November 2010 - galaxy-commits - lists.galaxyproject.org

galaxy-dist commit 5ec30f459e8e: Merge with d1baa724b393de6871df7249ebe35ecfe2054e31
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1290011973 18000 # Node ID 5ec30f459e8e4a1186f666f4879e14f082f17352 # Parent 7d46c23bb276790160fe05560aa87c3d41185a27 # Parent d1baa724b393de6871df7249ebe35ecfe2054e31 Merge with d1baa724b393de6871df7249ebe35ecfe2054e31

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galaxy-dist commit 29227c9c5992: Relax GTF sniffer ever so slightly so that Ensembl GTF files are sniffed correctly.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1290019719 18000 # Node ID 29227c9c599292f7608e61cdd4b2be424b7a7bfc # Parent 1ee9e2490e1968957f5f440a9dd08fb75aa3eb70 Relax GTF sniffer ever so slightly so that Ensembl GTF files are sniffed correctly. --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -965,7 +965,9 @@ class Gtf( Gff ): if len( attributes ) >= 2: try: # Imprecise: should check for a single space per the spec. - attr_name, attr_value = attributes[0].split(" ") + # strip() needed b/c Ensembl GTF files include an (illegal) + # space before attributes string. + attr_name, attr_value = attributes[0].strip().split(" ") if attr_name != 'gene_id': return False except:

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galaxy-dist commit 264c608b48d9: Fixed inconsistency in PerM loc.sample files
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1290012220 18000 # Node ID 264c608b48d9b0db2a142d820e32ec1d1fa550dd # Parent 5ec30f459e8e4a1186f666f4879e14f082f17352 Fixed inconsistency in PerM loc.sample files --- a/tool-data/perm_color_index.loc.sample +++ b/tool-data/perm_color_index.loc.sample @@ -13,7 +13,7 @@ #50, and stored in /depot/data/galaxy/phiX/perm_index/, #then the perm_color_index.loc entry would look something like this: # -#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index # #and your /depot/data/galaxy/phiX/perm_index/ directory #would contain the file phiX_color_F3_50.index: @@ -21,8 +21,8 @@ #Your perm_color_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#phiX_F4_50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#hg19_F3_50 /depot/data/galaxy/hg19/perm_index/hg19_color_F3_50.index -#hg19_F4_50 /depot/data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index # --- a/tool-data/perm_base_index.loc.sample +++ b/tool-data/perm_base_index.loc.sample @@ -21,8 +21,7 @@ #Your perm_base_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#phiX_F4_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#hg19_F3_50 /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index -#hg19_F4_50 /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index -# +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index +#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index

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galaxy-dist commit 1ee9e2490e19: Modifed tophat wrapper to work with data tables and fixed problem with index path; also got tests working
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1290013305 18000 # Node ID 1ee9e2490e1968957f5f440a9dd08fb75aa3eb70 # Parent 264c608b48d9b0db2a142d820e32ec1d1fa550dd Modifed tophat wrapper to work with data tables and fixed problem with index path; also got tests working --- /dev/null +++ b/test-data/tophat_in1.fasta @@ -0,0 +1,14 @@ +>test_chromosome +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +ACTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCC +ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC +AGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCT +ACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC +GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG +ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT +GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG +TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA --- /dev/null +++ b/test-data/tophat_in2.fastqsanger @@ -0,0 +1,400 @@ +@test_mRNA_150_290_0/1 +TCCTAAAAAGTCCGCCTCGGTCTCAGTCTCAAGTAGAAAAAGTCCCGTTGGCGATCCGTCTACGTCCGAGTAAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_8_197_1/1 +TCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGACACTACGGGGATGGCGACTAGGACTACGGACGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_82_255_2/1 +GAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAATATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_96_238_3/1 +GATCCGTCTACGTCCGCGTAAGATAATAAAGTACTAGTAGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_72_258_4/1 +GTAGAAAAAGTCCCGTTGCCCATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_107_286_5/1 +AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_122_299_6/1 +CAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_234_7/1 +AGTCTACGTCCGAGTCAGATAATAAACTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_57_231_8/1 +GGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCACCGACTGGACTATTTAGGACGATCGGACTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_8_155_9/1 +TACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTACAGTCGCTGCATCTGACGCTCGAAGTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_237_a/1 +ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_89_230_b/1 +TACGTCCGAGTGAGTTAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_105_276_c/1 +CCTCGATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_111_268_d/1 +CCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAATAATAGTGGCGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_151_286_e/1 +ACGTATTTGGCGCGCGGCCGTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_118_297_f/1 +AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_16_194_10/1 +TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_28_188_11/1 +TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGAACGGACTTAGAGCGTCAGATGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_36_218_12/1 +GAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGCCTTAGAGCGTCAGATGCAGCGACTGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_105_266_13/1 +AGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGGATCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_248_14/1 +ACTACGGGGATGACGACGAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGAACTTTTTAGGACGATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_89_245_15/1 +AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_218_16/1 +AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_46_195_17/1 +ATCCCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGACAAATATGTAGCGTCCTACTGCCCTCCTCAGTCCAATCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_126_282_18/1 +AGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_53_212_19/1 +TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATTTAGGACGATCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_11_190_1a/1 +GACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_52_261_1b/1 +CTACGGGAATGACGACTAGGGCTACGGAGGGACTTACAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_104_274_1c/1 +TCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_151_297_1d/1 +ACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_44_225_1e/1 +CCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCATATACGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_28_206_1f/1 +TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGACGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_48_249_20/1 +GTCCCGTTGCCGATCCGTCTCCGTCCGAGTAAGATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_75_235_21/1 +ACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGCACGATCGGACTGAGGAGGGCAGTAGAACGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_110_267_22/1 +CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_69_229_23/1 +ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTAGACGCTCAGCCGTAGGGCCGCGCGCCAAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_21_208_24/1 +GTAATAGTGGCGTATCGCAAGCTCGACGCTCAGGCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_42_209_25/1 +GGACGTGCCACTACGTGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_97_275_26/1 +ATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_36_146_27/1 +ACCTACTGCACTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGCATCTGACGCTCTAAGTCCGTCCGTAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_110_271_28/1 +ACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_38_199_29/1 +GCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_103_284_2a/1 +AAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_116_271_2b/1 +ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCTGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_77_256_2c/1 +GGACGGACTTAGAGCATCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_50_224_2d/1 +CGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_65_238_2e/1 +GACTAGGACTACGGACGGACTTAGAGCGTCAGAAGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_46_232_2f/1 +GTGCCACTACGGGGATGACGACTAGGACTACGGCCGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_26_189_30/1 +AGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTACCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_79_256_31/1 +AGAAAAAGTCCCGTTGCCGATCCGGCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATGGCAAGCTCGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_89_267_32/1 +CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGCCGTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_131_260_33/1 +GAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_73_240_34/1 +CTACGGACGGACTTAGAGCGTCAGATGCAGCGAATGGACTATTTAGGACGCTCGGACTGAGGAGGGCAGTAGGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_44_197_35/1 +ACGTGCAACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_128_252_36/1 +ACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAGGCCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_145_300_37/1 +GCAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTTCCGATCCGTCTACGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_85_275_38/1 +TTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGAAGCTACGTCTTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_48_207_39/1 +GCCCCTACGGGGATGACGACTAGGACTACGGACGGATTTAGACCGTCAGATGCAGCGACTGGACTATTTAGGACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_81_228_3a/1 +CCTACGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCATAGGGCCGCGCGCCAAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_75_277_3b/1 +ACGGACGGACTTAAAGCTTCAGATGCAGCGACAGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_30_231_3c/1 +CTACGTGCGAGTAAGATATTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTTAGCCGTAGGGCCGCGCGCCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_220_3d/1 +GAAGATAATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_104_278_3e/1 +CGCCTCGATTCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_44_193_3f/1 +ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGTCTATTTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_94_291_40/1 +CAGATGCAGCGACTGTACTATTTAGGACGACCTGACTGAGGAGGGTAGTAGGACGCTACGTATTTGGCGCGCGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_91_256_41/1 +CGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_23_186_42/1 +TCGACGCTCAGTCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTTCTGCCCTCCTCCGTCCGATCGTCCTAAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_92_266_43/1 +GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTCAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_92_250_44/1 +GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_106_253_45/1 +AAAAGTCCCGTTGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_5_197_46/1 +CTATCTGACTAGACTCGAGGCGCTTGCGTCTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_194_47/1 +TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_125_280_48/1 +CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGAAACGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_194_49/1 +ACTACGGGGATGACGACTAGGCCTACGGATGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_33_189_4a/1 +AGCCCGACGCTCAGCCGTAGGGCCGCGCGCCAAATAGGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_78_276_4b/1 +GACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGGCGCTAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_63_229_4c/1 +ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACACTCAGCCGTAGGGCCGCGCGCCAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_81_245_4d/1 +CGTTGCCGATCCGTCTACGTCCGAGTAAGATTATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_33_223_4e/1 +ACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_172_294_4f/1 +ACGGATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTCCTCGGACGTAGACGGATCGCCAACGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_88_257_50/1 +TAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_3_187_51/1 +TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_9_179_52/1 +TCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATGGTCCAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_85_268_53/1 +TTAGTGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_75_204_54/1 +ACGGACGGACTTCGAGCCTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_41_236_55/1 +AGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_56_183_56/1 +GGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTGGGACGATCGGACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_87_250_57/1 +AGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_82_271_58/1 +GACTTAGAGCGTCAGTTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_6_182_59/1 +TATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAGTACGGGGATGACGACTAGGACTACGGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_53_272_5a/1 +GATCCCAGTGTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_114_277_5b/1 +GCCTCGATCCCAGTCTCAAGCAGAAAAAGTCCCGTTGCCGTTCCGTCTACCTCCGAGTAAGATAATAAAGTAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_39_219_5c/1 +CTAGGACGTCCCACTATGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGGCTGGACTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_4_191_5d/1 +CAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGTGTCCTACTGCCCTACTCAGTCCGATCGTCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_73_259_5e/1 +CTACGGACGGACTTAGAGCGTCAGATGCTGCGACTGGACTATTTGGGACGATCGGACTGAGGAGGGCAGTAGGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_87_279_5f/1 +CCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_125_293_60/1 +CCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_111_297_61/1 +AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCGGATCCGTCTACGTCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_22_173_62/1 +AGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_116_295_63/1 +TCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII Binary file test-data/tophat_out1h.bam has changed --- a/test-data/tophat_in1.fq +++ /dev/null @@ -1,400 +0,0 @@ -@test_mRNA_150_290_0/1 -TCCTAAAAAGTCCGCCTCGGTCTCAGTCTCAAGTAGAAAAAGTCCCGTTGGCGATCCGTCTACGTCCGAGTAAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_8_197_1/1 -TCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGACACTACGGGGATGGCGACTAGGACTACGGACGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_82_255_2/1 -GAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAATATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_96_238_3/1 -GATCCGTCTACGTCCGCGTAAGATAATAAAGTACTAGTAGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_72_258_4/1 -GTAGAAAAAGTCCCGTTGCCCATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_107_286_5/1 -AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_122_299_6/1 -CAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_58_234_7/1 -AGTCTACGTCCGAGTCAGATAATAAACTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_57_231_8/1 -GGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCACCGACTGGACTATTTAGGACGATCGGACTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_8_155_9/1 -TACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTACAGTCGCTGCATCTGACGCTCGAAGTCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_51_237_a/1 -ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_89_230_b/1 -TACGTCCGAGTGAGTTAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_105_276_c/1 -CCTCGATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_111_268_d/1 -CCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAATAATAGTGGCGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_151_286_e/1 -ACGTATTTGGCGCGCGGCCGTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_118_297_f/1 -AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_16_194_10/1 -TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_28_188_11/1 -TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGAACGGACTTAGAGCGTCAGATGCAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_36_218_12/1 -GAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGCCTTAGAGCGTCAGATGCAGCGACTGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_105_266_13/1 -AGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGGATCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_51_248_14/1 -ACTACGGGGATGACGACGAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGAACTTTTTAGGACGATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_89_245_15/1 -AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_58_218_16/1 -AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_46_195_17/1 -ATCCCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGACAAATATGTAGCGTCCTACTGCCCTCCTCAGTCCAATCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_126_282_18/1 -AGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_53_212_19/1 -TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATTTAGGACGATCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_11_190_1a/1 -GACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_52_261_1b/1 -CTACGGGAATGACGACTAGGGCTACGGAGGGACTTACAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_104_274_1c/1 -TCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_151_297_1d/1 -ACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_44_225_1e/1 -CCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCATATACGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_28_206_1f/1 -TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGACGCAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_48_249_20/1 -GTCCCGTTGCCGATCCGTCTCCGTCCGAGTAAGATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_75_235_21/1 -ACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGCACGATCGGACTGAGGAGGGCAGTAGAACGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_110_267_22/1 -CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_69_229_23/1 -ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTAGACGCTCAGCCGTAGGGCCGCGCGCCAAAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_21_208_24/1 -GTAATAGTGGCGTATCGCAAGCTCGACGCTCAGGCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_42_209_25/1 -GGACGTGCCACTACGTGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_97_275_26/1 -ATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_36_146_27/1 -ACCTACTGCACTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGCATCTGACGCTCTAAGTCCGTCCGTAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_110_271_28/1 -ACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_38_199_29/1 -GCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_103_284_2a/1 -AAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_116_271_2b/1 -ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCTGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_77_256_2c/1 -GGACGGACTTAGAGCATCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_50_224_2d/1 -CGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_65_238_2e/1 -GACTAGGACTACGGACGGACTTAGAGCGTCAGAAGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_46_232_2f/1 -GTGCCACTACGGGGATGACGACTAGGACTACGGCCGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_26_189_30/1 -AGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTACCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_79_256_31/1 -AGAAAAAGTCCCGTTGCCGATCCGGCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATGGCAAGCTCGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_89_267_32/1 -CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGCCGTATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_131_260_33/1 -GAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_73_240_34/1 -CTACGGACGGACTTAGAGCGTCAGATGCAGCGAATGGACTATTTAGGACGCTCGGACTGAGGAGGGCAGTAGGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_44_197_35/1 -ACGTGCAACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_128_252_36/1 -ACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAGGCCAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_145_300_37/1 -GCAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTTCCGATCCGTCTACGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_85_275_38/1 -TTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGAAGCTACGTCTTTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_48_207_39/1 -GCCCCTACGGGGATGACGACTAGGACTACGGACGGATTTAGACCGTCAGATGCAGCGACTGGACTATTTAGGACG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_81_228_3a/1 -CCTACGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCATAGGGCCGCGCGCCAAATA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_75_277_3b/1 -ACGGACGGACTTAAAGCTTCAGATGCAGCGACAGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_30_231_3c/1 -CTACGTGCGAGTAAGATATTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTTAGCCGTAGGGCCGCGCGCCAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_58_220_3d/1 -GAAGATAATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_104_278_3e/1 -CGCCTCGATTCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_44_193_3f/1 -ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGTCTATTTAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_94_291_40/1 -CAGATGCAGCGACTGTACTATTTAGGACGACCTGACTGAGGAGGGTAGTAGGACGCTACGTATTTGGCGCGCGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_91_256_41/1 -CGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_23_186_42/1 -TCGACGCTCAGTCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTTCTGCCCTCCTCCGTCCGATCGTCCTAAATA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_92_266_43/1 -GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTCAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_92_250_44/1 -GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_106_253_45/1 -AAAAGTCCCGTTGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_5_197_46/1 -CTATCTGACTAGACTCGAGGCGCTTGCGTCTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_51_194_47/1 -TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_125_280_48/1 -CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGAAACGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_51_194_49/1 -ACTACGGGGATGACGACTAGGCCTACGGATGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_33_189_4a/1 -AGCCCGACGCTCAGCCGTAGGGCCGCGCGCCAAATAGGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_78_276_4b/1 -GACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGGCGCTAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_63_229_4c/1 -ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACACTCAGCCGTAGGGCCGCGCGCCAAAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_81_245_4d/1 -CGTTGCCGATCCGTCTACGTCCGAGTAAGATTATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_33_223_4e/1 -ACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_172_294_4f/1 -ACGGATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTCCTCGGACGTAGACGGATCGCCAACGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_88_257_50/1 -TAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_3_187_51/1 -TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_9_179_52/1 -TCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATGGTCCAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_85_268_53/1 -TTAGTGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_75_204_54/1 -ACGGACGGACTTCGAGCCTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_41_236_55/1 -AGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_56_183_56/1 -GGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTGGGACGATCGGACT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_87_250_57/1 -AGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_82_271_58/1 -GACTTAGAGCGTCAGTTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_6_182_59/1 -TATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAGTACGGGGATGACGACTAGGACTACGGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_53_272_5a/1 -GATCCCAGTGTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_114_277_5b/1 -GCCTCGATCCCAGTCTCAAGCAGAAAAAGTCCCGTTGCCGTTCCGTCTACCTCCGAGTAAGATAATAAAGTAATA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_39_219_5c/1 -CTAGGACGTCCCACTATGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGGCTGGACTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_4_191_5d/1 -CAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGTGTCCTACTGCCCTACTCAGTCCGATCGTCCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_73_259_5e/1 -CTACGGACGGACTTAGAGCGTCAGATGCTGCGACTGGACTATTTGGGACGATCGGACTGAGGAGGGCAGTAGGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_87_279_5f/1 -CCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_125_293_60/1 -CCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_111_297_61/1 -AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCGGATCCGTCTACGTCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_22_173_62/1 -AGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_116_295_63/1 -TCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII --- a/tools/ngs_rna/tophat_wrapper.py +++ b/tools/ngs_rna/tophat_wrapper.py @@ -30,7 +30,7 @@ def __main__(): parser.add_option( '-g', '--max_multihits', dest='max_multihits', help='Maximum number of alignments to be allowed' ) parser.add_option( '', '--seg-mismatches', dest='seg_mismatches', help='Number of mismatches allowed in each segment alignment for reads mapped independently' ) parser.add_option( '', '--seg-length', dest='seg_length', help='Minimum length of read segments' ) - + # Options for supplying own junctions parser.add_option( '-G', '--GTF', dest='gene_model_annotations', help='Supply TopHat with a list of gene model annotations. \ TopHat will use the exon records in this file to build \ @@ -58,18 +58,18 @@ def __main__(): parser.add_option( '', '--max-closure-intron', dest='max_closure_intron', help='Maximum intron length that may be found during closure search' ) parser.add_option( '', '--min-coverage-intron', dest='min_coverage_intron', help='Minimum intron length that may be found during coverage search' ) parser.add_option( '', '--max-coverage-intron', dest='max_coverage_intron', help='Maximum intron length that may be found during coverage search' ) - + # Wrapper options. parser.add_option( '-1', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' ) parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' ) parser.add_option( '', '--single-paired', dest='single_paired', help='' ) parser.add_option( '', '--settings', dest='settings', help='' ) - + (options, args) = parser.parse_args() - + # Creat bowtie index if necessary. tmp_index_dir = tempfile.mkdtemp() - if options.own_file != 'None': + if options.own_file: index_path = os.path.join( tmp_index_dir, os.path.split( options.own_file )[1] ) cmd_index = 'bowtie-build -f %s %s' % ( options.own_file, index_path ) try: @@ -98,12 +98,12 @@ def __main__(): stop_err( 'Error indexing reference sequence\n' + str( e ) ) else: index_path = options.index_path - + # Build tophat command. tmp_output_dir = tempfile.mkdtemp() cmd = 'tophat -o %s %s %s %s' reads = options.input1 - if options.input2 != 'None': + if options.input2: reads += ' ' + options.input2 opts = '-p %s' % options.num_threads if options.single_paired == 'paired': @@ -129,7 +129,7 @@ def __main__(): opts += ' -j %s' % options.raw_juncs if options.no_novel_juncs: opts += ' --no-novel-juncs' - + # Search type options. if options.coverage_search: opts += ' --coverage-search --min-coverage-intron %s --max-coverage-intron %s' % ( options.min_coverage_intron, options.max_coverage_intron ) @@ -143,13 +143,13 @@ def __main__(): opts += ' --microexon-search' if options.single_paired == 'paired': opts += ' --mate-std-dev %s' % options.mate_std_dev - if options.seg_mismatches != None: + if options.seg_mismatches: opts += ' --segment-mismatches %d' % int(options.seg_mismatches) - if options.seg_length != None: + if options.seg_length: opts += ' --segment-length %d' % int(options.seg_length) - if options.min_segment_intron != None: + if options.min_segment_intron: opts += ' --min-segment-intron %d' % int(options.min_segment_intron) - if options.max_segment_intron != None: + if options.max_segment_intron: opts += ' --max-segment-intron %d' % int(options.max_segment_intron) cmd = cmd % ( tmp_output_dir, opts, index_path, reads ) except Exception, e: @@ -160,7 +160,7 @@ def __main__(): shutil.rmtree( tmp_output_dir ) stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) ) print cmd - + # Run try: tmp_out = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name @@ -185,10 +185,10 @@ def __main__(): tmp_stderr.close() if returncode != 0: raise Exception, stderr - + # TODO: look for errors in program output. - - # Copy output files from tmp directory to specified files. + + # Copy output files from tmp directory to specified files. shutil.copyfile( os.path.join( tmp_output_dir, "junctions.bed" ), options.junctions_output_file ) shutil.copyfile( os.path.join( tmp_output_dir, "accepted_hits.bam" ), options.accepted_hits_output_file ) except Exception, e: --- a/test-data/tophat_in2.fq +++ /dev/null @@ -1,400 +0,0 @@ -@test_mRNA_150_290_0/2 -TACGTATTTGTCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATCCGCCACTATTACTTTATTATCTTACTCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_8_197_1/2 -GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_82_255_2/2 -GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_96_238_3/2 -GATGCAGCGACTGGACTATTTAGGACGATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGACC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_72_258_4/2 -ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_107_286_5/2 -TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_122_299_6/2 -GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_58_234_7/2 -GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_57_231_8/2 -CTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCCTAGGGCCGCGCGCCAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_8_155_9/2 -TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_51_237_a/2 -ATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_89_230_b/2 -AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_105_276_c/2 -ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_111_268_d/2 -CTATTTAAGACGTTCCGCCTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_151_286_e/2 -AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGATAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_118_297_f/2 -GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_16_194_10/2 -GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_28_188_11/2 -GCTCGACGCTCAGCCGTAGGGCCTCGCGCCAAATACGAAGCGTCCTACTGCCTTCCTCAGTCCGATCGTCCTAAA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_36_218_12/2 -AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_105_266_13/2 -ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_51_248_14/2 -TCCCGTTGCCGTTCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_89_245_15/2 -CGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAGAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_58_218_16/2 -GGATGACGACTAGGACTACGGACGGACTTAGAACGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_46_195_17/2 -GTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_126_282_18/2 -GGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_53_212_19/2 -TAAAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_11_190_1a/2 -AAGCTCGACGCTCAGCCGTAGGGCCACGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCCATCGACCTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_52_261_1b/2 -CAAGTAGAAAAAGTCCCGTTGCCGATCCTTCTACGTCCGAGTAAGATAATTAAGTAATAGTGGCGTATCGCAAGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_104_274_1c/2 -GAGTGTACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATGTGCCGCGCGGCCCTACGGCTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_151_297_1d/2 -AGTCCCGTCCTAAAATGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_44_225_1e/2 -ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCGGGTGCAGCGACTGGACTATTTAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_28_206_1f/2 -AATAGTGGCTTATCGCAAGCTCGACTCTCAGCCGTAGGGCCGCGCGCCAAATACGTGGCGTCCTACTGCCCTCCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_48_249_20/2 -GCCACTACGGGGATGACGACTAGGACGACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_75_235_21/2 -CCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCAACGCTCAGCCGTAGGGCCGTGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_110_267_22/2 -ACTAGTTAGGGCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAGTTGGCGCGCGGCCCTACGACTGAGCGTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_69_229_23/2 -AGGACTACGGACGGACTTATAGGGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_21_208_24/2 -GAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_42_209_25/2 -AGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_97_275_26/2 -CTCGATCCCAGTCTCAAGTAGAAAGAGTCCCGTTTCCGATCCGTCTACGTCCGACTAAGATAATAAAGTAATAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_36_146_27/2 -GCGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACAGACGGACTTAGAGCGTCAGATGCAGCGACTGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_110_271_28/2 -ATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTTCGTCCGAGTAAGATAATAAAGTAATAGTGGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_38_199_29/2 -GCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_103_284_2a/2 -CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_116_271_2b/2 -TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_77_256_2c/2 -AGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_50_224_2d/2 -CACTACGAGGATGACGTCTAGGACTACGGACGGACTTAGAGCGTCAGACGCAGCGACTGGACTATTTAGGACGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_65_238_2e/2 -GATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCGCAGCCGTAGGGCCGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_46_232_2f/2 -TCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_26_189_30/2 -GCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_79_256_31/2 -ACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_89_267_32/2 -AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGAGTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_131_260_33/2 -AAGTAAAAAAAGTCCCGTGGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCACAAGCT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_73_240_34/2 -CCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_44_197_35/2 -GTATCGCAAGCTCGACGATCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_128_252_36/2 -AAAGTCCCGTTCCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_145_300_37/2 -GACGCTACGTATTTGGCGCGGGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTAGTATATT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_85_275_38/2 -CTCGATCCCAGTCTCAAGTAGTAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAGAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_48_207_39/2 -TAAGAGTGGCGTATCGCAAGATCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTTCCCTCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_81_228_3a/2 -GGACTGAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGTAGTAGGACGCTACGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_75_277_3b/2 -GCCTCGATCCCAGTCTCAGGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_30_231_3c/2 -GCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_58_220_3d/2 -GGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_104_278_3e/2 -GACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTTTTTGGCGCGCGGCCCTACGGCTG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_44_193_3f/2 -CGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCTCTCCCCAGTCCGATCGTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_94_291_40/2 -GTCCCAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAATGTCGCGTTGCCGATCCGTCTACGTCCCAGGAAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_91_256_41/2 -AGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGAC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_23_186_42/2 -GGCGCTTGTGACTGAGCTAGGACGTGCCACTACGGGGATGAAGACTAGGACTACGGACGGACTTAGAGCGTCAGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_92_266_43/2 -GGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTCCGAGTAAGATAAGAAAGTAATAGTGGCGTATCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_92_250_44/2 -AGTCCCGTACCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_106_253_45/2 -CTGGACTATTTAGGTCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_5_197_46/2 -GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCCCGCCAAATACGTAGCGTCCTACTGCCCTCCTCCGTCCGAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_51_194_47/2 -ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_125_280_48/2 -TCCGCCTCGCTCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCAGAGTAAGATAATAAAGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_51_194_49/2 -CCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTGGCGTCCTACTGCCCTCCTCAGTCCGAACGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_33_189_4a/2 -ACTGAGCTAGGACGTGCCACTACGGGGATTACCACTAGGGCTACGGACGGACTTAGAGCGTCAGATGCAGCGACT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_78_276_4b/2 -CCTCGATCCTAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_63_229_4c/2 -ACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGGGACTGGACTATTTAGGACGATCGGACTGAGGAGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_81_245_4d/2 -GGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGATGAGGGCAGTAGGACGCTACGTA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_33_223_4e/2 -GAGTTAGATAATAAAGTAATAGTGGCTTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACCTAG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_172_294_4f/2 -CCCGTCCTAAAACGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGCTGCCGACCCGTCTACGTCCGAGT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_88_257_50/2 -GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_3_187_51/2 -CTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_9_179_52/2 -CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_85_268_53/2 -CCAGTCTCAAGTAGAAAAAGTCCCGTTGACGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTAT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_75_204_54/2 -TCGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCA -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_41_236_55/2 -TCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_56_183_56/2 -ACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_87_250_57/2 -AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_82_271_58/2 -ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATGCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_6_182_59/2 -CGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_53_272_5a/2 -TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_114_277_5b/2 -TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_39_219_5c/2 -AAGATAATAAAGTAATAGTGGCGTATCGCAAGCTGGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_4_191_5d/2 -ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_73_259_5e/2 -AGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATACAGTAATAGTGGCGTATCGCAAGCTC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_87_279_5f/2 -AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_125_293_60/2 -CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_111_297_61/2 -CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_22_173_62/2 -GTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGC -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -@test_mRNA_116_295_63/2 -TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT -+ -IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII --- /dev/null +++ b/test-data/tophat_out1j.bed @@ -0,0 +1,3 @@ +track name=junctions description="TopHat junctions" +test_chromosome 180 400 JUNC00000001 24 + 180 400 255,0,0 2 70,50 0,170 +test_chromosome 349 550 JUNC00000002 22 + 349 550 255,0,0 2 51,50 0,151 --- a/test-data/tophat_out1.bed +++ /dev/null @@ -1,3 +0,0 @@ -track name=junctions description="TopHat junctions" -test_chromosome 180 402 JUNC00000001 46 + 180 402 255,0,0 2 70,52 0,170 -test_chromosome 349 550 JUNC00000002 38 + 349 550 255,0,0 2 51,50 0,151 --- /dev/null +++ b/test-data/tophat_out2j.bed @@ -0,0 +1,3 @@ +track name=junctions description="TopHat junctions" +test_chromosome 180 402 JUNC00000001 46 + 180 402 255,0,0 2 70,52 0,170 +test_chromosome 349 550 JUNC00000002 38 + 349 550 255,0,0 2 51,50 0,151 --- /dev/null +++ b/test-data/tophat_out3j.bed @@ -0,0 +1,3 @@ +track name=junctions description="TopHat junctions" +test_chromosome 180 400 JUNC00000001 24 + 180 400 255,0,0 2 70,50 0,170 +test_chromosome 349 550 JUNC00000002 22 + 349 550 255,0,0 2 51,50 0,151 --- /dev/null +++ b/test-data/tophat_in3.fastqsanger @@ -0,0 +1,400 @@ +@test_mRNA_150_290_0/2 +TACGTATTTGTCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATCCGCCACTATTACTTTATTATCTTACTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_8_197_1/2 +GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_82_255_2/2 +GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_96_238_3/2 +GATGCAGCGACTGGACTATTTAGGACGATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_72_258_4/2 +ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_107_286_5/2 +TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_122_299_6/2 +GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_234_7/2 +GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_57_231_8/2 +CTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCCTAGGGCCGCGCGCCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_8_155_9/2 +TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_237_a/2 +ATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_89_230_b/2 +AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_105_276_c/2 +ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_111_268_d/2 +CTATTTAAGACGTTCCGCCTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_151_286_e/2 +AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGATAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_118_297_f/2 +GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_16_194_10/2 +GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_28_188_11/2 +GCTCGACGCTCAGCCGTAGGGCCTCGCGCCAAATACGAAGCGTCCTACTGCCTTCCTCAGTCCGATCGTCCTAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_36_218_12/2 +AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_105_266_13/2 +ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_248_14/2 +TCCCGTTGCCGTTCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_89_245_15/2 +CGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAGAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_218_16/2 +GGATGACGACTAGGACTACGGACGGACTTAGAACGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_46_195_17/2 +GTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_126_282_18/2 +GGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_53_212_19/2 +TAAAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_11_190_1a/2 +AAGCTCGACGCTCAGCCGTAGGGCCACGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCCATCGACCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_52_261_1b/2 +CAAGTAGAAAAAGTCCCGTTGCCGATCCTTCTACGTCCGAGTAAGATAATTAAGTAATAGTGGCGTATCGCAAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_104_274_1c/2 +GAGTGTACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATGTGCCGCGCGGCCCTACGGCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_151_297_1d/2 +AGTCCCGTCCTAAAATGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_44_225_1e/2 +ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCGGGTGCAGCGACTGGACTATTTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_28_206_1f/2 +AATAGTGGCTTATCGCAAGCTCGACTCTCAGCCGTAGGGCCGCGCGCCAAATACGTGGCGTCCTACTGCCCTCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_48_249_20/2 +GCCACTACGGGGATGACGACTAGGACGACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_75_235_21/2 +CCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCAACGCTCAGCCGTAGGGCCGTGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_110_267_22/2 +ACTAGTTAGGGCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAGTTGGCGCGCGGCCCTACGACTGAGCGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_69_229_23/2 +AGGACTACGGACGGACTTATAGGGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_21_208_24/2 +GAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_42_209_25/2 +AGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_97_275_26/2 +CTCGATCCCAGTCTCAAGTAGAAAGAGTCCCGTTTCCGATCCGTCTACGTCCGACTAAGATAATAAAGTAATAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_36_146_27/2 +GCGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACAGACGGACTTAGAGCGTCAGATGCAGCGACTGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_110_271_28/2 +ATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTTCGTCCGAGTAAGATAATAAAGTAATAGTGGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_38_199_29/2 +GCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_103_284_2a/2 +CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_116_271_2b/2 +TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_77_256_2c/2 +AGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_50_224_2d/2 +CACTACGAGGATGACGTCTAGGACTACGGACGGACTTAGAGCGTCAGACGCAGCGACTGGACTATTTAGGACGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_65_238_2e/2 +GATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCGCAGCCGTAGGGCCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_46_232_2f/2 +TCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_26_189_30/2 +GCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_79_256_31/2 +ACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_89_267_32/2 +AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGAGTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_131_260_33/2 +AAGTAAAAAAAGTCCCGTGGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCACAAGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_73_240_34/2 +CCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_44_197_35/2 +GTATCGCAAGCTCGACGATCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_128_252_36/2 +AAAGTCCCGTTCCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_145_300_37/2 +GACGCTACGTATTTGGCGCGGGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTAGTATATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_85_275_38/2 +CTCGATCCCAGTCTCAAGTAGTAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAGAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_48_207_39/2 +TAAGAGTGGCGTATCGCAAGATCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTTCCCTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_81_228_3a/2 +GGACTGAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGTAGTAGGACGCTACGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_75_277_3b/2 +GCCTCGATCCCAGTCTCAGGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_30_231_3c/2 +GCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_58_220_3d/2 +GGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_104_278_3e/2 +GACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTTTTTGGCGCGCGGCCCTACGGCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_44_193_3f/2 +CGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCTCTCCCCAGTCCGATCGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_94_291_40/2 +GTCCCAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAATGTCGCGTTGCCGATCCGTCTACGTCCCAGGAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_91_256_41/2 +AGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_23_186_42/2 +GGCGCTTGTGACTGAGCTAGGACGTGCCACTACGGGGATGAAGACTAGGACTACGGACGGACTTAGAGCGTCAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_92_266_43/2 +GGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTCCGAGTAAGATAAGAAAGTAATAGTGGCGTATCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_92_250_44/2 +AGTCCCGTACCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_106_253_45/2 +CTGGACTATTTAGGTCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_5_197_46/2 +GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCCCGCCAAATACGTAGCGTCCTACTGCCCTCCTCCGTCCGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_194_47/2 +ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_125_280_48/2 +TCCGCCTCGCTCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCAGAGTAAGATAATAAAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_51_194_49/2 +CCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTGGCGTCCTACTGCCCTCCTCAGTCCGAACGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_33_189_4a/2 +ACTGAGCTAGGACGTGCCACTACGGGGATTACCACTAGGGCTACGGACGGACTTAGAGCGTCAGATGCAGCGACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_78_276_4b/2 +CCTCGATCCTAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_63_229_4c/2 +ACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGGGACTGGACTATTTAGGACGATCGGACTGAGGAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_81_245_4d/2 +GGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGATGAGGGCAGTAGGACGCTACGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_33_223_4e/2 +GAGTTAGATAATAAAGTAATAGTGGCTTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACCTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_172_294_4f/2 +CCCGTCCTAAAACGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGCTGCCGACCCGTCTACGTCCGAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_88_257_50/2 +GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_3_187_51/2 +CTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_9_179_52/2 +CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_85_268_53/2 +CCAGTCTCAAGTAGAAAAAGTCCCGTTGACGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_75_204_54/2 +TCGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_41_236_55/2 +TCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_56_183_56/2 +ACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_87_250_57/2 +AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_82_271_58/2 +ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATGCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_6_182_59/2 +CGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_53_272_5a/2 +TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_114_277_5b/2 +TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_39_219_5c/2 +AAGATAATAAAGTAATAGTGGCGTATCGCAAGCTGGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_4_191_5d/2 +ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_73_259_5e/2 +AGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATACAGTAATAGTGGCGTATCGCAAGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_87_279_5f/2 +AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_125_293_60/2 +CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_111_297_61/2 +CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_22_173_62/2 +GTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_mRNA_116_295_63/2 +TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="tophat" name="Tophat" version="1.1.2"> +<tool id="tophat" name="Tophat" version="1.2.0"><description>Find splice junctions using RNA-seq data</description><requirements><requirement type="package">tophat</requirement> @@ -7,46 +7,41 @@ tophat_wrapper.py ## Change this to accommodate the number of threads you have available. --num-threads="4" - + ## Provide outputs. --junctions-output=$junctions --hits-output=$accepted_hits - + ## Handle reference file. #if $refGenomeSource.genomeSource == "history": --own-file=$refGenomeSource.ownFile - --indexes-path="None" #else: - --own-file="None" - --indexes-path=$refGenomeSource.index + --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes' ].get_fields() )[0][-1] }" #end if - + ## Are reads single-end or paired? --single-paired=$singlePaired.sPaired - + ## First input file always required. --input1=$singlePaired.input1 - + ## Set parms based on whether reads are single-end or paired. #if $singlePaired.sPaired == "single": - --input2="None" - -r "None" - --settings=$singlePaired.sParams.sSettingsType - #if $singlePaired.sParams.sSettingsType == "full": - --mate-std-dev="None" - -a $singlePaired.sParams.anchor_length - -m $singlePaired.sParams.splice_mismatches - -i $singlePaired.sParams.min_intron_length - -I $singlePaired.sParams.max_intron_length - -F $singlePaired.sParams.junction_filter - -g $singlePaired.sParams.max_multihits - --min-segment-intron $singlePaired.sParams.min_segment_intron - --max-segment-intron $singlePaired.sParams.max_segment_intron - --seg-mismatches=$singlePaired.sParams.seg_mismatches - --seg-length=$singlePaired.sParams.seg_length - - ## Supplying junctions parameters. - #if $singlePaired.sParams.own_junctions.use_junctions == "Yes": + --settings=$singlePaired.sParams.sSettingsType + #if $singlePaired.sParams.sSettingsType == "full": + -a $singlePaired.sParams.anchor_length + -m $singlePaired.sParams.splice_mismatches + -i $singlePaired.sParams.min_intron_length + -I $singlePaired.sParams.max_intron_length + -F $singlePaired.sParams.junction_filter + -g $singlePaired.sParams.max_multihits + --min-segment-intron $singlePaired.sParams.min_segment_intron + --max-segment-intron $singlePaired.sParams.max_segment_intron + --seg-mismatches=$singlePaired.sParams.seg_mismatches + --seg-length=$singlePaired.sParams.seg_length + + ## Supplying junctions parameters. + #if $singlePaired.sParams.own_junctions.use_junctions == "Yes": #if $singlePaired.sParams.own_junctions.gene_model_ann.use_annotations == "Yes": -G $singlePaired.sParams.own_junctions.gene_model_ann.gene_annotation_model #end if @@ -57,47 +52,47 @@ #if str($singlePaired.sParams.own_junctions.no_novel_juncs) == "Yes": --no-novel-juncs #end if - #end if - - #if $singlePaired.sParams.closure_search.use_search == "Yes": + #end if + + #if $singlePaired.sParams.closure_search.use_search == "Yes": --closure-search --min-closure-exon $singlePaired.sParams.closure_search.min_closure_exon --min-closure-intron $singlePaired.sParams.closure_search.min_closure_intron --max-closure-intron $singlePaired.sParams.closure_search.max_closure_intron - #else: + #else: --no-closure-search - #end if - #if $singlePaired.sParams.coverage_search.use_search == "Yes": + #end if + #if $singlePaired.sParams.coverage_search.use_search == "Yes": --coverage-search --min-coverage-intron $singlePaired.sParams.coverage_search.min_coverage_intron --max-coverage-intron $singlePaired.sParams.coverage_search.max_coverage_intron - #else: + #else: --no-coverage-search - #end if - ## TODO: No idea why the type conversion is necessary, but it seems to be. - #if str($singlePaired.sParams.microexon_search) == "Yes": + #end if + ## TODO: No idea why the type conversion is necessary, but it seems to be. + #if str($singlePaired.sParams.microexon_search) == "Yes": --microexon-search - #end if - #end if - #else: - --input2=$singlePaired.input2 - -r $singlePaired.mate_inner_distance - --settings=$singlePaired.pParams.pSettingsType - #if $singlePaired.pParams.pSettingsType == "full": - --mate-std-dev=$singlePaired.pParams.mate_std_dev - -a $singlePaired.pParams.anchor_length - -m $singlePaired.pParams.splice_mismatches - -i $singlePaired.pParams.min_intron_length - -I $singlePaired.pParams.max_intron_length - -F $singlePaired.pParams.junction_filter - -g $singlePaired.pParams.max_multihits - --min-segment-intron $singlePaired.pParams.min_segment_intron - --max-segment-intron $singlePaired.pParams.max_segment_intron - --seg-mismatches=$singlePaired.pParams.seg_mismatches - --seg-length=$singlePaired.pParams.seg_length - - ## Supplying junctions parameters. - #if $singlePaired.pParams.own_junctions.use_junctions == "Yes": + #end if + #end if + #else: + --input2=$singlePaired.input2 + -r $singlePaired.mate_inner_distance + --settings=$singlePaired.pParams.pSettingsType + #if $singlePaired.pParams.pSettingsType == "full": + --mate-std-dev=$singlePaired.pParams.mate_std_dev + -a $singlePaired.pParams.anchor_length + -m $singlePaired.pParams.splice_mismatches + -i $singlePaired.pParams.min_intron_length + -I $singlePaired.pParams.max_intron_length + -F $singlePaired.pParams.junction_filter + -g $singlePaired.pParams.max_multihits + --min-segment-intron $singlePaired.pParams.min_segment_intron + --max-segment-intron $singlePaired.pParams.max_segment_intron + --seg-mismatches=$singlePaired.pParams.seg_mismatches + --seg-length=$singlePaired.pParams.seg_length + + ## Supplying junctions parameters. + #if $singlePaired.pParams.own_junctions.use_junctions == "Yes": #if $singlePaired.pParams.own_junctions.gene_model_ann.use_annotations == "Yes": -G $singlePaired.pParams.own_junctions.gene_model_ann.gene_annotation_model #end if @@ -108,29 +103,29 @@ #if str($singlePaired.pParams.own_junctions.no_novel_juncs) == "Yes": --no-novel-juncs #end if - #end if - - #if $singlePaired.pParams.closure_search.use_search == "Yes": + #end if + + #if $singlePaired.pParams.closure_search.use_search == "Yes": --closure-search --min-closure-exon $singlePaired.pParams.closure_search.min_closure_exon --min-closure-intron $singlePaired.pParams.closure_search.min_closure_intron --max-closure-intron $singlePaired.pParams.closure_search.max_closure_intron - #else: + #else: --no-closure-search - #end if - #if $singlePaired.pParams.coverage_search.use_search == "Yes": + #end if + #if $singlePaired.pParams.coverage_search.use_search == "Yes": --coverage-search --min-coverage-intron $singlePaired.pParams.coverage_search.min_coverage_intron --max-coverage-intron $singlePaired.pParams.coverage_search.max_coverage_intron - #else: + #else: --no-coverage-search - #end if - ## TODO: No idea why the type conversion is necessary, but it seems to be. - #if str ($singlePaired.pParams.microexon_search) == "Yes": + #end if + ## TODO: No idea why the type conversion is necessary, but it seems to be. + #if str ($singlePaired.pParams.microexon_search) == "Yes": --microexon-search #end if - #end if - #end if + #end if + #end if </command><inputs><conditional name="refGenomeSource"> @@ -140,10 +135,7 @@ </param><when value="indexed"><param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_file="bowtie_indices.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> + <options from_data_table="tophat_indexes" /></param></when><when value="history"> @@ -186,7 +178,7 @@ <conditional name="gene_model_ann"><param name="use_annotations" type="select" label="Use Gene Annotation Model"><option value="No">No</option> - <option value="Yes">Yes</option> + <option value="Yes">Yes</option></param><when value="No" /><when value="Yes"> @@ -196,7 +188,7 @@ <conditional name="raw_juncs"><param name="use_juncs" type="select" label="Use Raw Junctions"><option value="No">No</option> - <option value="Yes">Yes</option> + <option value="Yes">Yes</option></param><when value="No" /><when value="Yes"> @@ -242,7 +234,7 @@ </param></when></conditional> - </when> + </when><when value="paired"><param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/><param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> @@ -276,7 +268,7 @@ <conditional name="gene_model_ann"><param name="use_annotations" type="select" label="Use Gene Annotation Model"><option value="No">No</option> - <option value="Yes">Yes</option> + <option value="Yes">Yes</option></param><when value="No" /><when value="Yes"> @@ -286,7 +278,7 @@ <conditional name="raw_juncs"><param name="use_juncs" type="select" label="Use Raw Junctions"><option value="No">No</option> - <option value="Yes">Yes</option> + <option value="Yes">Yes</option></param><when value="No" /><when value="Yes"> @@ -325,14 +317,14 @@ <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" /></when><when value="No" /> - </conditional> + </conditional><param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer."><option value="No">No</option><option value="Yes">Yes</option></param></when></conditional> - </when> + </when></conditional></inputs> @@ -342,38 +334,46 @@ </outputs><tests> - + <test> +  -<test> +  + <param name="genomeSource" value="history" /> + <param name="ownFile" ftype="fasta" value="tophat_in1.fasta" /> + <param name="sPaired" value="paired" /> + <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" /> + <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger" /> + <param name="mate_inner_distance" value="20" /> + <param name="pSettingsType" value="preSet" /> + <output name="junctions" file="tophat_out2j.bed" ftype="bed" /> + <output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" ftype="bam" /> + </test> +  + <test> + <param name="genomeSource" value="history"/> - <param name="ownFile" ftype="fasta" value="tophat_in3.fa"/> - <param name="sPaired" value="paired"/> - <param name="input1" ftype="fastqsanger" value="tophat_in1.fq"/> - <param name="input2" ftype="fastqsanger" value="tophat_in2.fq"/> - <param name="mate_inner_distance" value="20"/> - <param name="pSettingsType" value="preSet"/> - <output name="junctions" file="tophat_out1.bed"/> -  - <output name="accepted_hits" file="tophat_out2.bam" lines_diff="100000"/> - </test> - + <test> +  - -</tests> + </tests><help> **Tophat Overview** Binary file test-data/tophat_out3h.bam has changed Binary file test-data/tophat_out2.bam has changed --- a/test-data/tophat_in3.fa +++ /dev/null @@ -1,14 +0,0 @@ ->test_chromosome -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -ACTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCC -ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC -AGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCT -ACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC -GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG -ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT -GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG -TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA --- a/tool_data_table_conf.xml.sample +++ b/tool_data_table_conf.xml.sample @@ -1,3 +1,4 @@ +<tables><table name="all_fasta" comment_char="#"> @@ -34,7 +35,7 @@ <columns>value, dbkey, name, path</columns><file path="tool-data/bwa_index.loc" /></table> -  + <table name="indexed_maf_files"><columns>name, value, dbkey, species</columns><file path="tool-data/maf_index.loc" /> @@ -65,9 +66,8 @@ <file path="tool-data/srma_index.loc" /></table> -</tables> Binary file test-data/tophat_out4h.bam has changed --- /dev/null +++ b/test-data/tophat_out4j.bed @@ -0,0 +1,3 @@ +track name=junctions description="TopHat junctions" +test_chromosome 180 402 JUNC00000001 46 + 180 402 255,0,0 2 70,52 0,170 +test_chromosome 349 550 JUNC00000002 38 + 349 550 255,0,0 2 51,50 0,151 Binary file test-data/tophat_out2h.bam has changed

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galaxy-dist commit 1bf064c8ab88: Fixed functional tests and samples grid alignment bug
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1289928056 18000 # Node ID 1bf064c8ab88621dd58890f6cd56ad4900d10d6b # Parent 2e2ee0289d67d244954aa05bfe315dbb5ff413eb Fixed functional tests and samples grid alignment bug --- a/test/functional/test_sample_tracking.py +++ b/test/functional/test_sample_tracking.py @@ -341,7 +341,7 @@ class TestFormsAndRequests( TwillTestCas request_id=self.security.encode_id( request1.id ), strings_displayed=[ 'History of sequencing request "%s"' % request1.name, request1.states.NEW, - 'Request created' ], + 'Sequencing request created' ], strings_not_displayed=[ request1.states.SUBMITTED, request1.states.COMPLETE, request1.states.REJECTED ] ) @@ -412,7 +412,7 @@ class TestFormsAndRequests( TwillTestCas self.add_samples( cntrller='requests', request_id=self.security.encode_id( request1.id ), sample_value_tuples=sample_value_tuples, - strings_displayed=[ 'Add Samples to Request "%s"' % request1.name, + strings_displayed=[ 'Add Samples to Sequencing Request "%s"' % request1.name, '<input type="text" name="sample_0_name" value="Sample_1" size="10"/>' ], # sample name input field strings_displayed_after_submit=strings_displayed_after_submit ) # check the new sample field values on the request page @@ -446,7 +446,7 @@ class TestFormsAndRequests( TwillTestCas self.edit_samples( cntrller='requests', request_id=self.security.encode_id( request1.id ), sample_value_tuples=new_sample_value_tuples, - strings_displayed=[ 'Edit Current Samples of Request "%s"' % request1.name, + strings_displayed=[ 'Edit Current Samples of Sequencing Request "%s"' % request1.name, '<input type="text" name="sample_0_name" value="Sample1" size="10"/>' ], # sample name input field strings_displayed_after_submit=strings_displayed_after_submit ) # check the changed sample field values on the request page @@ -465,14 +465,14 @@ class TestFormsAndRequests( TwillTestCas self.submit_request( cntrller='requests', request_id=self.security.encode_id( request1.id ), request_name=request1.name, - strings_displayed_after_submit=[ 'The request has been submitted.' ] ) + strings_displayed_after_submit=[ 'The sequencing request has been submitted.' ] ) refresh( request1 ) # Make sure the request is showing in the 'submitted' filter self.check_request_grid( cntrller='requests', state=request1.states.SUBMITTED, strings_displayed=[ request1.name ] ) # Make sure the request's state is now set to 'submitted' - assert request1.state is not request1.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" \ + assert request1.state is not request1.states.SUBMITTED, "The state of the sequencing request '%s' should be set to '%s'" \ % ( request1.name, request1.states.SUBMITTED ) # the sample state should appear once for each sample strings_displayed_count = [ ( request1.type.states[0].name, len( request1.samples ) ) ] @@ -485,8 +485,8 @@ class TestFormsAndRequests( TwillTestCas strings_displayed_count=strings_displayed_count, strings_not_displayed=strings_not_displayed ) strings_displayed=[ 'History of sequencing request "%s"' % request1.name, - 'Request submitted by %s' % regular_user1.email, - 'Request created' ] + 'Sequencing request submitted by %s' % regular_user1.email, + 'Sequencing request created' ] strings_displayed_count = [ ( request1.states.SUBMITTED, 1 ) ] self.view_request_history( cntrller='requests', request_id=self.security.encode_id( request1.id ), @@ -519,7 +519,7 @@ class TestFormsAndRequests( TwillTestCas self.add_bar_codes( cntrller='requests_admin', request_id=self.security.encode_id( request1.id ), bar_codes=bar_codes, - strings_displayed=[ 'Edit Current Samples of Request "%s"' % request1.name ], + strings_displayed=[ 'Edit Current Samples of Sequencing Request "%s"' % request1.name ], strings_displayed_after_submit=strings_displayed_after_submit ) # the second sample state should appear once for each sample strings_displayed_count = [ ( request1.type.states[1].name, len( request1.samples ) ), @@ -538,7 +538,7 @@ class TestFormsAndRequests( TwillTestCas # check history of each sample for sample in request1.samples: strings_displayed = [ 'Events for Sample "%s"' % sample.name, - 'Request submitted and sample state set to %s' % request1.type.states[0].name, + 'Sequencing request submitted and sample state set to %s' % request1.type.states[0].name, request1.type.states[0].name, request1.type.states[1].name ] self.view_sample_history( cntrller='requests_admin', @@ -558,9 +558,9 @@ class TestFormsAndRequests( TwillTestCas if index > 1: # status message if index == len( request_type1.states ) - 1: - status_msg = 'All samples of this request are in the final sample state (%s).' % state.name + status_msg = 'All samples of this sequencing request are in the final sample state (%s).' % state.name else: - status_msg = 'All samples of this request are in the (%s) sample state. ' % state.name + status_msg = 'All samples of this sequencing request are in the (%s) sample state. ' % state.name # check email notification message email_msg = '' if state.id in [ email_state.id for email_state in email_notification_sample_states ]: @@ -568,7 +568,7 @@ class TestFormsAndRequests( TwillTestCas self.change_sample_state( request_id=self.security.encode_id( request1.id ), sample_ids=[ sample.id for sample in request1.samples ], new_sample_state_id=self.security.encode_id( state.id ), - strings_displayed=[ 'Edit Current Samples of Request "%s"' % request1.name ], + strings_displayed=[ 'Edit Current Samples of Sequencing Request "%s"' % request1.name ], strings_displayed_after_submit = [ status_msg, email_msg ] ) # check request history page if index == len( request_type1.states ) - 1: @@ -584,7 +584,7 @@ class TestFormsAndRequests( TwillTestCas self.check_request_grid( cntrller='requests_admin', state='Complete', strings_displayed=[ request1.name ] ) - assert request1.state is not request1.states.COMPLETE, "The state of the request '%s' should be set to '%s'" \ + assert request1.state is not request1.states.COMPLETE, "The state of the sequencing request '%s' should be set to '%s'" \ % ( request1.name, request1.states.COMPLETE ) # def test_045_admin_create_request_on_behalf_of_regular_user( self ): --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -113,27 +113,23 @@ </script></%def> -<%def name="render_editable_sample_row( cntrller, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )"> +<%def name="render_editable_sample_row( cntrller, request, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )"><% + trans.sa_session.refresh( request ) is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + is_rejected = request.is_rejected + is_complete = request.is_complete + is_submitted = request.is_submitted + is_unsubmitted = request.is_unsubmitted if sample: - trans.sa_session.refresh( sample.request ) - is_complete = sample.request.is_complete - is_rejected = request.is_rejected - is_submitted = sample.request.is_submitted - is_unsubmitted = sample.request.is_unsubmitted can_delete_samples = editing_samples and request.samples and ( ( is_admin and not is_complete ) or is_unsubmitted ) display_checkboxes = editing_samples and ( is_complete or is_rejected or is_submitted ) - display_bar_code = request.samples and ( is_complete or is_rejected or is_submitted ) display_datasets = request.samples and ( is_complete or is_submitted ) else: - is_complete = False - is_submitted = False - is_unsubmitted = False can_delete_samples = False display_checkboxes = False - display_bar_code = False display_datasets = False + display_bar_code = request.samples and ( is_complete or is_rejected or is_submitted ) %><% if display_checkboxes and trans.security.encode_id( sample.id ) in encoded_selected_sample_ids: @@ -152,15 +148,13 @@ </td> %if display_bar_code: <td valign="top"> - %if is_admin: + %if is_admin and is_submitted: <input type="text" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}" size="10"/> %else: ${sample_widget['bar_code']} <input type="hidden" name="sample_${sample_widget_index}_bar_code" value="${sample_widget['bar_code']}"/> %endif </td> - %else: - <td></td> %endif %if sample: %if is_unsubmitted: @@ -305,7 +299,7 @@ sample = None %> %if editing_samples: - <tr>${render_editable_sample_row( cntrller, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )}</tr> + <tr>${render_editable_sample_row( cntrller, request, sample, sample_widget_index, sample_widget, encoded_selected_sample_ids )}</tr> %elif sample: <tr><td> @@ -401,7 +395,7 @@ </tr> %else: ## The Add sample button was clicked for this sample_widget - <tr>${render_editable_sample_row( cntrller, None, sample_widget_index, sample_widget, encoded_selected_sample_ids )}</tr> + <tr>${render_editable_sample_row( cntrller, request, None, sample_widget_index, sample_widget, encoded_selected_sample_ids )}</tr> %endif %endfor </tbody>

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galaxy-dist commit a68c74ec8cfb: OpenID support for Galaxy.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1290006822 18000 # Node ID a68c74ec8cfbc641db4b6fe424e3f77b9f3c5d3c # Parent 56431b214df16653a966b96bf399c7646da267b8 OpenID support for Galaxy. --- a/eggs.ini +++ b/eggs.ini @@ -44,6 +44,7 @@ Paste = 1.6 PasteDeploy = 1.3.3 PasteScript = 1.7.3 pexpect = 2.4 +python_openid = 2.2.5 Routes = 1.12.3 SQLAlchemy = 0.5.6 sqlalchemy_migrate = 0.5.4 --- /dev/null +++ b/templates/user/openid_manage.mako @@ -0,0 +1,17 @@ +## Template generates a grid that enables user to select items. +<%namespace file="../grid_base.mako" import="make_grid" /> +<%namespace file="login.mako" import="render_openid_form" /> + +<%inherit file="../grid_base.mako" /> + +<%def name="grid_body( grid )"> + ${make_grid( grid )} + <h2>Associate more OpenIDs</h2> + ${render_openid_form( kwargs['referer'], True, kwargs['openid_providers'] )} +</%def> + +<%def name="center_panel()"> + <div style="margin: 1em;"> + ${grid_body( grid )} + </div> +</%def> Binary file static/images/openid-16x16.gif has changed --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1953,6 +1953,12 @@ class UserAddress( object ): html = html + '<br/>' + 'Phone: ' + self.phone return html +class UserOpenID( object ): + def __init__( self, user=None, session=None, openid=None ): + self.user = user + self.session = session + self.openid = openid + class Page( object ): def __init__( self ): self.id = None --- a/templates/user/index.mako +++ b/templates/user/index.mako @@ -15,6 +15,9 @@ %if trans.app.config.enable_api: <li><a href="${h.url_for( controller='user', action='api_keys' )}">${_('Manage your API Keys')}</a> for new histories</li> %endif + %if trans.app.config.enable_openid: + <li><a href="${h.url_for( controller='user', action='openid_manage' )}">${ ('Manage OpenIDs')}</a> linked to your account</li> + %endif %else: <li><a href="${h.url_for( controller='user', action='show_info', webapp='community' )}">${_('Manage your information')}</a></li> %endif --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0062_user_openid_table.py @@ -0,0 +1,48 @@ +""" +Migration script to create table for associating sessions and users with +OpenIDs. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +# Table to add + +UserOpenID_table = Table( "galaxy_user_openid", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, index=True, default=now, onupdate=now ), + Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "openid", TEXT, index=True, unique=True ), + ) + +def upgrade(): + print __doc__ + metadata.reflect() + + # Create galaxy_user_openid table + try: + UserOpenID_table.create() + except Exception, e: + log.debug( "Creating galaxy_user_openid table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + + # Drop galaxy_user_openid table + try: + UserOpenID_table.drop() + except Exception, e: + log.debug( "Dropping galaxy_user_openid table failed: %s" % str( e ) ) --- a/templates/user/login.mako +++ b/templates/user/login.mako @@ -1,23 +1,77 @@ -<%inherit file="/base.mako"/> +<%! + def inherit(context): + if context.get('use_panels'): + if context.get('webapp'): + webapp = context.get('webapp') + else: + webapp = 'galaxy' + return '/webapps/%s/base_panels.mako' % webapp + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.active_view=active_view + self.message_box_visible=False +%> +</%def> + <%namespace file="/message.mako" import="render_msg" /> -%if redirect_url: - <script type="text/javascript"> - top.location.href = '${redirect_url}'; - </script> -%endif +<%def name="center_panel()"> + ${body()} +</%def> -%if not redirect_url and message: - ${render_msg( message, status )} -%endif +<%def name="body()"> -%if not trans.user: + %if redirect_url: + <script type="text/javascript"> + top.location.href = '${redirect_url}'; + </script> + %endif + + %if context.get('use_panels'): + <div style="margin: 1em;"> + %else: + <div> + %endif + + %if message: + ${render_msg( message, status )} + %endif + + %if not trans.user: + + ${render_login_form()} + + %if trans.app.config.enable_openid: + <br/> + ${render_openid_form( referer, False, openid_providers )} + %endif + + %endif + + </div> + +</%def> + +<%def name="render_login_form( form_action=None )"> + + <% + if form_action is None: + form_action = h.url_for( controller='user', action='login', use_panels=use_panels ) + %> + %if header: ${header} %endif <div class="toolForm"><div class="toolFormTitle">Login</div> - <form name="login" id="login" action="${h.url_for( controller='user', action='login' )}" method="post" > + <form name="login" id="login" action="${form_action}" method="post" ><div class="form-row"><label>Email address:</label><input type="text" name="email" value="${email}" size="40"/> @@ -36,4 +90,32 @@ </div></form></div> -%endif + +</%def> + +<%def name="render_openid_form( referer, auto_associate, openid_providers )"> + + <div class="toolForm"> + <div class="toolFormTitle">OpenID Login</div> + <form name="openid" id="openid" action="${h.url_for( controller='user', action='openid_auth' )}" method="post" > + <div class="form-row"> + <label>OpenID URL:</label> + <input type="text" name="openid_url" size="60" style="background-image:url('${h.url_for( '/static/images/openid-16x16.gif' )}' ); background-repeat: no-repeat; padding-right: 20px; background-position: 99% 50%;"/> + <input type="hidden" name="webapp" value="${webapp}" size="40"/> + <input type="hidden" name="referer" value="${referer}" size="40"/> + <input type="hidden" name="auto_associate" value="${auto_associate}" size="40"/> + </div> + <div class="form-row"> + Or, authenticate with your <select name="openid_provider"> + %for provider in openid_providers.keys(): + <option>${provider}</option> + %endfor + </select> account. + </div> + <div class="form-row"> + <input type="submit" name="login_button" value="Login"/> + </div> + </form> + </div> + +</%def> --- a/lib/galaxy/eggs/__init__.py +++ b/lib/galaxy/eggs/__init__.py @@ -321,6 +321,7 @@ class GalaxyConfig( object ): "pbs_python": lambda: "pbs" in self.config.get( "app:main", "start_job_runners" ).split(","), "threadframe": lambda: self.config.get( "app:main", "use_heartbeat" ), "guppy": lambda: self.config.get( "app:main", "use_memdump" ), + "python_openid": lambda: self.config.get( "app:main", "enable_openid" ), "GeneTrack": lambda: sys.version_info[:2] >= ( 2, 5 ), "pysam": check_pysam() }.get( egg_name, lambda: True )() --- /dev/null +++ b/templates/user/openid_associate.mako @@ -0,0 +1,75 @@ +<%! + def inherit(context): + if context.get('use_panels'): + if context.get('webapp'): + webapp = context.get('webapp') + else: + webapp = 'galaxy' + return '/webapps/%s/base_panels.mako' % webapp + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.active_view=active_view + self.message_box_visible=False +%> +</%def> + +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="login.mako" import="render_login_form" /> +<%namespace file="register.mako" import="render_registration_form" /> + +<%def name="center_panel()"> + ${body()} +</%def> + +<%def name="body()"> + + %if context.get('use_panels'): + <div style="margin: 1em;"> + %else: + <div> + %endif + + %if message: + ${render_msg( message, status )} + %endif + + <h2>OpenID Account Association</h2> + <div> + OpenIDs must be associated with a Galaxy account before they can be used for authentication. This only needs to be done once per OpenID. You may associate your OpenID with an existing Galaxy account, or create a new one. + </div> + <br/> + + %if len( openids ) > 1: + <div> + The following OpenIDs will be associated with the account chosen or created below. + <ul> + %for openid in openids: + <li>${openid.openid}</li> + %endfor + </ul> + </div> + %else: + <div> + The OpenID <strong>${openids[0].openid}</strong> will be associated with the account chosen or created. + </div> + %endif + <br/> + + <% form_action = h.url_for( use_panels=use_panels ) %> + + ${render_login_form( form_action=form_action )} + + <br/> + + ${render_registration_form( form_action=form_action )} + + </div> + +</%def> --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -22,8 +22,18 @@ ## An admin user may be creating a new user account, in which case we want to display the registration form. ## But if the current user is not an admin user, then don't display the registration form. %if trans.user_is_admin() or not trans.user: + ${render_registration_form()} +%endif + +<%def name="render_registration_form( form_action=None )"> + + <% + if form_action is None: + form_action = h.url_for( controller='user', action='create', admin_view=admin_view ) + %> + <div class="toolForm"> - <form name="registration" id="registration" action="${h.url_for( controller='user', action='create', admin_view=admin_view )}" method="post" > + <form name="registration" id="registration" action="${form_action}" method="post" ><div class="toolFormTitle">Create account</div><div class="form-row"><label>Email address:</label> @@ -83,4 +93,5 @@ </div></form></div> -%endif + +</%def> --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -324,6 +324,10 @@ use_interactive = True # WYSIWYG editor that is very similar to a word processor. #enable_pages = False +# Enable authentication via OpenID. Allows users to log in to their Galaxy +# account by authenticating with an OpenID provider. +#enable_openid = False + # Enable the (experimental! beta!) Web API. Documentation forthcoming. #enable_api = False --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -68,6 +68,15 @@ UserAddress.table = Table( "user_address Column( "deleted", Boolean, index=True, default=False ), Column( "purged", Boolean, index=True, default=False ) ) +UserOpenID.table = Table( "galaxy_user_openid", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, index=True, default=now, onupdate=now ), + Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "openid", TEXT, index=True, unique=True ), + ) + History.table = Table( "history", metadata, Column( "id", Integer, primary_key=True), Column( "create_time", DateTime, default=now ), @@ -968,6 +977,17 @@ assign_mapper( context, UserAddress, Use order_by=desc(UserAddress.table.c.update_time)), ) ) +assign_mapper( context, UserOpenID, UserOpenID.table, + properties=dict( + session=relation( GalaxySession, + primaryjoin=( UserOpenID.table.c.session_id == GalaxySession.table.c.id ), + backref='openids', + order_by=desc( UserOpenID.table.c.update_time ) ), + user=relation( User, + primaryjoin=( UserOpenID.table.c.user_id == User.table.c.id ), + backref='openids', + order_by=desc( UserOpenID.table.c.update_time ) ) ) ) + assign_mapper( context, ValidationError, ValidationError.table ) --- a/templates/display_common.mako +++ b/templates/display_common.mako @@ -85,6 +85,8 @@ class_plural = "Forms" elif a_class == model.RequestType: class_plural = "sequencer configurations" + elif a_class == model.UserOpenID: + class_plural = "OpenIDs" else: class_plural = a_class.__name__ + "s" return class_plural --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -60,6 +60,10 @@ class UniverseApplication( object ): self.heartbeat = None self.memdump = None self.memory_usage = None + # Container for OpenID authentication routines + if self.config.enable_openid: + from galaxy.web.framework import openid_manager + self.openid_manager = openid_manager.OpenIDManager( self.config.openid_consumer_cache_path ) # Start the heartbeat process if configured and available if self.config.use_heartbeat: from galaxy.util import heartbeat --- /dev/null +++ b/lib/galaxy/web/framework/openid_manager.py @@ -0,0 +1,53 @@ +""" +Mange the OpenID consumer and related data stores. +""" + +import os, pickle, logging + +from galaxy import eggs +eggs.require( 'python-openid' ) + +import openid +from openid import oidutil +from openid.store import filestore +from openid.consumer import consumer +from openid.extensions import sreg + +log = logging.getLogger( __name__ ) +def oidlog( message, level=0 ): + log.debug( message ) +oidutil.log = oidlog + +class OpenIDManager( object ): + def __init__( self, cache_path ): + self.session_path = os.path.join( cache_path, 'session' ) + self.store_path = os.path.join( cache_path, 'store' ) + for dir in self.session_path, self.store_path: + if not os.path.exists( dir ): + os.makedirs( dir ) + self.store = filestore.FileOpenIDStore( self.store_path ) + def get_session( self, trans ): + session_file = os.path.join( self.session_path, str( trans.galaxy_session.id ) ) + if not os.path.exists( session_file ): + pickle.dump( dict(), open( session_file, 'w' ) ) + return pickle.load( open( session_file ) ) + def persist_session( self, trans, oidconsumer ): + session_file = os.path.join( self.session_path, str( trans.galaxy_session.id ) ) + pickle.dump( oidconsumer.session, open( session_file, 'w' ) ) + def get_consumer( self, trans ): + return consumer.Consumer( self.get_session( trans ), self.store ) + def add_sreg( self, trans, request, required=None, optional=None ): + if required is None: + required = [] + if optional is None: + optional = [] + sreg_request = sreg.SRegRequest( required=required, optional=optional ) + request.addExtension( sreg_request ) + def get_sreg( self, info ): + return sreg.SRegResponse.fromSuccessResponse( info ) + + # so I don't have to expose all of openid.consumer.consumer + FAILURE = consumer.FAILURE + SUCCESS = consumer.SUCCESS + CANCEL = consumer.CANCEL + SETUP_NEEDED = consumer.SETUP_NEEDED --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -39,9 +39,11 @@ class Configuration( object ): # Where dataset files are stored self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root ) self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) + self.openid_consumer_cache_path = resolve_path( kwargs.get( "openid_consumer_cache_path", "database/openid_consumer_cache" ), self.root ) self.cookie_path = kwargs.get( "cookie_path", "/" ) # web API self.enable_api = string_as_bool( kwargs.get( 'enable_api', False ) ) + self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) # Communication with a sequencer self.enable_sequencer_communication = string_as_bool( kwargs.get( 'enable_sequencer_communication', False ) ) # dataset Track files @@ -161,7 +163,17 @@ class Configuration( object ): if not os.path.isdir( path ): raise ConfigurationError("Directory does not exist: %s" % path ) # Create the directories that it makes sense to create - for path in self.file_path, self.new_file_path, self.job_working_directory, self.cluster_files_directory, self.template_cache, self.ftp_upload_dir, self.library_import_dir, self.user_library_import_dir, self.nginx_upload_store, './static/genetrack/plots', os.path.join( self.tool_data_path, 'shared', 'jars' ): + for path in self.file_path, \ + self.new_file_path, \ + self.job_working_directory, \ + self.cluster_files_directory, \ + self.template_cache, \ + self.ftp_upload_dir, \ + self.library_import_dir, \ + self.user_library_import_dir, \ + self.nginx_upload_store, \ + './static/genetrack/plots', \ + os.path.join( self.tool_data_path, 'shared', 'jars' ): if path not in [ None, False ] and not os.path.isdir( path ): try: os.makedirs( path ) --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -1,9 +1,10 @@ """ Contains the user interface in the Universe class """ +from galaxy.web.framework.helpers import time_ago, grids from galaxy.web.base.controller import * from galaxy.model.orm import * -from galaxy import util +from galaxy import util, model import logging, os, string, re, smtplib, socket from random import choice from email.MIMEText import MIMEText @@ -26,48 +27,337 @@ require_login_creation_template = requir VALID_USERNAME_RE = re.compile( "^[a-z0-9\-]+$" ) +OPENID_PROVIDERS = { 'Google' : 'https://www.google.com/accounts/o8/id', + 'Yahoo!' : 'http://yahoo.com', + 'AOL/AIM' : 'http://openid.aol.com', + 'Flickr' : 'http://flickr.com', + 'Launchpad' : 'http://login.launchpad.net', + } + +class UserOpenIDGrid( grids.Grid ): + use_panels = False + title = "OpenIDs linked to your account" + model_class = model.UserOpenID + template = '/user/openid_manage.mako' + default_filter = { "openid" : "All" } + default_sort_key = "-create_time" + columns = [ + grids.TextColumn( "OpenID URL", key="openid" ), + grids.GridColumn( "Created", key="create_time", format=time_ago ), + ] + operations = [ + grids.GridOperation( "Delete", async_compatible=True ), + ] + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( self.model_class ).filter( self.model_class.user_id == trans.user.id ) + class User( BaseController, UsesFormDefinitionWidgets ): + user_openid_grid = UserOpenIDGrid() @web.expose def index( self, trans, webapp='galaxy', **kwd ): return trans.fill_template( '/user/index.mako', webapp=webapp ) @web.expose + def openid_auth( self, trans, webapp='galaxy', **kwd ): + if not trans.app.config.enable_openid: + return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' ) + message = 'Unspecified failure authenticating via OpenID' + status = kwd.get( 'status', 'done' ) + openid_url = kwd.get( 'openid_url', '' ) + openid_provider = kwd.get( 'openid_provider', '' ) + referer = kwd.get( 'referer', trans.request.referer ) + auto_associate = util.string_as_bool( kwd.get( 'auto_associate', False ) ) + use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) + action = 'login' + if auto_associate: + action = 'openid_manage' + if not referer: + referer = url_for( '/' ) + consumer = trans.app.openid_manager.get_consumer( trans ) + process_url = trans.request.base.rstrip( '/' ) + url_for( controller='user', action='openid_process', referer=referer, auto_associate=auto_associate ) + if not openid_url and openid_provider and openid_provider in OPENID_PROVIDERS: + openid_url = OPENID_PROVIDERS[openid_provider] + if openid_url: + request = None + try: + request = consumer.begin( openid_url ) + if request is None: + message = 'No OpenID services are available at %s' % openid_url + except Exception, e: + message = 'Failed to begin OpenID authentication: %s' % str( e ) + if request is not None: + trans.app.openid_manager.add_sreg( trans, request, optional=[ 'nickname', 'email' ] ) + if request.shouldSendRedirect(): + redirect_url = request.redirectURL( + trans.request.base, process_url ) + trans.app.openid_manager.persist_session( trans, consumer ) + trans.response.send_redirect( redirect_url ) + return + else: + form = request.htmlMarkup( trans.request.base, process_url, form_tag_attrs={'id':'openid_message','target':'_top'} ) + trans.app.openid_manager.persist_session( trans, consumer ) + return form + return trans.response.send_redirect( url_for( controller='user', + action=action, + use_panels=use_panels, + message=message, + status='error' ) ) + @web.expose + def openid_process( self, trans, webapp='galaxy', **kwd ): + if not trans.app.config.enable_openid: + return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' ) + auto_associate = util.string_as_bool( kwd.get( 'auto_associate', False ) ) + action = 'login' + if auto_associate: + action = 'openid_manage' + if trans.app.config.bugs_email is not None: + contact = '<a href="mailto:%s">contact support</a>' % trans.app.config.bugs_email + else: + contact = 'contact support' + message = 'Verification failed for an unknown reason. Please contact support for assistance.' + status = 'error' + consumer = trans.app.openid_manager.get_consumer( trans ) + info = consumer.complete( kwd, trans.request.url ) + display_identifier = info.getDisplayIdentifier() + redirect_url = kwd.get( 'referer', url_for( '/' ) ) + if info.status == trans.app.openid_manager.FAILURE and display_identifier: + message = "Login via OpenID failed. The technical reason for this follows, please include this message in your email if you need to %s to resolve this problem: %s" % ( contact, info.message ) + return trans.response.send_redirect( url_for( controller='user', + action=action, + use_panels=True, + message=message, + status='error' ) ) + elif info.status == trans.app.openid_manager.SUCCESS: + if info.endpoint.canonicalID: + display_identifier = info.endpoint.canonicalID + user_openid = trans.sa_session.query( trans.app.model.UserOpenID ).filter( trans.app.model.UserOpenID.table.c.openid == display_identifier ).first() + if not user_openid: + user_openid = trans.app.model.UserOpenID( session=trans.galaxy_session, openid=display_identifier ) + elif not user_openid.user and user_openid.session.id != trans.galaxy_session.id: + user_openid.session = trans.galaxy_session + elif user_openid.user and not auto_associate: + trans.handle_user_login( user_openid.user, webapp ) + trans.log_event( "User logged in via OpenID: %s" % display_identifier ) + trans.response.send_redirect( redirect_url ) + return + if auto_associate and trans.user: + # The user is already logged in and requested association from + # the user prefs as opposed to using the OpenID form on the + # login page. + if user_openid.user and user_openid.user.id != trans.user.id: + message = "The OpenID <strong>%s</strong> is already associated with another Galaxy account, <strong>%s</strong>. Please disassociate it from that account before attempting to associate it with a new account." % ( display_identifier, user_openid.user.email ) + status = "error" + elif user_openid.user and user_openid.user.id == trans.user.id: + message = "The OpenID <strong>%s</strong> is already associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) + status = "warning" + else: + user_openid.user_id = trans.user.id + trans.sa_session.add( user_openid ) + trans.sa_session.flush() + trans.log_event( "User associated OpenID: %s" % display_identifier ) + message = "The OpenID <strong>%s</strong> has been associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) + status = "done" + trans.response.send_redirect( url_for( controller='user', + action='openid_manage', + use_panels=True, + message=message, + status=status ) ) + return + trans.sa_session.add( user_openid ) + trans.sa_session.flush() + message = "OpenID authentication was successful, but you need to associate your OpenID with a Galaxy account." + sreg_resp = trans.app.openid_manager.get_sreg( info ) + try: + username = sreg_resp.get( 'nickname', '' ) + except AttributeError: + username = '' + try: + email = sreg_resp.get( 'email', '' ) + except AttributeError: + email = '' + trans.response.send_redirect( url_for( controller='user', + action='openid_associate', + use_panels=True, + username=username, + email=email, + message=message, + status='warning' ) ) + elif info.status == trans.app.openid_manager.CANCEL: + message = "Login via OpenID was cancelled by an action at the OpenID provider's site." + status = "warning" + elif info.status == trans.app.openid_manager.SETUP_NEEDED: + if info.setup_url: + return trans.response.send_redirect( info.setup_url ) + else: + message = "Unable to log in via OpenID. Setup at the provider is required before this OpenID can be used. Please visit your provider's site to complete this step." + return trans.response.send_redirect( url_for( controller='user', + action=action, + use_panels=True, + message=message, + status=status ) ) + @web.expose + def openid_associate( self, trans, webapp='galaxy', **kwd ): + if not trans.app.config.enable_openid: + return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' ) + use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + email = kwd.get( 'email', '' ) + username = kwd.get( 'username', '' ) + referer = kwd.get( 'referer', trans.request.referer ) + params = util.Params( kwd ) + admin_view = util.string_as_bool( params.get( 'admin_view', False ) ) + openids = trans.galaxy_session.openids + if not openids: + return trans.show_error_message( 'You have not successfully completed an OpenID authentication in this session. You can do so on the <a href="%s">login</a> page.' % url_for( controller='user', action='login', use_panels=use_panels ) ) + elif admin_view: + return trans.show_error_message( 'Associating OpenIDs with accounts cannot be done by administrators.' ) + if kwd.get( 'login_button', False ): + message, status, user, success = self.__validate_login( trans, webapp, **kwd ) + if success: + for openid in openids: + openid.user = user + trans.sa_session.add( openid ) + trans.sa_session.flush() + for openid in openids: + trans.log_event( "User associated OpenID: %s" % openid.openid ) + redirect_url = referer + if not redirect_url: + redirect_url = url_for( '/' ) + trans.response.send_redirect( redirect_url ) + return + if kwd.get( 'create_user_button', False ): + password = kwd.get( 'password', '' ) + confirm = kwd.get( 'confirm', '' ) + subscribe = params.get( 'subscribe', '' ) + subscribe_checked = CheckboxField.is_checked( subscribe ) + error = '' + if not trans.app.config.allow_user_creation and not trans.user_is_admin(): + error = 'User registration is disabled. Please contact your Galaxy administrator for an account.' + else: + # Check email and password validity + error = self.__validate( trans, params, email, password, confirm, username, webapp ) + if not error: + # all the values are valid + message, status, user, success = self.__register( trans, webapp, email, password, username, subscribe_checked, kwd ) + if success: + trans.handle_user_login( user, webapp ) + trans.log_event( "User created a new account" ) + trans.log_event( "User logged in" ) + for openid in openids: + openid.user = user + trans.sa_session.add( openid ) + trans.sa_session.flush() + for openid in openids: + trans.log_event( "User associated OpenID: %s" % openid.openid ) + redirect_url = referer + if not redirect_url: + redirect_url = url_for( '/' ) + trans.response.send_redirect( redirect_url ) + else: + message = error + status = 'error' + if webapp == 'galaxy': + user_info_select, user_info_form, widgets = self.__user_info_ui( trans, **kwd ) + else: + user_info_select = [] + user_info_form = [] + widgets = [] + return trans.fill_template( '/user/openid_associate.mako', + webapp=webapp, + email=email, + password='', + confirm='', + username=username, + header='', + use_panels=use_panels, + redirect_url='', + referer='', + refresh_frames=[], + message=message, + status=status, + active_view="user", + subscribe_checked=False, + admin_view=False, + user_info_select=user_info_select, + user_info_form=user_info_form, + widgets=widgets, + openids=openids ) + @web.expose + @web.require_login( 'manage OpenIDs' ) + def openid_disassociate( self, trans, webapp='galaxy', **kwd ): + if not trans.app.config.enable_openid: + return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' ) + params = util.Params( kwd ) + ids = params.get( 'id', None ) + message = params.get( 'message', None ) + status = params.get( 'status', None ) + use_panels = params.get( 'use_panels', False ) + user_openids = [] + if not ids: + message = 'You must select at least one OpenID to disassociate from your Galaxy account.' + status = 'error' + else: + ids = util.listify( params.id ) + for id in ids: + id = trans.security.decode_id( id ) + user_openid = trans.sa_session.query( trans.app.model.UserOpenID ).get( int( id ) ) + if not user_openid or ( trans.user.id != user_openid.user_id ): + message = 'The selected OpenID(s) are not associated with your Galaxy account.' + status = 'error' + user_openids = [] + break + user_openids.append( user_openid ) + if user_openids: + deleted_urls = [] + for user_openid in user_openids: + trans.sa_session.delete( user_openid ) + deleted_urls.append( user_openid.openid ) + trans.sa_session.flush() + for deleted_url in deleted_urls: + trans.log_event( "User disassociated OpenID: %s" % deleted_url ) + message = '%s OpenIDs were disassociated from your Galaxy account.' % len( ids ) + status = 'done' + trans.response.send_redirect( url_for( controller='user', + action='openid_manage', + use_panels=use_panels, + message=message, + status=status ) ) + @web.expose + @web.require_login( 'manage OpenIDs' ) + def openid_manage( self, trans, webapp='galaxy', **kwd ): + if not trans.app.config.enable_openid: + return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' ) + use_panels = kwd.get( 'use_panels', False ) + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "delete": + trans.response.send_redirect( url_for( controller='user', + action='openid_disassociate', + use_panels=use_panels, + id=kwd['id'] ) ) + kwd['referer'] = url_for( controller='user', action='openid_manage', use_panels=True ) + kwd['openid_providers'] = OPENID_PROVIDERS + return self.user_openid_grid( trans, **kwd ) + @web.expose def login( self, trans, webapp='galaxy', redirect_url='', refresh_frames=[], **kwd ): referer = kwd.get( 'referer', trans.request.referer ) - use_panels = util.string_as_bool( kwd.get( 'use_panels', True ) ) + use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) header = '' user = None email = kwd.get( 'email', '' ) if kwd.get( 'login_button', False ): - password = kwd.get( 'password', '' ) - referer = kwd.get( 'referer', '' ) if webapp == 'galaxy' and not refresh_frames: if trans.app.config.require_login: refresh_frames = [ 'masthead', 'history', 'tools' ] else: refresh_frames = [ 'masthead', 'history' ] - user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email==email ).first() - if not user: - message = "No such user" - status = 'error' - elif user.deleted: - message = "This account has been marked deleted, contact your Galaxy administrator to restore the account." - status = 'error' - elif user.external: - message = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it." - status = 'error' - elif not user.check_password( password ): - message = "Invalid password" - status = 'error' - else: - trans.handle_user_login( user, webapp ) - trans.log_event( "User logged in" ) - message = 'You are now logged in as %s.<br>You can <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \ - ( user.email, referer, url_for( '/' ) ) - if trans.app.config.require_login: - message += ' <a target="_top" href="%s">Click here</a> to continue to the home page.' % web.url_for( '/static/welcome.html' ) + message, status, user, success = self.__validate_login( trans, webapp, **kwd ) + if success and referer: redirect_url = referer + elif success: + redirect_url = url_for( '/' ) if not user and trans.app.config.require_login: if trans.app.config.allow_user_creation: header = require_login_creation_template % web.url_for( action='create' ) @@ -83,7 +373,37 @@ class User( BaseController, UsesFormDefi refresh_frames=refresh_frames, message=message, status=status, + openid_providers=OPENID_PROVIDERS, active_view="user" ) + def __validate_login( self, trans, webapp='galaxy', **kwd ): + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + email = kwd.get( 'email', '' ) + password = kwd.get( 'password', '' ) + referer = kwd.get( 'referer', trans.request.referer ) + success = False + user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email==email ).first() + if not user: + message = "No such user" + status = 'error' + elif user.deleted: + message = "This account has been marked deleted, contact your Galaxy administrator to restore the account." + status = 'error' + elif user.external: + message = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it." + status = 'error' + elif not user.check_password( password ): + message = "Invalid password" + status = 'error' + else: + trans.handle_user_login( user, webapp ) + trans.log_event( "User logged in" ) + message = 'You are now logged in as %s.<br>You can <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \ + ( user.email, referer, url_for( '/' ) ) + if trans.app.config.require_login: + message += ' <a target="_top" href="%s">Click here</a> to continue to the home page.' % web.url_for( '/static/welcome.html' ) + success = True + return ( message, status, user, success ) @web.expose def logout( self, trans, webapp='galaxy' ): if webapp == 'galaxy': @@ -138,54 +458,25 @@ class User( BaseController, UsesFormDefi error = self.__validate( trans, params, email, password, confirm, username, webapp ) if not error: # all the values are valid - user = trans.app.model.User( email=email ) - user.set_password_cleartext( password ) - user.username = username - trans.sa_session.add( user ) - trans.sa_session.flush() - trans.app.security_agent.create_private_user_role( user ) - message = 'Now logged in as %s.<br><a target="_top" href="%s">Return to the home page.</a>' % ( user.email, url_for( '/' ) ) - if webapp == 'galaxy': - # We set default user permissions, before we log in and set the default history permissions - trans.app.security_agent.user_set_default_permissions( user, - default_access_private=trans.app.config.new_user_dataset_access_role_default_private ) - # save user info - self.__save_user_info( trans, user, action='create', new_user=True, **kwd ) - if subscribe_checked: - # subscribe user to email list - if trans.app.config.smtp_server is None: - error = "Now logged in as " + user.email + ". However, subscribing to the mailing list has failed because mail is not configured for this Galaxy instance." - else: - msg = MIMEText( 'Join Mailing list.\n' ) - to = msg[ 'To' ] = trans.app.config.mailing_join_addr - frm = msg[ 'From' ] = email - msg[ 'Subject' ] = 'Join Mailing List' - try: - s = smtplib.SMTP() - s.connect( trans.app.config.smtp_server ) - s.sendmail( frm, [ to ], msg.as_string() ) - s.close() - except: - error = "Now logged in as " + user.email + ". However, subscribing to the mailing list has failed." - if not error and not admin_view: - # The handle_user_login() method has a call to the history_set_default_permissions() method - # (needed when logging in with a history), user needs to have default permissions set before logging in - trans.handle_user_login( user, webapp ) - trans.log_event( "User created a new account" ) - trans.log_event( "User logged in" ) - elif not error: - trans.response.send_redirect( web.url_for( controller='admin', - action='users', - message='Created new user account (%s)' % user.email, - status='done' ) ) - elif not admin_view: + message, status, user, success = self.__register( trans, webapp, email, password, username, subscribe_checked, kwd ) + if success and not admin_view and webapp != 'galaxy': # Must be logging into the community space webapp trans.handle_user_login( user, webapp ) - if not error: - redirect_url = referer - if error: - message=error - status='error' + redirect_url = referer + if success and not admin_view: + # The handle_user_login() method has a call to the history_set_default_permissions() method + # (needed when logging in with a history), user needs to have default permissions set before logging in + trans.handle_user_login( user, webapp ) + trans.log_event( "User created a new account" ) + trans.log_event( "User logged in" ) + elif success: + trans.response.send_redirect( web.url_for( controller='admin', + action='users', + message='Created new user account (%s)' % user.email, + status='done' ) ) + else: + message = error + status = 'error' if webapp == 'galaxy': user_info_select, user_info_form, widgets = self.__user_info_ui( trans, **kwd ) else: @@ -209,6 +500,57 @@ class User( BaseController, UsesFormDefi refresh_frames=refresh_frames, message=message, status=status ) + def __register( self, trans, webapp, email, password, username, subscribe_checked, kwd ): + status = kwd.get( 'status', 'done' ) + admin_view = util.string_as_bool( kwd.get( 'admin_view', False ) ) + user = trans.app.model.User( email=email ) + user.set_password_cleartext( password ) + user.username = username + trans.sa_session.add( user ) + trans.sa_session.flush() + trans.app.security_agent.create_private_user_role( user ) + error = '' + if webapp == 'galaxy': + # We set default user permissions, before we log in and set the default history permissions + trans.app.security_agent.user_set_default_permissions( user, + default_access_private=trans.app.config.new_user_dataset_access_role_default_private ) + # save user info + self.__save_user_info( trans, user, action='create', new_user=True, **kwd ) + if subscribe_checked: + # subscribe user to email list + if trans.app.config.smtp_server is None: + error = "Now logged in as " + user.email + ". However, subscribing to the mailing list has failed because mail is not configured for this Galaxy instance." + else: + msg = MIMEText( 'Join Mailing list.\n' ) + to = msg[ 'To' ] = trans.app.config.mailing_join_addr + frm = msg[ 'From' ] = email + msg[ 'Subject' ] = 'Join Mailing List' + try: + s = smtplib.SMTP() + s.connect( trans.app.config.smtp_server ) + s.sendmail( frm, [ to ], msg.as_string() ) + s.close() + except: + error = "Now logged in as " + user.email + ". However, subscribing to the mailing list has failed." + if not error and not admin_view: + # The handle_user_login() method has a call to the history_set_default_permissions() method + # (needed when logging in with a history), user needs to have default permissions set before logging in + trans.handle_user_login( user, webapp ) + trans.log_event( "User created a new account" ) + trans.log_event( "User logged in" ) + elif not error: + trans.response.send_redirect( web.url_for( controller='admin', + action='users', + message='Created new user account (%s)' % user.email, + status='done' ) ) + if error: + message = error + status = 'error' + success = False + else: + message = 'Now logged in as %s.<br><a target="_top" href="%s">Return to the home page.</a>' % ( user.email, url_for( '/' ) ) + success = True + return ( message, status, user, success ) def __save_user_info(self, trans, user, action, new_user=True, **kwd): ''' This method saves the user information for new users as well as editing user --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -29,12 +29,19 @@ ## <%def name="center_panel()"> - ${make_grid( grid )} + ${self.grid_body( grid )} </%def> ## Render the grid's basic elements. Each of these elements can be subclassed. <%def name="body()"> - ${make_grid( grid )} + ${self.grid_body( grid )} +</%def> + +## Because body() is special and always exists even if not explicitly defined, +## it's not possible to override body() in the topmost template in the chain. +## Because of this, override grid_body() instead. +<%def name="grid_body( grid )"> + ${self.make_grid( grid )} </%def><%def name="title()">${grid.title}</%def>

1 0

galaxy-dist commit 2e2ee0289d67: Fix BLAST+ regression from changeset 535d276c92bc (loc file columns)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1289925107 0 # Node ID 2e2ee0289d67d244954aa05bfe315dbb5ff413eb # Parent d2d0c199c20ddf942e1e2587dc9aede8acd9cebc Fix BLAST+ regression from changeset 535d276c92bc (loc file columns) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -40,10 +40,13 @@ blastn </param><when value="db"><param name="database" type="select" label="Nucleotide BLAST database"> -  + <options from_file="blastdb.loc"> - <column name="name" index="2"/> - <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="value" index="2"/></options></param><param name="subject" type="hidden" value="" /> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -41,10 +41,13 @@ blastp </param><when value="db"><param name="database" type="select" label="Protein BLAST database"> -  + <options from_file="blastdb_p.loc"> - <column name="name" index="2"/> - <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="value" index="2"/></options></param><param name="subject" type="hidden" value="" /> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -39,10 +39,13 @@ tblastx </param><when value="db"><param name="database" type="select" label="Nucleotide BLAST database"> -  + <options from_file="blastdb.loc"> - <column name="name" index="2"/> - <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="value" index="2"/></options></param><param name="subject" type="hidden" value="" /> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -40,10 +40,13 @@ blastx </param><when value="db"><param name="database" type="select" label="Protein BLAST database"> -  + <options from_file="blastdb_p.loc"> - <column name="name" index="2"/> - <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="value" index="2"/></options></param><param name="subject" type="hidden" value="" /> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -40,10 +40,13 @@ tblastn </param><when value="db"><param name="database" type="select" label="Nucleotide BLAST database"> -  + <options from_file="blastdb.loc"> - <column name="name" index="2"/> - <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="value" index="2"/></options></param><param name="subject" type="hidden" value="" />

1 0

galaxy-dist commit 7bded9108bd8: More miscellaneous Sample Tracking cleanup and bug fixes, move supported form_builder field types from form_builder.BaseField to Request.model and Sample.model.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1290007512 18000 # Node ID 7bded9108bd8297ea609e9ec06bbe516b5f0b83a # Parent a68c74ec8cfbc641db4b6fe424e3f77b9f3c5d3c More miscellaneous Sample Tracking cleanup and bug fixes, move supported form_builder field types from form_builder.BaseField to Request.model and Sample.model. --- a/templates/admin/requests/edit_request_type.mako +++ b/templates/admin/requests/edit_request_type.mako @@ -28,7 +28,7 @@ </div><div class="form-row"><label> - Sequencing Request Form definition: + Sequencing request form definition: </label><select name="form_id"> %for form in forms: @@ -42,7 +42,7 @@ </div><div class="form-row"><label> - Sample Form definition: + Sample form definition: </label><select name="form_id"> %for form in forms: --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -18,12 +18,6 @@ class BaseField(object): return ' disabled="disabled"' else: return '' - @staticmethod - def form_field_types(): - return ['TextField', 'TextArea', 'SelectField', 'CheckboxField', 'AddressField', 'WorkflowField'] - @staticmethod - def sample_field_types(): - return ['TextField', 'SelectField', 'CheckboxField', 'WorkflowField'] class TextField(BaseField): """ @@ -559,8 +553,8 @@ class AddressField(BaseField): self.select_address.add_option( 'Add a new address', 'new' ) return self.select_address.get_html( disabled=disabled ) + address_html -class WorkflowField(BaseField): - def __init__(self, name, user=None, value=None, params=None): +class WorkflowField( BaseField ): + def __init__( self, name, user=None, value=None, params=None ): self.name = name self.user = user self.value = value @@ -580,7 +574,7 @@ class WorkflowField(BaseField): else: self.select_workflow.add_option( a.name, str( a.id ) ) return self.select_workflow.get_html( disabled=disabled ) - + def get_suite(): """Get unittest suite for this module""" import doctest, sys @@ -592,11 +586,11 @@ def build_select_field( trans, objs, lab selected_value='none', refresh_on_change=False, multiple=False, display=None, size=None ): """ Build a SelectField given a set of objects. The received params are: - - objs: the set of object used to populate the option list + - objs: the set of objects used to populate the option list - label_attr: the attribute of each obj (e.g., name, email, etc ) whose value is used to populate each option label. If the string 'self' is passed as label_attr, each obj in objs is assumed to be a string, so the obj itself is used - select_field_name: the name of the SelectField - - initial_value: the vlaue of the first option in the SelectField - allows for an option telling the user to select something + - initial_value: the value of the first option in the SelectField - allows for an option telling the user to select something - selected_value: the value of the currently selected option - refresh_on_change: True if the SelectField should perform a refresh_on_change """ --- a/templates/admin/requests/view_request_type.mako +++ b/templates/admin/requests/view_request_type.mako @@ -38,7 +38,7 @@ <div style="clear: both"></div></div><div class="form-row"> - <label>Sequencing Request form definition</label> + <label>Sequencing request form definition</label> ${request_type.request_form.name} </div><div class="form-row"> --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1495,12 +1495,11 @@ class MetadataFile( object ): class FormDefinition( object ): # The following form_builder classes are supported by the FormDefinition class. - # AddressField, CheckboxField, SelectField, TextArea, TextField, WorkflowField supported_field_types = [ AddressField, CheckboxField, SelectField, TextArea, TextField, WorkflowField ] types = Bunch( REQUEST = 'Sequencing Request Form', SAMPLE = 'Sequencing Sample Form', LIBRARY_INFO_TEMPLATE = 'Library information template', - USER_INFO = 'User Information' ) + USER_INFO = 'User Information' ) def __init__( self, name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None ): self.name = name self.desc = desc @@ -1792,6 +1791,8 @@ class RequestTypePermissions( object ): self.role = role class Sample( object ): + # The following form_builder classes are supported by the Sample class. + supported_field_types = [ CheckboxField, SelectField, TextField, WorkflowField ] bulk_operations = Bunch( CHANGE_STATE = 'Change state', SELECT_LIBRARY = 'Select data library and folder' ) api_collection_visible_keys = ( 'id', 'name' ) --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -588,12 +588,8 @@ class RequestsCommon( BaseController, Us request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) except: return invalid_id_redirect( trans, cntrller, request_id ) - events_list = [] - for event in request.events: - events_list.append( ( event.state, time_ago( event.update_time ), event.comment ) ) return trans.fill_template( '/requests/common/view_request_history.mako', cntrller=cntrller, - events_list=events_list, request=request ) @web.expose @web.require_login( "edit email notification settings" ) @@ -777,7 +773,7 @@ class RequestsCommon( BaseController, Us search_box=search_box ) @web.expose @web.require_login( "sample events" ) - def sample_events( self, trans, cntrller, **kwd ): + def view_sample_history( self, trans, cntrller, **kwd ): params = util.Params( kwd ) status = params.get( 'status', 'done' ) message = util.restore_text( params.get( 'message', '' ) ) @@ -786,15 +782,8 @@ class RequestsCommon( BaseController, Us sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) except: return invalid_id_redirect( trans, cntrller, sample_id ) - events_list = [] - for event in sample.events: - events_list.append( ( event.state.name, - event.state.desc, - time_ago( event.update_time ), - event.comment ) ) - return trans.fill_template( '/requests/common/sample_events.mako', + return trans.fill_template( '/requests/common/view_sample_history.mako', cntrller=cntrller, - events_list=events_list, sample=sample ) @web.expose @web.require_login( "add sample" ) @@ -1054,9 +1043,9 @@ class RequestsCommon( BaseController, Us # selected sets of samples. If samples are selected, the sample_operation param # will have a value other than 'none', and the samples param will be a list of # encoded sample ids. There are currently only 2 multi-select operations; - # 'Change state' and 'Select data library and folder'. If sample_operation is - # 'none, then the samples param will be a list of sample objects. - if sample_operation == 'Change state': + # model.Sample.bulk_operations.CHANGE_STATE and model.sample.bulk_operations.SELECT_LIBRARY. + # If sample_operation is 'none, then the samples param will be a list of sample objects. + if sample_operation == trans.model.Sample.bulk_operations.CHANGE_STATE: sample_state_id = params.get( 'sample_state_id', None ) if sample_state_id in [ None, 'none' ]: message = "Select a new state from the <b>Change current state</b> list before clicking the <b>Save</b> button." @@ -1090,7 +1079,7 @@ class RequestsCommon( BaseController, Us cntrller=cntrller, action='update_request_state', request_id=trans.security.encode_id( request.id ) ) ) - elif sample_operation == 'Select data library and folder': + elif sample_operation == trans.model.sample.bulk_operations.SELECT_LIBRARY: # TODO: fix the code so that the sample_operation_select_field does not use # sample_0_library_id as it's name. it should use something like sample_operation_library_id # and sample_operation_folder_id because the name sample_0_library_id should belong to the --- a/lib/galaxy/web/controllers/forms.py +++ b/lib/galaxy/web/controllers/forms.py @@ -64,12 +64,12 @@ class FormsGrid( grids.Grid ): ] class Forms( BaseController ): - # Empty form field + # Empty TextField empty_field = { 'label': '', 'helptext': '', 'visible': True, 'required': False, - 'type': BaseField.form_field_types()[0], + 'type': model.TextField.__name__, 'selectlist': [], 'layout': 'none', 'default': '' } @@ -597,12 +597,12 @@ class Forms( BaseController ): self.selectbox_options = [] # if the form is for defining samples, then use the sample field types # which does not include TextArea & AddressField - if form_type == trans.app.model.FormDefinition.types.SAMPLE: - for ft in BaseField.sample_field_types(): - self.fieldtype.add_option(ft, ft) + if form_type == trans.model.FormDefinition.types.SAMPLE: + for ft in trans.model.Sample.supported_field_types: + self.fieldtype.add_option( ft.__name__, ft.__name__ ) else: - for ft in BaseField.form_field_types(): - self.fieldtype.add_option(ft, ft) + for ft in trans.model.Request.supported_field_types: + self.fieldtype.add_option( ft.__name__, ft__name__ ) self.required = SelectField('field_required_'+str(index), display='radio') self.required.add_option('Required', 'required') self.required.add_option('Optional', 'optional', selected=True) @@ -632,22 +632,22 @@ class Forms( BaseController ): field[ 'selectlist' ] = ['', ''] # if the form is for defining samples, then use the sample field types # which does not include TextArea & AddressField - if form_type == trans.app.model.FormDefinition.types.SAMPLE: - for ft in BaseField.sample_field_types(): - if ft == field['type']: - self.fieldtype.add_option(ft, ft, selected=True) + if form_type == trans.model.FormDefinition.types.SAMPLE: + for ft in trans.model.Sample.supported_field_types: + if ft.__name__ == field[ 'type' ]: + self.fieldtype.add_option( ft.__name__, ft__name__, selected=True ) if ft == 'SelectField': - self.selectbox_ui(field) + self.selectbox_ui( field ) else: - self.fieldtype.add_option(ft, ft) + self.fieldtype.add_option( ft.__name__, ft.__name__ ) else: - for ft in BaseField.form_field_types(): - if ft == field['type']: - self.fieldtype.add_option(ft, ft, selected=True) + for ft in trans.model.Request.supported_field_types: + if ft.__name__ == field[ 'type' ]: + self.fieldtype.add_option( ft.__name__, ft.__name__, selected=True ) if ft == 'SelectField': - self.selectbox_ui(field) + self.selectbox_ui( field ) else: - self.fieldtype.add_option(ft, ft) + self.fieldtype.add_option( ft.__name__, ft.__name__ ) # required/optional if field['required'] == 'required': self.required = SelectField('field_required_'+str(self.index), display='radio') --- a/templates/admin/requests/create_request_type.mako +++ b/templates/admin/requests/create_request_type.mako @@ -39,7 +39,7 @@ <div style="clear: both"></div></div> %endfor - <div class="toolFormTitle">Possible sample states</div> + <div class="toolFormTitle">Sample states</div> %if len(rt_states_widgets): %for index, info in enumerate(rt_states_widgets): ${render_state( index, info[0], info[1] )} --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -160,7 +160,7 @@ %if is_unsubmitted: <td>Unsubmitted</td> %else: - <td valign="top"><a href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${sample.state.name}</a></td> + <td valign="top"><a href="${h.url_for( controller='requests_common', action='view_sample_history', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${sample.state.name}</a></td> %endif %else: <td></td> @@ -334,7 +334,7 @@ %if is_unsubmitted: <td>Unsubmitted</td> %else: - <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='sample_events', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td> + <td><a id="sampleState-${sample.id}" href="${h.url_for( controller='requests_common', action='view_sample_history', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">${render_sample_state( sample )}</a></td> %endif %if sample_widget_library and library_cntrller is not None: <td><a href="${h.url_for( controller='library_common', action='browse_library', cntrller=library_cntrller, id=trans.security.encode_id( sample_widget_library.id ) )}">${sample_widget_library.name}</a></td> --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1536,7 +1536,7 @@ class TwillTestCase( unittest.TestCase ) self.visit_url( "%s/requests_common/view_request_history?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) self.check_page( strings_displayed, strings_displayed_count, strings_not_displayed ) def view_sample_history( self, cntrller, sample_id, strings_displayed=[], strings_displayed_count=[], strings_not_displayed=[] ): - self.visit_url( "%s/requests_common/sample_events?cntrller=%s&sample_id=%s" % ( self.url, cntrller, sample_id ) ) + self.visit_url( "%s/requests_common/view_sample_history?cntrller=%s&sample_id=%s" % ( self.url, cntrller, sample_id ) ) self.check_page( strings_displayed, strings_displayed_count, strings_not_displayed ) def edit_basic_request_info( self, cntrller, request_id, name, new_name='', new_desc='', new_fields=[], strings_displayed=[], strings_displayed_after_submit=[] ): --- a/templates/requests/common/edit_basic_request_info.mako +++ b/templates/requests/common/edit_basic_request_info.mako @@ -8,7 +8,6 @@ is_unsubmitted = request.is_unsubmitted can_add_samples = is_unsubmitted can_reject = is_admin and is_submitted - can_select_datasets = is_admin and ( is_complete or is_submitted ) can_submit_request = request.samples and is_unsubmitted %> @@ -24,9 +23,6 @@ %if can_reject: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> %endif - %if can_select_datasets: - <a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> - %endif </div></ul> --- /dev/null +++ b/templates/requests/common/view_sample_history.mako @@ -0,0 +1,38 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<% from galaxy.web.framework.helpers import time_ago %> + +<br/><br/> +<ul class="manage-table-actions"> + <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li> +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +<h3>History of sample "${sample.name}"</h3> + +<div class="toolForm"> + <table class="grid"> + <thead> + <tr> + <th>State</th> + <th>Description</th> + <th>Last Updated</th> + <th>Comments</th> + </tr> + </thead> + <tbody> + %for event in sample.events: + <tr> + <td><b>${event.state.name}</b></td> + <td>${event.state.desc}</td> + <td>${time_ago( event.update_time )}</td> + <td>${event.comment}</td> + </tr> + %endfor + </tbody> + </table> +</div> --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -44,8 +44,6 @@ class Configuration( object ): # web API self.enable_api = string_as_bool( kwargs.get( 'enable_api', False ) ) self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) - # Communication with a sequencer - self.enable_sequencer_communication = string_as_bool( kwargs.get( 'enable_sequencer_communication', False ) ) # dataset Track files self.track_store_path = kwargs.get( "track_store_path", "${extra_files_path}/tracks") self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root ) --- a/templates/requests/common/view_request_history.mako +++ b/templates/requests/common/view_request_history.mako @@ -2,6 +2,8 @@ <%namespace file="/message.mako" import="render_msg" /><% + from galaxy.web.framework.helpers import time_ago + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() is_complete = request.is_complete is_submitted = request.is_submitted @@ -41,16 +43,16 @@ <thead><tr><th>State</th> - <th>Last Update</th> + <th>Last Updated</th><th>Comments</th></tr></thead><tbody> - %for state, updated, comments in events_list: - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td><b><a>${state}</a></b></td> - <td><a>${updated}</a></td> - <td><a>${comments}</a></td> + %for event in request.events: + <tr> + <td><b>${event.state}</b></td> + <td>${time_ago( event.update_time )}</td> + <td>${event.comment}</td></tr> %endfor </tbody> --- a/templates/requests/common/sample_events.mako +++ /dev/null @@ -1,44 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="title()">Events for Sample ${sample.name}</%def> - -<h2>Events for Sample "${sample.name}"</h2> -<ul class="manage-table-actions"> - <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li> -</ul> -<h3>Sequencing Request "${sample.request.name}"</h3> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="form-row"> - <div class="toolParamHelp" style="clear: both;"> - <b>Possible states: </b> - <% states = " > ".join([ ss.name for ss in sample.request.type.states ]) %> - ${states} - </div> - </div> - <table class="grid"> - <thead> - <tr> - <th>State</th> - <th>Description</th> - <th>Last Update</th> - <th>Comments</th> - </tr> - </thead> - <tbody> - %for state, desc, updated, comments in events_list: - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td><b><a>${state}</a></b></td> - <td><a>${desc}</a></td> - <td><a>${updated}</a></td> - <td><a>${comments}</a></td> - </tr> - %endfor - </tbody> - </table> -</div>

1 0

galaxy-dist commit 918a25ed14f5: Bug fix due to my last commit - Requests do not have supported_field_types, FormDefinitions do.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1290008781 18000 # Node ID 918a25ed14f5427f70970b0c436159fc58fd111e # Parent 7bded9108bd8297ea609e9ec06bbe516b5f0b83a Bug fix due to my last commit - Requests do not have supported_field_types, FormDefinitions do. --- a/lib/galaxy/web/controllers/forms.py +++ b/lib/galaxy/web/controllers/forms.py @@ -601,7 +601,7 @@ class Forms( BaseController ): for ft in trans.model.Sample.supported_field_types: self.fieldtype.add_option( ft.__name__, ft.__name__ ) else: - for ft in trans.model.Request.supported_field_types: + for ft in trans.model.FormDefinition.supported_field_types: self.fieldtype.add_option( ft.__name__, ft__name__ ) self.required = SelectField('field_required_'+str(index), display='radio') self.required.add_option('Required', 'required') @@ -641,7 +641,7 @@ class Forms( BaseController ): else: self.fieldtype.add_option( ft.__name__, ft.__name__ ) else: - for ft in trans.model.Request.supported_field_types: + for ft in trans.model.FormDefinition.supported_field_types: if ft.__name__ == field[ 'type' ]: self.fieldtype.add_option( ft.__name__, ft.__name__, selected=True ) if ft == 'SelectField':

1 0

galaxy-dist commit 56431b214df1: Don't 'use strict' as FF4 beta doesn't support it
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1289944688 18000 # Node ID 56431b214df16653a966b96bf399c7646da267b8 # Parent 394d8186f666b506cd0a93aefb7a079e0c9ec59b Don't 'use strict' as FF4 beta doesn't support it --- a/static/scripts/jquery.jstore.js +++ b/static/scripts/jquery.jstore.js @@ -15,7 +15,7 @@ * http://creativecommons.org/licenses/by/3.0/us */ -"use strict"; +//"use strict"; /*global Class, window, jQuery, ActiveXObject, google */ --- a/static/scripts/class.js +++ b/static/scripts/class.js @@ -5,7 +5,7 @@ * Inspired by base2 and Prototype */ -"use strict"; +//"use strict"; (function () { --- a/static/scripts/packed/jquery.jstore.js +++ b/static/scripts/packed/jquery.jstore.js @@ -14,4 +14,4 @@ * Licensed under the Creative Commons Attribution 3.0 United States License: * http://creativecommons.org/licenses/by/3.0/us */ -"use strict";(function(i,n){var h="JSTORE_ENGINE_UNSTABLE",t="JSTORE_UNKNOWN_ENGINE_REQUESTED",r="JSTORE_ENGINE_NAMESPACE_COLLISION",j="JSTORE_RESOURCE_NAMESPACE_COLLISION",m="JSTORE_ENGINE_UNAVAILABLE",o="JSTORE_INVALID_FLAVOR",f=(function(){try{return new RegExp('^("(\\\\.|[^"\\\\\\n\\r])*?"|[,:{}\\[\\]0-9.\\-+Eaeflnr-u \\n\\r\\t])+?$')}catch(I){return(/^(true|false|null|\[.*\]|\{.*\}|".*"|\d+|\d+\.\d+)$/)}}()),b="jstore-html5-local",y="jstore-html5-sql",F="jstore-flash",G="jstore-google-gears",A="jstore-msie",u,E={},D={},C={},c=false,d={},q={project:undefined,flash:"jStore.Flash.html",json:"browser.json.js"},l;function z(I){switch(I){case b:case y:case F:case G:case A:return true;default:return false}}function g(I,J){return !I?false:I.constructor.toString().match(new RegExp(J+"\$\$","i"))!==null}function s(K,I,J){if(g(K,"Function")){return K.apply(I||E,g(J,"Array")?J:[J])}}function p(J,I){i.ajax({url:J,complete:I||i.noop(),type:"GET",dataType:"script",cache:false})}func tion 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s.updateCache(true)}}},function(){return B("9.0.0")});e(G,{limit:-1,init:function(J,I){this.database=google.gears.factory.create("beta.database");this.database.open("jstore-"+J);this.database.execute("CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)");this._super(J,I)},updateCache:function(){var I=this.database.execute("SELECT k,v FROM jstore");while(I.isValidRow()){this.data[I.field(0)]=k(I.field(1));I.next()}I.close();this._super()},__set:function(I,J){this.database.execute("BEGIN");this.database.execute("INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)",[I,x(J)]);this.database.execute("COMMIT")},__remove:function(I){this.database.execute("BEGIN");this.database.execute("DELETE FROM jstore WHERE k = ?",[I]);this.database.execute("COMMIT")}},function(){return n.google!==undefined&&n.google.gears!==undefined});e(A,{limit:parseInt(10000,16),init:function(J,I){this.database=i('<div style="display:none;behavior:url(\'#default#userData\')" id="jstore-'+J+'"></div>').appendTo(document.body).get(0);this._super(J,I)},updateCache:function(){this.database.load(this.project);var K=document.getElementById("jstore-"+this.project),L=K.XMLDocument,I,J=0;if(L&&L.documentElement&&L.documentElement.attributes){I=L.documentElement;for(;J<I.attributes.length;++J){this.data[I.attributes.item(J).nodeName]=k(I.attributes.item(J).nodeValue)}}this._super()},__set:function(I,J){this.database.setAttribute(I,x(J));this.database.save(this.project)},__remove:function(I){this.database.removeAttribute(I);this.database.save(this.project)}},function(){return n.ActiveXObject!==undefined})}(jQuery,window)); +(function(i,n){var h="JSTORE_ENGINE_UNSTABLE",t="JSTORE_UNKNOWN_ENGINE_REQUESTED",r="JSTORE_ENGINE_NAMESPACE_COLLISION",j="JSTORE_RESOURCE_NAMESPACE_COLLISION",m="JSTORE_ENGINE_UNAVAILABLE",o="JSTORE_INVALID_FLAVOR",f=(function(){try{return new RegExp('^("(\\\\.|[^"\\\\\\n\\r])*?"|[,:{}\\[\\]0-9.\\-+Eaeflnr-u 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N=H().match(/\d+/g),L=I.match(/\d+/g),J=0,K,M;for(;J<3;J++){K=parseInt(N[J],10);M=parseInt(L[J],10);if(K<M){return false}else{if(K>M){return true}}}return true}i.extend(E,{enginePriority:[b,y,F,A],available:{},isReady:false,isFlashReady:false,flavors:{local:b,sql:y,flash:F,gears:G,msie:A},init:function(J,K,I){i.extend(q,{project:J},K);i(function(){if(n.JSON===undefined){p(q.json)}if(I!==undefined){E.create(I,J,"default")}else{a()}});return E},create:function(I,M,J){M=M||q.project||location.hostname.replace(/\./g,"-")||"unknown";if(!z(I)){throw o}if(D[I]===undefined){throw m}var L=(J!==undefined?J+".":"")+M+"."+I,K;if(C[L]!==undefined){throw j}K=C[L]=new D[I](M,L);K.ready(function(){E.trigger("jstore-engine-ready",[K])});if(I===F&&!E.isFlashReady){if(l===undefined){c=true}n.jstore_ready=function(){E.isFlashReady=true ;E.trigger("flash-ready");if(l===undefined){v()}n.flash_ready=undefined};n.jstore_error=function(N){E.trigger("jstore-error",["JSTORE_FLASH_EXCEPTION",null,N])};i('<iframe style="height:1px;width:1px;position:absolute;left:0;top:0;margin-left:-100px;" id="jStoreFlashFrame" src="'+q.flash+'"></iframe>').appendTo("body")}else{if(l===undefined){l=L;v()}}return K},engine:function(I){return C[I]},activeEngine:function(I){if(I!==undefined){if(C[I]===undefined){throw t}else{l=I}}return C[l]},bind:function(J,K,I){I=I||"jstore";if(d[I]===undefined){d[I]={}}if(d[I][J]===undefined){d[I][J]=[K]}else{d[I][J].push(K)}return E},trigger:function(K,J,I){I=I||"jstore";if(d[I]!==undefined){if(d[I][K]!==undefined){i.each(d[I][K],function(){s(this,E,J)})}}return E},error:function(I){E.bind("jstore-error",I)},ready:function(I){if(E.isReady){s(I)}else{E.bind("jstore-ready",I)}return E},engineReady:function(I){if(E.isReady){s(I)}else{E.bind("jstore-engine-ready",I)}return E},store:function(I,J){ret urn J===undefined?E.get(I):E.set(I,J)},remove:function(I){return E.activeEngine().remove(I)},get:function(I){return E.activeEngine().get(I)},set:function(I,J){return E.activeEngine().set(I,J)}});u=Class.extend({project:undefined,jri:undefined,flavor:undefined,database:undefined,data:undefined,limit:undefined,isReady:undefined,init:function(J,I){this.project=J;this.jri=I;this.data={};this.isReady=false;this.updateCache()},updateCache:function(){this.isReady=true;this.trigger("engine-ready",[this])},bind:function(I,J){E.bind(I,J,this.jri)},trigger:function(J,I){E.trigger(J,I,this.jri)},ready:function(I){if(this.isReady){s(I,this)}else{this.bind("engine-ready",I)}},get:function(I){this.__interruptAccess();return this.data[I]},set:function(I,J){this.__interruptAccess();I=w(I);try{this.__set(I,J)}catch(K){E.trigger("jstore-error",["JSTORE_STORAGE_FAILURE",this.jri,K])}this.data[I]=J;return J},remove:function(J){this.__interruptAccess();J=w(J);try{this.__remove(J)}catch(K){E.trigg er("jstore-error",["JSTORE_REMOVE_FAILURE",this.jri,K])}var I=this.data[J];this.data[J]=undefined;return I},__interruptAccess:function(){if(!this.isReady){throw h}},__set:function(I,J){return},__remove:function(I){return}});i.extend(i.fn,{store:function(I,J){if(J===undefined){E.get(I)}else{E.set(I,J)}return this},removeStore:function(I){E.activeEngine().remove(I);return this},getStore:function(I){return E.activeEngine().get(I)},setStore:function(I,J){E.activeEngine().set(I,J);return this}});n.jStore=i.jStore=E;e(b,{limit:parseInt(500000,16),init:function(J,I){this.database=n.globalStorage===undefined?n.localStorage:n.globalStorage[location.hostname];this._super(J,I)},updateCache:function(){var J,K;for(J in this.database){var I=false;if(this.database.hasOwnProperty){if(this.database.hasOwnProperty(J)){I=true}}else{if(this.database.getItem(J)!==null){I=true}}if(I){K=this.database.getItem(J);this.data[J]=k(K&&K.value?K.value:K)}}this._super()},__set:function(I,J){this.database. setItem(I,x(J))},__remove:function(I){this.database.removeItem(I)}},function(){return n.localStorage!==undefined||n.globalStorage!==undefined});e(y,{limit:parseInt(32000,16),init:function(J,I){this.database=n.openDatabase("jstore-"+J,"1.0",J,this.limit);if(!this.database){throw"JSTORE_SQL_NO_DB"}this.database.transaction(function(K){K.executeSql("CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)")});this._super(J,I)},updateCache:function(){var I=this,J=this._super;this.database.transaction(function(K){K.executeSql("SELECT k,v FROM jstore",[],function(O,L){var N=L.rows,M=0,P;for(;M<N.length;++M){P=N.item(M);I.data[P.k]=k(P.v)}J.apply(I)})})},__set:function(I,J){this.database.transaction(function(K){K.executeSql("INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)",[I,x(J)])})},__remove:function(I){this.database.transaction(function(J){J.executeSql("DELETE FROM jstore WHERE k = ?",[I])})}},function(){return n.openDatabase!==undefined});e(F,{ limit:-1,init:function(K,J){var I=this;E.bind("flash-ready",function(){I.__flashReadyListener()});this._super(K,J)},updateCache:function(I){if(I===true){var J,K=this.database.jstore_get_all();for(J in K){if(K.hasOwnProperty(J)){this.data[J]=k(this.database.jstore_get(J))}}this._super()}},__set:function(I,J){if(!this.database.jstore_set(I,x(J))){E.trigger("jstore-error",["JSTORE_STORAGE_FAILURE",this.jri,"Flash Exception"])}},__remove:function(I){this.database.jstore_remove(I)},__flashReadyListener:function(){var I=i("#jStoreFlashFrame")[0],J;if(I.Document!==undefined&&g(I.Document.jStoreFlash.jstore_get,"Function")){this.database=I.Document.jStoreFlash}else{if(I.contentWindow&&I.contentWindow.document){J=i(I.contentWindow.document);if(g(i("object",J)[0].jstore_get,"Function")){this.database=i("object",J)[0]}else{if(g(i("embed",J)[0].jstore_get,"Function")){this.database=i("embed",J)[0]}}}}if(this.database===undefined){throw"JSTORE_FLASH_REFERENCE_ISSUE"}else{this.updateCache (true)}}},function(){return B("9.0.0")});e(G,{limit:-1,init:function(J,I){this.database=google.gears.factory.create("beta.database");this.database.open("jstore-"+J);this.database.execute("CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)");this._super(J,I)},updateCache:function(){var I=this.database.execute("SELECT k,v FROM jstore");while(I.isValidRow()){this.data[I.field(0)]=k(I.field(1));I.next()}I.close();this._super()},__set:function(I,J){this.database.execute("BEGIN");this.database.execute("INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)",[I,x(J)]);this.database.execute("COMMIT")},__remove:function(I){this.database.execute("BEGIN");this.database.execute("DELETE FROM jstore WHERE k = ?",[I]);this.database.execute("COMMIT")}},function(){return n.google!==undefined&&n.google.gears!==undefined});e(A,{limit:parseInt(10000,16),init:function(J,I){this.database=i('<div style="display:none;behavior:url(\'#default#userData\')" id="jstore-'+ J+'"></div>').appendTo(document.body).get(0);this._super(J,I)},updateCache:function(){this.database.load(this.project);var K=document.getElementById("jstore-"+this.project),L=K.XMLDocument,I,J=0;if(L&&L.documentElement&&L.documentElement.attributes){I=L.documentElement;for(;J<I.attributes.length;++J){this.data[I.attributes.item(J).nodeName]=k(I.attributes.item(J).nodeValue)}}this._super()},__set:function(I,J){this.database.setAttribute(I,x(J));this.database.save(this.project)},__remove:function(I){this.database.removeAttribute(I);this.database.save(this.project)}},function(){return n.ActiveXObject!==undefined})}(jQuery,window)); --- a/static/scripts/packed/class.js +++ b/static/scripts/packed/class.js @@ -4,4 +4,4 @@ * Copyright (c) 2008 John Resig (http://ejohn.org/blog/simple-javascript-inheritance/) * Inspired by base2 and Prototype */ -"use strict";(function(){var a=false,b=/xyz/.test(function(){xyz})?/\b_super\b/:/.*/;this.Class=function(){};Class.extend=function(g){var f=this.prototype;a=true;var e=new this();a=false;for(var d in g){e[d]=(typeof g[d]==="function"&&typeof f[d]==="function"&&b.test(g[d])?(function(h,i){return function(){var k=this._super;this._super=f[h];var j=i.apply(this,arguments);this._super=k;return j}}(d,g[d])):g[d])}function c(){if(!a&&this.init){this.init.apply(this,arguments)}}c.prototype=e;c.constructor=c;c.extend=arguments.callee;return c}}()); +(function(){var a=false,b=/xyz/.test(function(){xyz})?/\b_super\b/:/.*/;this.Class=function(){};Class.extend=function(g){var f=this.prototype;a=true;var e=new this();a=false;for(var d in g){e[d]=(typeof g[d]==="function"&&typeof f[d]==="function"&&b.test(g[d])?(function(h,i){return function(){var k=this._super;this._super=f[h];var j=i.apply(this,arguments);this._super=k;return j}}(d,g[d])):g[d])}function c(){if(!a&&this.init){this.init.apply(this,arguments)}}c.prototype=e;c.constructor=c;c.extend=arguments.callee;return c}}());

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