August 2009 - galaxy-dev - lists.galaxyproject.org

Specifying a PATH for local binaries?
by Chris Cole 10 Aug '09

10 Aug '09

Hi all, I'm trying install some local tools, but only locally to the galaxy user (e.g. ~/local_tools/bin). In order to avoid specifying the full path in each and every tool's XML file how can I specify a PATH for galaxy to find the binaries? It seems that Galaxy ignores the default $PATH although SGE can. Cheers, Chris

2 5

[hg] galaxy 2537: In tool tests, only add a file once if it is r...
by Greg Von Kuster 06 Aug '09

06 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/11a2d159e280 changeset: 2537:11a2d159e280 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Aug 05 12:59:24 2009 -0400 description: In tool tests, only add a file once if it is required. 1 file(s) affected in this change: lib/galaxy/tools/test.py diffs (29 lines): diff -r 1ba58ed85a5f -r 11a2d159e280 lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py Wed Aug 05 11:54:34 2009 -0400 +++ b/lib/galaxy/tools/test.py Wed Aug 05 12:59:24 2009 -0400 @@ -25,7 +25,7 @@ for input_name, input_value in self.tool.inputs.items(): if isinstance( input_value, grouping.Conditional ) or isinstance( input_value, grouping.Repeat ): self.__expand_grouping_for_data_input(name, value, extra, input_name, input_value) - elif isinstance( self.tool.inputs[name], parameters.DataToolParameter ): + elif isinstance( self.tool.inputs[name], parameters.DataToolParameter ) and ( value, extra ) not in self.required_files: self.required_files.append( ( value, extra ) ) except: pass self.inputs.append( ( name, value, extra ) ) @@ -37,7 +37,7 @@ if name != grouping_value.test_param.name: for case in grouping_value.cases: for case_input_name, case_input_value in case.inputs.items(): - if case_input_name == name and isinstance( case_input_value, basic.DataToolParameter ): + if case_input_name == name and isinstance( case_input_value, basic.DataToolParameter ) and ( value, extra ) not in self.required_files: self.required_files.append( ( value, extra ) ) return True elif isinstance( case_input_value, grouping.Conditional ): @@ -49,6 +49,6 @@ # with the same name ( "input2" ) is not yet supported in our test code ( the lat one added is the only # one used ). for input_name, input_value in grouping_value.inputs.items(): - if input_name == name and isinstance( input_value, basic.DataToolParameter ): + if input_name == name and isinstance( input_value, basic.DataToolParameter ) and ( value, extra ) not in self.required_files: self.required_files.append( ( value, extra ) ) return True

1 0

[hg] galaxy 2536: Testing framework will now click the add butto...
by Greg Von Kuster 06 Aug '09

06 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/1ba58ed85a5f changeset: 2536:1ba58ed85a5f user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Aug 05 11:54:34 2009 -0400 description: Testing framework will now click the add button for nested repeats when repeat content has been specfied. 3 file(s) affected in this change: test-data/joiner_out4.bed test/base/twilltestcase.py tools/filters/joiner.xml diffs (133 lines): diff -r 93d502caec2a -r 1ba58ed85a5f test-data/joiner_out4.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/joiner_out4.bed Wed Aug 05 11:54:34 2009 -0400 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + NoChrom +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + NoChrom +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - NoChrom +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + NoChrom +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - NoChrom +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - NoChrom +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + NoChrom +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - NoChrom +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + NoChrom +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + NoChrom +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - NoChrom +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + NoChrom +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - NoChrom +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - NoChrom +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + NoChrom +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - NoChrom +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 - diff -r 93d502caec2a -r 1ba58ed85a5f test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Aug 05 11:19:46 2009 -0400 +++ b/test/base/twilltestcase.py Wed Aug 05 11:54:34 2009 -0400 @@ -650,9 +650,17 @@ break # To help with debugging a tool, print out the form controls when the test fails print "form '%s' contains the following controls ( note the values )" % f.name + control_names = [] for i, control in enumerate( f.controls ): print "control %d: %s" % ( i, str( control ) ) try: + #check if a repeat element needs to be added + if control.name not in kwd and control.name.endswith( '_add' ): + #control name doesn't exist, could be repeat + repeat_startswith = control.name[0:-4] + if repeat_startswith and not [ c_name for c_name in control_names if c_name.startswith( repeat_startswith ) ] and [ c_name for c_name in kwd.keys() if c_name.startswith( repeat_startswith ) ]: + tc.submit( control.name ) + return self.submit_form( form_no=form_no, button=button, **kwd ) # Check for refresh_on_change attribute, submit a change if required if 'refresh_on_change' in control.attrs.keys(): changed = False @@ -677,6 +685,7 @@ except Exception, e: log.debug( "In submit_form, continuing, but caught exception: %s" % str( e ) ) continue + control_names.append( control.name ) # No refresh_on_change attribute found in current form, so process as usual for control_name, control_value in kwd.items(): if not isinstance( control_value, list ): diff -r 93d502caec2a -r 1ba58ed85a5f tools/filters/joiner.xml --- a/tools/filters/joiner.xml Wed Aug 05 11:19:46 2009 -0400 +++ b/tools/filters/joiner.xml Wed Aug 05 11:54:34 2009 -0400 @@ -98,7 +98,7 @@ <param name="fill_empty_columns_switch" value="no_fill"/> <output name="out_file1" file="joiner_out2.bed"/> </test> -<test> + <test> <param name="input1" value="1.bed"/> <param name="input2" value="2.bed"/> <param name="field1" value="2"/> @@ -110,6 +110,22 @@ <param name="column_fill_type" value="single_fill_value"/> <param name="fill_value" value="~"/> <output name="out_file1" file="joiner_out3.bed"/> + </test> + <test> + <param name="input1" value="1.bed"/> + <param name="input2" value="2.bed"/> + <param name="field1" value="2"/> + <param name="field2" value="2"/> + <param name="unmatched" value="Yes"/> + <param name="partial" value="Yes"/> + <param name="fill_empty_columns_switch" value="fill_empty"/> + <param name="fill_columns_by" value="fill_all"/> + <param name="column_fill_type" value="fill_value_by_column"/> + <param name="column_number1" value="6"/> + <param name="fill_value1" value="+"/> + <param name="column_number2" value="1"/> + <param name="fill_value2" value="NoChrom"/> + <output name="out_file1" file="joiner_out4.bed"/> </test> </tests> <help>

1 0

[hg] galaxy 2531: Renamed test files and fixed output datatype p...
by Greg Von Kuster 06 Aug '09

06 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0d5182c4870b changeset: 2531:0d5182c4870b user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Tue Aug 04 16:32:57 2009 -0400 description: Renamed test files and fixed output datatype problem with solid-to-fastq tool 7 file(s) affected in this change: test-data/s2fq_out1.fastqsanger test-data/s2fq_out1.tabular test-data/s2fq_out2.fastqsanger test-data/s2fq_out2.tabular test-data/s2fq_out3.fastqsanger test-data/s2fq_out3.tabular tools/next_gen_conversion/solid_to_fastq.xml diffs (1981 lines): diff -r dd1b55dd3c22 -r 0d5182c4870b test-data/s2fq_out1.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_out1.fastqsanger Tue Aug 04 16:32:57 2009 -0400 @@ -0,0 +1,576 @@ +@1831_573_1004/1 +AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG ++ +><C&&9952+C>5<.?<79,=42<292:<(9/-7 +@1831_573_1050/1 +TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ++ +;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, +@1831_573_1067/1 +AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++ +++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ +@1831_573_1219/1 +CGCCCTATAATAATACAGCGCGTTAGACCGCTCA ++ +@@=4/+)5)408?'665>*/5?<61';<3,:,5- +@1831_573_1242/1 +GCTGAATCGCACCTAGCAACTATAGCCGGGCCGC ++ +>>::>17=A5?@@=;7A=;2.60>82<8=74+;; +@1831_573_1333/1 +AGAATCGTTACCACACACTGCGTCTGGGTATCCG ++ +='@#%3=.>)/34*117,,/6-4+.9742456<) +@1831_573_1362/1 +CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC ++ +B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? +@1831_573_1448/1 +TCACGCCGGTCCTTGACTGGCGTTCTCTTCGAGG ++ +7=A)?,.@A@@:@@<=/7)@<-#8662%9613&+ +@1831_573_1490/1 +CTCGTCATGTTACGCAAAGGCACGTCACAGCACC ++ +@@@?,@??@$><=>+%/*>*1,)?26&12'9%7. +@1831_573_1523/1 +ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ++ +,//*,#8''.6''6'2&27/80)%&#0'%#*,2' +@1831_573_1578/1 +CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ++ +?=@<@C@?@@??=>@;7<<8<694)3511(+1<. +@1831_573_1647/1 +AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT ++ +?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 +@1831_573_1684/1 +TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT ++ +>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? +@1831_573_1769/1 +TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC ++ +54749&&767%/7;3$-7;3#,3//#,45/#&06 +@1831_573_1853/1 +CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC ++ +4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& +@1831_573_1943/1 +ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC ++ +>/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, +@1831_573_1977/1 +GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC ++ +@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 +@1831_574_109/1 +TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT ++ +7651#4817>@65<2:84716=788<1995.7?6 +@1831_574_148/1 +CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC ++ +;->3;;3>//>0;;7=,=4-4/+>029<9<624; +@1831_574_185/1 +CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC ++ +<4;%%@7>#*>97%6;+8$#<07%1372$%<54# +@1831_574_243/1 +AGGCACCGTAACTCAGGACATTCTCGATTAGTTA ++ +@@@95@=9?*><45$<@<4%@9?7#=?>7&>?97 +@1831_574_257/1 +ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC ++ +>>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& +@1831_574_293/1 +TGCTGCAAATAAACATACAGCCTTCTAATGACTA ++ +')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% +@1831_574_389/1 +CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA ++ +)$>/>8):2@:213;;.1)@3%64%+)<7)+$92 +@1831_574_575/1 +TTCTTGGCAAGCGCAGATTATGCGTTCCGCCTAG ++ +?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< +@1831_574_592/1 +TCATTTACCACGTCAGGGTCGGAGTCATTCATTA ++ +3-5)19,,<@>4067<2.-864346;9<1/;212 +@1831_574_617/1 +AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC ++ +>@?;>?=@==@>@=5?@+@:@40@><:0)')64- +@1831_574_725/1 +GACAAGATGGCTATTATTTACAATCCGATCTGCA ++ +'>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 +@1831_574_734/1 +CCTGTACGAAAGAACGTAGGCATGGGCTGGGGGG ++ +-&.$2&<*(-%):/)%5:)/%7+,9034*A.?70 +@1831_574_824/1 +AGCGCAAATTATGCGTTCCGCCTAGCGGAGAACT ++ +@@@;;),+@<-<7;<&89??&29?<$2:A<);8? +@1831_574_959/1 +CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC ++ +A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 +@1831_574_1062/1 +ACCGGTAATATAAGGCAACATGATTACGGCCACG ++ +@821<//:136/8<1/5.427.;>288/0<1$)/ +@1831_574_1092/1 +GACTGGCGAAATCATCGCGGAAAAACCCCTATCA ++ +8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 +@1831_574_1103/1 +ATCTCCTGATTAGACATATCTCCGTAGCTCACGC ++ +??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 +@1831_574_1116/1 +CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC ++ +(a)++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 +@1831_574_1194/1 +TTATCACATTTGGGGATCGGAAGGGACTACTTCG ++ +5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 +@1831_574_1204/1 +CTTACTGGTCTGCTGGACATATAGTGGCGATGAA ++ +A5A5B@5:;@@,.9?A1?#.?;3),>82%)='7* +@1831_574_1306/1 +ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA ++ +2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 +@1831_574_1387/1 +GTACTTCTCAATGCTGCACTACTATGTACGCCCC ++ +?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' +@1831_574_1431/1 +GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC ++ +7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 +@1831_574_1560/1 +GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC ++ +))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ +@1831_574_1591/1 +TGAGCACTTATGGCTAGGCGTAGGGGACCGTGAG ++ +=<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 +@1831_574_1624/1 +ACGGGAAGGGCTGGAATCTACCCAGTAGGCATTG ++ +<6.&(,7-+))7..'/;43.)927.(<85&13-) +@1831_574_1826/1 +TACGTCGCGACCGAGCGTTATATAGTCTGACCCC ++ +@<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ +@1831_574_1903/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ +@1831_574_1961/1 +GTTTCACTTCGGTTATTAAGAAACCCAAATGGAA ++ +>-07-@>(2'@<#064@%5%@@6.&<<(9)=:47 +@1831_575_54/1 +TTTCTTATGGGTAGAACAGCTGCCACTGACTGAA ++ +=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 +@1831_575_80/1 +TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT ++ +?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& +@1831_575_192/1 +AACTACGCCCCTTAATTACACAGCGCGTTAGACC ++ +:8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' +@1831_575_197/1 +TTCGCCTACACTTAGATACCTCTTAAACTCAATG ++ +-:?463@A:88?6?437<=.2&1.;@67.4@%2, +@1831_575_223/1 +ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA ++ +?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' +@1831_575_420/1 +CCCACATGGAAAACACTCACCGCCGAACAGAGCG ++ +2?.>?(-''2+..@),$%1@;')1)?+)7.').. +@1831_575_434/1 +ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC ++ +@@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) +@1831_575_444/1 +TAGGCGACCGTGAGGACAAGAGCTGTTGCCTTGA ++ +2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> +@1831_575_459/1 +CTTATCAGCACACGGTTTACCAGTCCGACTCCAA ++ +@@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. +@1831_575_506/1 +CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC ++ +?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* +@1831_575_569/1 +AGCAGACTGCTGTAACACGGTGTGGTGTAAGGAT ++ +'9-,@29+479%&>9#&08=>7#9>,69/+'*3) +@1831_575_622/1 +CCAAATCCGGCCCAGTAAGTGTCCTGTCGCACCC ++ +A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ +@1831_575_644/1 +CTTGAATGGCGATCTCGTCGAGGAAATACCACTA ++ +<8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 +@1831_575_663/1 +GGCAACTTATCCGCATTGGTCCCACTGGAGCGCA ++ +@@@@A</;A>@6>0792<5966:?;25+:><1,+ +@1831_575_681/1 +TCTCCTGATTAGACATATCACTGTTGAACACAGC ++ +72?.)25;96-14'*.03'#4#++$)/8+%/((& +@1831_575_711/1 +TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC ++ +%+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& +@1831_575_730/1 +CACACAGGAACCATAGCGTATGTTATTCACCCCC ++ +%8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& +@1831_575_904/1 +ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC ++ +<><.689@@7@<54:4=@>69=:+6-=42;8<:# +@1831_575_938/1 +TCATCAGGGAAGGCTAGGGGTTTACACTATTCGA ++ +:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 +@1831_575_970/1 +TGACTCCTACAGTCTTTATAGTACCGAGGGAGGC ++ +@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 +@1831_575_991/1 +TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA ++ +>>;7???/4<:::,#&*%'$--5-#(7)&&,-)% +@1831_575_1138/1 +TTGAAAGACCTGAACGCGATTTCATGTTTACTGC ++ +=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 +@1831_575_1157/1 +TCGCTGTTTAGATTTCGGGAGGGTACTTCAGTGC ++ +B@B>?A?A@?9'?;?&8?@@6;<@=+<:99+965 +@1831_575_1180/1 +GAATTCACGGCAGTGTTATCACCGTTTCCTTCCA ++ +<B>5?':/78?;1;55:997@@>94=7<186->7 +@1831_575_1283/1 +GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT ++ +C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 +@1831_575_1302/1 +CGACTATTCGTTTCGTCTAGAACGTGACACTAGC ++ +12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* +@1831_575_1310/1 +CTTGCTCTCGAGCTATGCCTCAGGACACGCCCTT ++ +<<>663?99@(@7=11@:@@/7??<@<;>'3-7; +@1831_575_1321/1 +CAACACAGTTGAACGGCGGAGGAGTAAAGATGCG ++ +;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 +@1831_575_1373/1 +CGCTACCGGTTCCAACGGCTGCCTGACTCGCGGA ++ +@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< +@1831_575_1419/1 +TGGGGAATATAACAGCGTAGCGTTGAACACTAGA ++ +//3->&-.->%11/@&/&7:<,-1=,+2<6'%&< +@1831_575_1436/1 +TGCATCTAGCGCGTATTGCGAGCCTTACGGATTC ++ +2@=;39*3<*4<:>52>>9'7:<='0=>1'136< +@1831_575_1442/1 +TCTGACAAGGTTCCTGCACCTGCGTCTGAGAGGG ++ +>58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> +@1831_575_1454/1 +CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT ++ +4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, +@1831_575_1500/1 +CACAAAAGGTCCCTACCTGTCTACCCTACATAGC ++ +?@@?A@?8<6<:985=99999==B3<5<<,7?>9 +@1831_575_1535/1 +CTCGACGATATGACCGCCAGCCACTTAACTCCGC ++ +B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< +@1831_575_1724/1 +TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA ++ +<B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 +@1831_575_1829/1 +CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC ++ +2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 +@1831_575_1898/1 +CTTACCATATCATCTCAACCCATAACAGCACTTA ++ +B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, +@1831_575_1964/1 +GACAGACCATGAGGCTGAAGACTACTAAGTGCGT ++ +>39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ +@1831_576_32/1 +TACGCAACGATTTATGGCCTTATAATTGAGGCCA ++ +<>?>?=7<2)522;><<@40@>704<>5=23@+& +@1831_576_74/1 +ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA ++ +=@@?@>(??<B5?@@@9<@><+><;@';>6961? +@1831_576_86/1 +ATGAAAACGCATTAGGACAACCATAATGGCCTCA ++ +811)2:*.++5</:3+43924*))/:,6&29)2/ +@1831_576_89/1 +GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA ++ +)69+,'.4=-,>/>(*$#)3030*'(,%)2##$, +@1831_576_266/1 +ATGGGGTCACTCGACCTAATCCCGCGGCTTTGGT ++ +@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 +@1831_576_327/1 +GCCGTTCTACTCTAGCTGCAACTTGCGATTGCTA ++ +@?@6@@;<@?><@>==3@:==<3@@>53<9><6= +@1831_576_331/1 +GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA ++ +-2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. +@1831_576_387/1 +ACACGCCATGATCCGATAAGAAGGGAACGTAAGG ++ +8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) +@1831_576_406/1 +AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC ++ +4<>%%14:*4656)&<251&2+3#&19,6&4>5( +@1831_576_449/1 +CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA ++ ++'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* +@1831_576_519/1 +TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC ++ +=46<97@>2/6?;2<4A881>9121+<1/4.9+7 +@1831_576_603/1 +CAATATGTCTTAGTCGTGACTCGGCAACTTATCC ++ +@46=@C.??<A79@@;-<@@>29B?>55<B7598 +@1831_576_655/1 +GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG ++ +@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% +@1831_576_677/1 +TTTACTCAGTTGATACATCACTGTAGCACATAGG ++ +290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% +@1831_576_718/1 +CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT ++ +4###$0###%(#########,####%####$### +@1831_576_722/1 +CGTATGATGGCGAGTCTTTATAATCCAATCTGAA ++ +*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') +@1831_576_754/1 +AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA ++ +4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* +@1831_576_815/1 +TAGGCCTGATATGACACGATCACAGTGCAACATC ++ +3>@?9>@?B=>=;>A???=>:25=4.25?6<57. +@1831_576_882/1 +TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG ++ +26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 +@1831_576_898/1 +AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT ++ +@@C2?C>?<>@886B?;?.??87=B<8<15??=. +@1831_576_923/1 +CTGGACATGAGAGACTGCACGCGGTACACGTCGG ++ +6.51=;.699<96>;;49<;;11;<@59:9=647 +@1831_576_930/1 +CTGGCATGTACGTCCATGTCAGACGAGCAGAACT ++ +#*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# +@1831_576_1019/1 +GATGCGCGCTGTCATGGCATCGAACCATCGGTCG ++ +<$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- +@1831_576_1068/1 +AAGAGTGACTCACTTACCGGGATGCGATGGAGCC ++ +>><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 +@1831_576_1131/1 +AGTTCGGGAAGGGCTGGAATCTACCCAGTAGGCA ++ +04@#@/@,4>9?2+?1571@',>=;(759;*92< +@1831_576_1168/1 +CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA ++ +@CC6@@2?9=>7?;76<;467@;9,0%26'',4$ +@1831_576_1207/1 +CAACCTGACTAAACGGGGATACGCTGGCGCTACA ++ +$>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 +@1831_576_1289/1 +TAGCGCAAGTCCAGAATGTTCATAGACTCGCGAT ++ +9<>1B@@;7@@663==28,5':8<<,.=2>>.50 +@1831_576_1329/1 +CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA ++ +>&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 +@1831_576_1367/1 +GGTCTCATCCGTTCCAATCGGGACTTTGACCAGT ++ +?@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 +@1831_576_1416/1 +TAGCGTTCAACGTCGATCTCATCTTGCCGATGGC ++ +';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ +@1831_576_1461/1 +GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA ++ +1&74#(#(&##$#,'###%#%%#*#&%%##%%%' +@1831_576_1605/1 +AGTGCAACATCTGCTTTGCTTATCAGCACACGGC ++ +<@C@@>1;@:;<<@@9@???9<3?5-21=4877, +@1831_576_1664/1 +CGCGCACAACTCGCCATGATACGACAAGACCCGA ++ +@?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) +@1831_576_1671/1 +GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT ++ +@?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% +@1831_576_1729/1 +CGTTTCGTCTACAACGTGACACTAGCACAGTATA ++ +?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> +@1831_576_1880/1 +TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT ++ +515/792,:,7/%/05,%$):+#8%2(1754))3 +@1831_576_1982/1 +AATGTCGTCAGACGACTTTGGCGCGAAAACCATA ++ +@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ +@1831_576_1987/1 +AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA ++ +##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ +@1831_576_2014/1 +CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT ++ +@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 +@1831_576_2028/1 +ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA ++ +<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ +@1831_577_40/1 +CCCCGCGTTACGAACGAGAGAAATCTCTTATAAT ++ +2/4('.')(<*?#$)%&<,/39<(.2,+<=@611 +@1831_577_119/1 +TCCCACAAGCCATTGACATGCTCGCTCTAAACAG ++ +>?C11)-1/)#;#/,850*+.+$$5550+%-.40 +@1831_577_133/1 +TGCTTGTACGGTCTAACGGGGTATGGGTTTCTGG ++ +4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) +@1831_577_255/1 +ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG ++ +<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# +@1831_577_281/1 +TATGTACGTCGCGTACACTCCGGGGCCCGCAAAA ++ +-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? +@1831_577_288/1 +CATCCGAGGCTATCAAGGCGTAAGCACTGACCTA ++ +;/79??&=B::298*6.7/+4&21,7,6?.7#'6 +@1831_577_322/1 +GAATGCTGGAGTACATTATGACAAACTATCGGAG ++ +=;>4506;255464-<#7+194&2<?65968)7/ +@1831_577_362/1 +CGATTAGTTACCACTCGTATTCGCACGCCCAGGA ++ +2B?:@?@<?958=,3:,90:&'-99,6<5.($+6 +@1831_577_382/1 +GTCGCGTATTCCCCGATGCTATGTAGACTTGCAA ++ +2957/:1))=76(*24;,3+:<.&.&-=1=2/5* +@1831_577_464/1 +TAGAGGCACCCTAACTCAGGGCTTTCTCGATTAG ++ +=<7/<826)>#.'&4204+5#/041.7*91&756 +@1831_577_488/1 +TGAATAGTTATGGCCAGAATGTCTGCACCGATAC ++ +48.,*>6566<?8=<=<2>6;94>;=9>@8924@ +@1831_577_511/1 +GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT ++ +7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ +@1831_577_545/1 +ACCGCTCTTTGGGTATGGGGCAATCTGGCATGTT ++ +><<9?<>?A<481@<@8==@76/61<95.5988- +@1831_577_559/1 +GTGCCACTATGTTCGACAGACCCTAAGGCGGAAG ++ +<@;??@>@?/2<.@1=>12=61/;=?.&2+92)' +@1831_577_562/1 +GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ++ +((&*&0%)1%)#($2-,***%/-,,))&,-.1'* +@1831_577_637/1 +GCCTTCGCGGGAGCATATCAGTCGATACATCCCA ++ +-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, +@1831_577_641/1 +TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT ++ +47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' +@1831_577_692/1 +CCGGTGAGAATTACATCGCGAGTACGCCCAAGGA ++ +B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< diff -r dd1b55dd3c22 -r 0d5182c4870b test-data/s2fq_out1.tabular --- a/test-data/s2fq_out1.tabular Tue Aug 04 12:05:12 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,576 +0,0 @@ -@1831_573_1004/1 -AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG -+ -><C&&9952+C>5<.?<79,=42<292:<(9/-7 -@1831_573_1050/1 -TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT -+ -;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, -@1831_573_1067/1 -AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG -+ -++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ -@1831_573_1219/1 -CGCCCTATAATAATACAGCGCGTTAGACCGCTCA -+ -@@=4/+)5)408?'665>*/5?<61';<3,:,5- -@1831_573_1242/1 -GCTGAATCGCACCTAGCAACTATAGCCGGGCCGC -+ ->>::>17=A5?@@=;7A=;2.60>82<8=74+;; -@1831_573_1333/1 -AGAATCGTTACCACACACTGCGTCTGGGTATCCG -+ -='@#%3=.>)/34*117,,/6-4+.9742456<) -@1831_573_1362/1 -CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC -+ -B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? -@1831_573_1448/1 -TCACGCCGGTCCTTGACTGGCGTTCTCTTCGAGG -+ -7=A)?,.@A@@:@@<=/7)@<-#8662%9613&+ -@1831_573_1490/1 -CTCGTCATGTTACGCAAAGGCACGTCACAGCACC -+ -@@@?,@??@$><=>+%/*>*1,)?26&12'9%7. -@1831_573_1523/1 -ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG -+ -,//*,#8''.6''6'2&27/80)%&#0'%#*,2' -@1831_573_1578/1 -CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC -+ -?=@<@C@?@@??=>@;7<<8<694)3511(+1<. -@1831_573_1647/1 -AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT -+ -?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 -@1831_573_1684/1 -TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT -+ ->1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? -@1831_573_1769/1 -TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC -+ -54749&&767%/7;3$-7;3#,3//#,45/#&06 -@1831_573_1853/1 -CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC -+ -4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& -@1831_573_1943/1 -ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC -+ ->/*1,),@-)'0*>5'$/?6(a)/.&?8/(')A43, -@1831_573_1977/1 -GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC -+ -@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 -@1831_574_109/1 -TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT -+ -7651#4817>@65<2:84716=788<1995.7?6 -@1831_574_148/1 -CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC -+ -;->3;;3>//>0;;7=,=4-4/+>029<9<624; -@1831_574_185/1 -CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC -+ -<4;%%@7>#*>97%6;+8$#<07%1372$%<54# -@1831_574_243/1 -AGGCACCGTAACTCAGGACATTCTCGATTAGTTA -+ -@@@95@=9?*><45$<@<4%@9?7#=?>7&>?97 -@1831_574_257/1 -ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC -+ ->>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& -@1831_574_293/1 -TGCTGCAAATAAACATACAGCCTTCTAATGACTA -+ -')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% -@1831_574_389/1 -CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA -+ -)$>/>8):2@:213;;.1)@3%64%+)<7)+$92 -@1831_574_575/1 -TTCTTGGCAAGCGCAGATTATGCGTTCCGCCTAG -+ -?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< -@1831_574_592/1 -TCATTTACCACGTCAGGGTCGGAGTCATTCATTA -+ -3-5)19,,<@>4067<2.-864346;9<1/;212 -@1831_574_617/1 -AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC -+ ->@?;>?=@==@>@=5?@+@:@40@><:0)')64- -@1831_574_725/1 -GACAAGATGGCTATTATTTACAATCCGATCTGCA -+ -'>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 -@1831_574_734/1 -CCTGTACGAAAGAACGTAGGCATGGGCTGGGGGG -+ --&.$2&<*(-%):/)%5:)/%7+,9034*A.?70 -@1831_574_824/1 -AGCGCAAATTATGCGTTCCGCCTAGCGGAGAACT -+ -@@@;;),+@<-<7;<&89??&29?<$2:A<);8? -@1831_574_959/1 -CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC -+ -A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 -@1831_574_1062/1 -ACCGGTAATATAAGGCAACATGATTACGGCCACG -+ -@821<//:136/8<1/5.427.;>288/0<1$)/ -@1831_574_1092/1 -GACTGGCGAAATCATCGCGGAAAAACCCCTATCA -+ -8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 -@1831_574_1103/1 -ATCTCCTGATTAGACATATCTCCGTAGCTCACGC -+ -??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 -@1831_574_1116/1 -CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC -+ -(a)++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 -@1831_574_1194/1 -TTATCACATTTGGGGATCGGAAGGGACTACTTCG -+ -5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 -@1831_574_1204/1 -CTTACTGGTCTGCTGGACATATAGTGGCGATGAA -+ -A5A5B@5:;@@,.9?A1?#.?;3),>82%)='7* -@1831_574_1306/1 -ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA -+ -2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 -@1831_574_1387/1 -GTACTTCTCAATGCTGCACTACTATGTACGCCCC -+ -?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' -@1831_574_1431/1 -GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC -+ -7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 -@1831_574_1560/1 -GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC -+ -))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ -@1831_574_1591/1 -TGAGCACTTATGGCTAGGCGTAGGGGACCGTGAG -+ -=<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 -@1831_574_1624/1 -ACGGGAAGGGCTGGAATCTACCCAGTAGGCATTG -+ -<6.&(,7-+))7..'/;43.)927.(<85&13-) -@1831_574_1826/1 -TACGTCGCGACCGAGCGTTATATAGTCTGACCCC -+ -@<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ -@1831_574_1903/1 -AGTGCAACATCTGCTTTGCTTATCAGCACACGGC -+ -956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ -@1831_574_1961/1 -GTTTCACTTCGGTTATTAAGAAACCCAAATGGAA -+ ->-07-@>(2'@<#064@%5%@@6.&<<(9)=:47 -@1831_575_54/1 -TTTCTTATGGGTAGAACAGCTGCCACTGACTGAA -+ -=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 -@1831_575_80/1 -TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT -+ -?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& -@1831_575_192/1 -AACTACGCCCCTTAATTACACAGCGCGTTAGACC -+ -:8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' -@1831_575_197/1 -TTCGCCTACACTTAGATACCTCTTAAACTCAATG -+ --:?463@A:88?6?437<=.2&1.;@67.4@%2, -@1831_575_223/1 -ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA -+ -?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' -@1831_575_420/1 -CCCACATGGAAAACACTCACCGCCGAACAGAGCG -+ -2?.>?(-''2+..@),$%1@;')1)?+)7.').. -@1831_575_434/1 -ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC -+ -@@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) -@1831_575_444/1 -TAGGCGACCGTGAGGACAAGAGCTGTTGCCTTGA -+ -2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> -@1831_575_459/1 -CTTATCAGCACACGGTTTACCAGTCCGACTCCAA -+ -@@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. -@1831_575_506/1 -CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC -+ -?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* -@1831_575_569/1 -AGCAGACTGCTGTAACACGGTGTGGTGTAAGGAT -+ -'9-,@29+479%&>9#&08=>7#9>,69/+'*3) -@1831_575_622/1 -CCAAATCCGGCCCAGTAAGTGTCCTGTCGCACCC -+ -A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ -@1831_575_644/1 -CTTGAATGGCGATCTCGTCGAGGAAATACCACTA -+ -<8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 -@1831_575_663/1 -GGCAACTTATCCGCATTGGTCCCACTGGAGCGCA -+ -@@@@A</;A>@6>0792<5966:?;25+:><1,+ -@1831_575_681/1 -TCTCCTGATTAGACATATCACTGTTGAACACAGC -+ -72?.)25;96-14'*.03'#4#++$)/8+%/((& -@1831_575_711/1 -TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC -+ -%+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& -@1831_575_730/1 -CACACAGGAACCATAGCGTATGTTATTCACCCCC -+ -%8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& -@1831_575_904/1 -ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC -+ -<><.689@@7@<54:4=@>69=:+6-=42;8<:# -@1831_575_938/1 -TCATCAGGGAAGGCTAGGGGTTTACACTATTCGA -+ -:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 -@1831_575_970/1 -TGACTCCTACAGTCTTTATAGTACCGAGGGAGGC -+ -@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 -@1831_575_991/1 -TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA -+ ->>;7???/4<:::,#&*%'$--5-#(7)&&,-)% -@1831_575_1138/1 -TTGAAAGACCTGAACGCGATTTCATGTTTACTGC -+ -=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 -@1831_575_1157/1 -TCGCTGTTTAGATTTCGGGAGGGTACTTCAGTGC -+ -B@B>?A?A@?9'?;?&8?@@6;<@=+<:99+965 -@1831_575_1180/1 -GAATTCACGGCAGTGTTATCACCGTTTCCTTCCA -+ -<B>5?':/78?;1;55:997@@>94=7<186->7 -@1831_575_1283/1 -GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT -+ -C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 -@1831_575_1302/1 -CGACTATTCGTTTCGTCTAGAACGTGACACTAGC -+ -12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* -@1831_575_1310/1 -CTTGCTCTCGAGCTATGCCTCAGGACACGCCCTT -+ -<<>663?99@(@7=11@:@@/7??<@<;>'3-7; -@1831_575_1321/1 -CAACACAGTTGAACGGCGGAGGAGTAAAGATGCG -+ -;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 -@1831_575_1373/1 -CGCTACCGGTTCCAACGGCTGCCTGACTCGCGGA -+ -@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< -@1831_575_1419/1 -TGGGGAATATAACAGCGTAGCGTTGAACACTAGA -+ -//3->&-.->%11/@&/&7:<,-1=,+2<6'%&< -@1831_575_1436/1 -TGCATCTAGCGCGTATTGCGAGCCTTACGGATTC -+ -2@=;39*3<*4<:>52>>9'7:<='0=>1'136< -@1831_575_1442/1 -TCTGACAAGGTTCCTGCACCTGCGTCTGAGAGGG -+ ->58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> -@1831_575_1454/1 -CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT -+ -4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, -@1831_575_1500/1 -CACAAAAGGTCCCTACCTGTCTACCCTACATAGC -+ -?@@?A@?8<6<:985=99999==B3<5<<,7?>9 -@1831_575_1535/1 -CTCGACGATATGACCGCCAGCCACTTAACTCCGC -+ -B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< -@1831_575_1724/1 -TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA -+ -<B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 -@1831_575_1829/1 -CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC -+ -2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 -@1831_575_1898/1 -CTTACCATATCATCTCAACCCATAACAGCACTTA -+ -B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, -@1831_575_1964/1 -GACAGACCATGAGGCTGAAGACTACTAAGTGCGT -+ ->39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ -@1831_576_32/1 -TACGCAACGATTTATGGCCTTATAATTGAGGCCA -+ -<>?>?=7<2)522;><<@40@>704<>5=23@+& -@1831_576_74/1 -ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA -+ -=@@?@>(??<B5?@@@9<@><+><;@';>6961? -@1831_576_86/1 -ATGAAAACGCATTAGGACAACCATAATGGCCTCA -+ -811)2:*.++5</:3+43924*))/:,6&29)2/ -@1831_576_89/1 -GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA -+ -)69+,'.4=-,>/>(*$#)3030*'(,%)2##$, -@1831_576_266/1 -ATGGGGTCACTCGACCTAATCCCGCGGCTTTGGT -+ -@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 -@1831_576_327/1 -GCCGTTCTACTCTAGCTGCAACTTGCGATTGCTA -+ -@?@6@@;<@?><@>==3@:==<3@@>53<9><6= -@1831_576_331/1 -GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA -+ --2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. -@1831_576_387/1 -ACACGCCATGATCCGATAAGAAGGGAACGTAAGG -+ -8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) -@1831_576_406/1 -AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC -+ -4<>%%14:*4656)&<251&2+3#&19,6&4>5( -@1831_576_449/1 -CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA -+ -+'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* -@1831_576_519/1 -TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC -+ -=46<97@>2/6?;2<4A881>9121+<1/4.9+7 -@1831_576_603/1 -CAATATGTCTTAGTCGTGACTCGGCAACTTATCC -+ -@46=@C.??<A79@@;-<@@>29B?>55<B7598 -@1831_576_655/1 -GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG -+ -@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% -@1831_576_677/1 -TTTACTCAGTTGATACATCACTGTAGCACATAGG -+ -290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% -@1831_576_718/1 -CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT -+ -4###$0###%(#########,####%####$### -@1831_576_722/1 -CGTATGATGGCGAGTCTTTATAATCCAATCTGAA -+ -*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') -@1831_576_754/1 -AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA -+ -4//#(.$)'',>(&#1$<,##%((,#5?#0*%1* -@1831_576_815/1 -TAGGCCTGATATGACACGATCACAGTGCAACATC -+ -3>@?9>@?B=>=;>A???=>:25=4.25?6<57. -@1831_576_882/1 -TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG -+ -26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 -@1831_576_898/1 -AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT -+ -@@C2?C>?<>@886B?;?.??87=B<8<15??=. -@1831_576_923/1 -CTGGACATGAGAGACTGCACGCGGTACACGTCGG -+ -6.51=;.699<96>;;49<;;11;<@59:9=647 -@1831_576_930/1 -CTGGCATGTACGTCCATGTCAGACGAGCAGAACT -+ -#*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# -@1831_576_1019/1 -GATGCGCGCTGTCATGGCATCGAACCATCGGTCG -+ -<$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- -@1831_576_1068/1 -AAGAGTGACTCACTTACCGGGATGCGATGGAGCC -+ ->><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 -@1831_576_1131/1 -AGTTCGGGAAGGGCTGGAATCTACCCAGTAGGCA -+ -04@#@/@,4>9?2+?1571@',>=;(759;*92< -@1831_576_1168/1 -CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA -+ -@CC6@@2?9=>7?;76<;467@;9,0%26'',4$ -@1831_576_1207/1 -CAACCTGACTAAACGGGGATACGCTGGCGCTACA -+ -$>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 -@1831_576_1289/1 -TAGCGCAAGTCCAGAATGTTCATAGACTCGCGAT -+ -9<>1B@@;7@@663==28,5':8<<,.=2>>.50 -@1831_576_1329/1 -CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA -+ ->&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 -@1831_576_1367/1 -GGTCTCATCCGTTCCAATCGGGACTTTGACCAGT -+ -?@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 -@1831_576_1416/1 -TAGCGTTCAACGTCGATCTCATCTTGCCGATGGC -+ -';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ -@1831_576_1461/1 -GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA -+ -1&74#(#(&##$#,'###%#%%#*#&%%##%%%' -@1831_576_1605/1 -AGTGCAACATCTGCTTTGCTTATCAGCACACGGC -+ -<@C@@>1;@:;<<@@9@???9<3?5-21=4877, -@1831_576_1664/1 -CGCGCACAACTCGCCATGATACGACAAGACCCGA -+ -@?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) -@1831_576_1671/1 -GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT -+ -@?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% -@1831_576_1729/1 -CGTTTCGTCTACAACGTGACACTAGCACAGTATA -+ -?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> -@1831_576_1880/1 -TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT -+ -515/792,:,7/%/05,%$):+#8%2(1754))3 -@1831_576_1982/1 -AATGTCGTCAGACGACTTTGGCGCGAAAACCATA -+ -@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ -@1831_576_1987/1 -AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA -+ -##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ -@1831_576_2014/1 -CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT -+ -@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 -@1831_576_2028/1 -ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA -+ -<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ -@1831_577_40/1 -CCCCGCGTTACGAACGAGAGAAATCTCTTATAAT -+ -2/4('.')(<*?#$)%&<,/39<(.2,+<=@611 -@1831_577_119/1 -TCCCACAAGCCATTGACATGCTCGCTCTAAACAG -+ ->?C11)-1/)#;#/,850*+.+$$5550+%-.40 -@1831_577_133/1 -TGCTTGTACGGTCTAACGGGGTATGGGTTTCTGG -+ -4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) -@1831_577_255/1 -ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG -+ -<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# -@1831_577_281/1 -TATGTACGTCGCGTACACTCCGGGGCCCGCAAAA -+ --:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? -@1831_577_288/1 -CATCCGAGGCTATCAAGGCGTAAGCACTGACCTA -+ -;/79??&=B::298*6.7/+4&21,7,6?.7#'6 -@1831_577_322/1 -GAATGCTGGAGTACATTATGACAAACTATCGGAG -+ -=;>4506;255464-<#7+194&2<?65968)7/ -@1831_577_362/1 -CGATTAGTTACCACTCGTATTCGCACGCCCAGGA -+ -2B?:@?@<?958=,3:,90:&'-99,6<5.($+6 -@1831_577_382/1 -GTCGCGTATTCCCCGATGCTATGTAGACTTGCAA -+ -2957/:1))=76(*24;,3+:<.&.&-=1=2/5* -@1831_577_464/1 -TAGAGGCACCCTAACTCAGGGCTTTCTCGATTAG -+ -=<7/<826)>#.'&4204+5#/041.7*91&756 -@1831_577_488/1 -TGAATAGTTATGGCCAGAATGTCTGCACCGATAC -+ -48.,*>6566<?8=<=<2>6;94>;=9>@8924@ -@1831_577_511/1 -GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT -+ -7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ -@1831_577_545/1 -ACCGCTCTTTGGGTATGGGGCAATCTGGCATGTT -+ -><<9?<>?A<481@<@8==@76/61<95.5988- -@1831_577_559/1 -GTGCCACTATGTTCGACAGACCCTAAGGCGGAAG -+ -<@;??@>@?/2<.@1=>12=61/;=?.&2+92)' -@1831_577_562/1 -GTTCCACTACGTTCCACGCAAAGGAATCCGAATC -+ -((&*&0%)1%)#($2-,***%/-,,))&,-.1'* -@1831_577_637/1 -GCCTTCGCGGGAGCATATCAGTCGATACATCCCA -+ --,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, -@1831_577_641/1 -TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT -+ -47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' -@1831_577_692/1 -CCGGTGAGAATTACATCGCGAGTACGCCCAAGGA -+ -B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< diff -r dd1b55dd3c22 -r 0d5182c4870b test-data/s2fq_out2.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_out2.fastqsanger Tue Aug 04 16:32:57 2009 -0400 @@ -0,0 +1,192 @@ +@1378_11_329/2 +GTTCGTGGCCGGTGGGTGTTTGGG ++ +###$$#$#$&#####$'$#$###$ +@1378_17_1788/2 +TGGGTGGATGTGTTGTCGTTCATG ++ +#$#$###$#$#######$#$#### +@1378_25_2035/2 +GTGCGTCGGGGAGGGTGCTGTCGG ++ +######%#$%#$$###($###&&% +@1378_28_770/2 +GGTTGGGAGTTGGCGCGCGTGGTT ++ +###$##%%$####%#%$#%%#($$ +@1378_33_1945/2 +GGGGGGGGGGGGGGGGGGGGGGGG ++ +.6;?;55697>8779457986264 +@1378_34_789/2 +GGGCTTGCGTTAGTGAGAGGTTGT ++ +###%$%$%%###$####$###$#& +@1378_35_263/2 +GGCGGGGGGGGGGGGGGGGGGGGG ++ +$%%&,)3/)%$-6'$&5&#$''5. +@1378_43_186/2 +GCTAGGGTTTGGGTTTGCGGTGGG ++ +$%#$########%##%#$###'#' +@1378_51_1671/2 +GGTGTTGTTCGGATGTAGCGTGGG ++ +##%$$####$########$##0## +@1378_56_324/2 +GCTGGGTGATCTAAGGAATGTAAT ++ +#$#####$$$#$$$$##%###*(# +@1378_56_773/2 +TCTGGTCGGTTTCGGGGAGTGGAA ++ +##%%#&$###$#$##%$####%%$ +@1378_62_2027/2 +GTTGGCCTGGCCTGCCGTGCTGCG ++ +*##),/%##$)#%##1$#'%.#&# +@1378_62_2029/2 +GGCGGTGTGTGGTGCGGCTGTGCG ++ +/$$$=(####%####)$$%$-&%# +@1378_67_1795/2 +CGTGCCAACGACCGTCCTACGGAG ++ +@@.?7@@@.@:@A<<>>=>70<@7 +@1378_68_466/2 +GTGTCATCTGAGGTAAAGCATTGT ++ +/##$09#$#.=$#$76+$%1'### +@1378_68_1692/2 +TGTTCGATTTAGGTCTTGCCTCGC ++ +###%%$%%##%$#$##$###$$#$ +@1378_80_664/2 +TGTCTGCGTTGTATCTCTGGTGTA ++ +%##%,%$$#&$$###$#$%##'%# +@1378_85_1786/2 +CCCTAGGAGCGTATACCGGACGAG ++ +,'&/%/@,&1,&'/)&,6&&1)(( +@1378_86_1011/2 +AGGCGATGGGATATTATTTTACTT ++ +:$###)%##$9$###1$$#$2### +@1378_86_1789/2 +GGCCAGGTACTAATAAATTCAACA ++ +1.51/&%#'$,*?%#6&0$$5,20 +@1378_91_1596/2 +GCTTTTTCATTCGGTGCCTTTGGA ++ +'>%/3%=()8'#.%?50$&5>%)% +@1378_94_1595/2 +GCGGGTTAACCCAGTACCTCTGGC ++ +,8@6'>8<76>@@(->9)7'*941 +@1378_95_1039/2 +GTTCTGTGCCAGGTGAGGTACGGA ++ +&##,./#$&)6##+,'#$$0(##$ +@1378_95_1767/2 +CTAATTGACCGGGCAAGCTATTAA ++ +',,2'(10/>:=/7).3&%6&)&6 +@1378_96_1037/2 +CTGCTGGGCCATTTGACTTACTCA ++ +'$#+#(##-%5##+*&###-.$$$ +@1378_96_1764/2 +TCTTTGTAACCCACTTAGTATTTC ++ +4='28>.@4881B807:822>%)1 +@1378_98_1574/2 +AGGCGAGTGTGGGGGTTGTTTGAG ++ ++%%$#)##%##$####%###$%$# +@1378_107_1647/2 +GGTCTGGTTCTATGTTGGTCGACT ++ +###'$$#$$$(#%###(#$##$%# +@1378_111_829/2 +GGTCTTCTATGGTGCTAAATTAGT ++ +$##'&###$##)#%($#$%#$'%# +@1378_111_1900/2 +GCACGCCTTTGGGCTAAGCCGTAA ++ +)$)'#%$########$'#&%$#(# +@1378_112_1483/2 +TGGAGTGGTGTGTTTGCTGAGCCA ++ +#$#)#############$#%#%'% +@1378_125_1287/2 +TGACGTGGGTTGTCCCGTGAGATT ++ +##$%%#$###$##$$#&%##$(%% +@1378_126_468/2 +AAAAAACGGGCCGGGCGGACTAGG ++ +@@B@@@>@2>1+?:92)>@8&&<+ +@1378_127_664/2 +TCGCTTTGCCTATGTTTGTTCGGA ++ +#%$%#&##$%#%%###$$###)-' +@1378_129_463/2 +AAAAAAAAAAAAAAAAAAAAAAAA ++ +,)&20%8'(&35-***1-2&+510 +@1378_129_875/2 +GACCTTTACGTATTGGGGGTTGGC ++ +###)###+###$##$#&%##$,#$ +@1378_140_1251/2 +TTTCCTTCGTGTGCGTGCGGAGTG ++ +#%#%$##$$$######.$$$%#%( +@1378_141_809/2 +TCTCGTGGTTTCTTTTTTATGTGT ++ +##%)##$$#####%$#$#%%#'## +@1378_144_983/2 +GTTCGTTCGTGGTGTACGAGGGTG ++ +#(#%#####($#%##$$#%##%#) +@1378_153_270/2 +GGCCGTGTGCGGGTGTAGATTGGA ++ +%$##($######&##$&$$$$%## +@1378_155_1689/2 +CGCGTTCGGACAAAGCTAGCACCT ++ +@4@@=6=@@<4:@@681@@@.24. +@1378_157_1580/2 +GGGATTGAAGGGATGTATGCTAGG ++ +#%$&%#$$'%$%#$##*#%$$$$# +@1378_161_317/2 +AATCCATACCCACAAAAGCAGGCC ++ +.&%','(@''?7//+&)+2.+)0) +@1378_177_735/2 +CGAGCCCTAAACCATGAGATCGGA ++ +@@B>@AC9@A<B8@=9>7@5)>,0 +@1378_181_1684/2 +TTTCTGTTGTGGTTTTGTTGGGGT ++ +$##'$%'##%##$%$#$$####$* +@1378_187_1407/2 +TTGGGTGAAATCTTGTCGAGTGGA ++ +####&##$$###$#####%##%%) +@1378_203_721/2 +CCTTTACGATCATAAACCATGACC ++ +9<&./1&@;12')?<1',?/)&/. +@1378_206_2039/2 +CCCCCCCCCCCCCCCCCCCCCCCC ++ +?=>>?=:;<>>4::<=56199(05 diff -r dd1b55dd3c22 -r 0d5182c4870b test-data/s2fq_out2.tabular --- a/test-data/s2fq_out2.tabular Tue Aug 04 12:05:12 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,192 +0,0 @@ -@1378_11_329/2 -GTTCGTGGCCGGTGGGTGTTTGGG -+ -###$$#$#$&#####$'$#$###$ -@1378_17_1788/2 -TGGGTGGATGTGTTGTCGTTCATG -+ -#$#$###$#$#######$#$#### -@1378_25_2035/2 -GTGCGTCGGGGAGGGTGCTGTCGG -+ -######%#$%#$$###($###&&% -@1378_28_770/2 -GGTTGGGAGTTGGCGCGCGTGGTT -+ -###$##%%$####%#%$#%%#($$ -@1378_33_1945/2 -GGGGGGGGGGGGGGGGGGGGGGGG -+ -.6;?;55697>8779457986264 -@1378_34_789/2 -GGGCTTGCGTTAGTGAGAGGTTGT -+ -###%$%$%%###$####$###$#& -@1378_35_263/2 -GGCGGGGGGGGGGGGGGGGGGGGG -+ -$%%&,)3/)%$-6'$&5&#$''5. -@1378_43_186/2 -GCTAGGGTTTGGGTTTGCGGTGGG -+ -$%#$########%##%#$###'#' -@1378_51_1671/2 -GGTGTTGTTCGGATGTAGCGTGGG -+ -##%$$####$########$##0## -@1378_56_324/2 -GCTGGGTGATCTAAGGAATGTAAT -+ -#$#####$$$#$$$$##%###*(# -@1378_56_773/2 -TCTGGTCGGTTTCGGGGAGTGGAA -+ -##%%#&$###$#$##%$####%%$ -@1378_62_2027/2 -GTTGGCCTGGCCTGCCGTGCTGCG -+ -*##),/%##$)#%##1$#'%.#&# -@1378_62_2029/2 -GGCGGTGTGTGGTGCGGCTGTGCG -+ -/$$$=(####%####)$$%$-&%# -@1378_67_1795/2 -CGTGCCAACGACCGTCCTACGGAG -+ -@@.?7@@@.@:@A<<>>=>70<@7 -@1378_68_466/2 -GTGTCATCTGAGGTAAAGCATTGT -+ -/##$09#$#.=$#$76+$%1'### -@1378_68_1692/2 -TGTTCGATTTAGGTCTTGCCTCGC -+ -###%%$%%##%$#$##$###$$#$ -@1378_80_664/2 -TGTCTGCGTTGTATCTCTGGTGTA -+ -%##%,%$$#&$$###$#$%##'%# -@1378_85_1786/2 -CCCTAGGAGCGTATACCGGACGAG -+ -,'&/%/@,&1,&'/)&,6&&1)(( -@1378_86_1011/2 -AGGCGATGGGATATTATTTTACTT -+ -:$###)%##$9$###1$$#$2### -@1378_86_1789/2 -GGCCAGGTACTAATAAATTCAACA -+ -1.51/&%#'$,*?%#6&0$$5,20 -@1378_91_1596/2 -GCTTTTTCATTCGGTGCCTTTGGA -+ -'>%/3%=()8'#.%?50$&5>%)% -@1378_94_1595/2 -GCGGGTTAACCCAGTACCTCTGGC -+ -,8@6'>8<76>@@(->9)7'*941 -@1378_95_1039/2 -GTTCTGTGCCAGGTGAGGTACGGA -+ -&##,./#$&)6##+,'#$$0(##$ -@1378_95_1767/2 -CTAATTGACCGGGCAAGCTATTAA -+ -',,2'(10/>:=/7).3&%6&)&6 -@1378_96_1037/2 -CTGCTGGGCCATTTGACTTACTCA -+ -'$#+#(##-%5##+*&###-.$$$ -@1378_96_1764/2 -TCTTTGTAACCCACTTAGTATTTC -+ -4='28>.@4881B807:822>%)1 -@1378_98_1574/2 -AGGCGAGTGTGGGGGTTGTTTGAG -+ -+%%$#)##%##$####%###$%$# -@1378_107_1647/2 -GGTCTGGTTCTATGTTGGTCGACT -+ -###'$$#$$$(#%###(#$##$%# -@1378_111_829/2 -GGTCTTCTATGGTGCTAAATTAGT -+ -$##'&###$##)#%($#$%#$'%# -@1378_111_1900/2 -GCACGCCTTTGGGCTAAGCCGTAA -+ -)$)'#%$########$'#&%$#(# -@1378_112_1483/2 -TGGAGTGGTGTGTTTGCTGAGCCA -+ -#$#)#############$#%#%'% -@1378_125_1287/2 -TGACGTGGGTTGTCCCGTGAGATT -+ -##$%%#$###$##$$#&%##$(%% -@1378_126_468/2 -AAAAAACGGGCCGGGCGGACTAGG -+ -@@B@@@>@2>1+?:92)>@8&&<+ -@1378_127_664/2 -TCGCTTTGCCTATGTTTGTTCGGA -+ -#%$%#&##$%#%%###$$###)-' -@1378_129_463/2 -AAAAAAAAAAAAAAAAAAAAAAAA -+ -,)&20%8'(&35-***1-2&+510 -@1378_129_875/2 -GACCTTTACGTATTGGGGGTTGGC -+ -###)###+###$##$#&%##$,#$ -@1378_140_1251/2 -TTTCCTTCGTGTGCGTGCGGAGTG -+ -#%#%$##$$$######.$$$%#%( -@1378_141_809/2 -TCTCGTGGTTTCTTTTTTATGTGT -+ -##%)##$$#####%$#$#%%#'## -@1378_144_983/2 -GTTCGTTCGTGGTGTACGAGGGTG -+ -#(#%#####($#%##$$#%##%#) -@1378_153_270/2 -GGCCGTGTGCGGGTGTAGATTGGA -+ -%$##($######&##$&$$$$%## -@1378_155_1689/2 -CGCGTTCGGACAAAGCTAGCACCT -+ -@4@@=6=@@<4:@@681@@@.24. -@1378_157_1580/2 -GGGATTGAAGGGATGTATGCTAGG -+ -#%$&%#$$'%$%#$##*#%$$$$# -@1378_161_317/2 -AATCCATACCCACAAAAGCAGGCC -+ -.&%','(@''?7//+&)+2.+)0) -@1378_177_735/2 -CGAGCCCTAAACCATGAGATCGGA -+ -@@B>@AC9@A<B8@=9>7@5)>,0 -@1378_181_1684/2 -TTTCTGTTGTGGTTTTGTTGGGGT -+ -$##'$%'##%##$%$#$$####$* -@1378_187_1407/2 -TTGGGTGAAATCTTGTCGAGTGGA -+ -####&##$$###$#####%##%%) -@1378_203_721/2 -CCTTTACGATCATAAACCATGACC -+ -9<&./1&@;12')?<1',?/)&/. -@1378_206_2039/2 -CCCCCCCCCCCCCCCCCCCCCCCC -+ -?=>>?=:;<>>4::<=56199(05 diff -r dd1b55dd3c22 -r 0d5182c4870b test-data/s2fq_out3.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/s2fq_out3.fastqsanger Tue Aug 04 16:32:57 2009 -0400 @@ -0,0 +1,192 @@ +@1378_11_329/1 +AGACCGGGCGGGGTGGCGTTCGGT ++ +%##+'#######%###$#$##$(# +@1378_17_1788/1 +TGCCGTGTCTTGCTAACGCCGATT ++ +#'#$$#$###%%##$$$$###### +@1378_25_2035/1 +CTGCGTGTTGGTGTCTACTGGGGT ++ +#%#'##$#$##&%#%$$$%#%#'# +@1378_28_770/1 +CTGCTATGCCGGCCGCCTGCCCCT ++ +%##(#$$#%$#$%###$%%$##$# +@1378_33_1945/1 +GGGGGGGGGGGGGGGGGGGGGGGG ++ ++9;64287788752796/576352 +@1378_34_789/1 +ATGGTGGCTGACGCGTTTGACTGT ++ +#$##%#$##$&$#%##$##$###$ +@1378_35_263/1 +GGGCGGGGGGCGGCGGGGGGGGGG ++ +),,#%'$)'-(%&%'%',%%&&(& +@1378_43_186/1 +ATACTAGTTGGGACGCGTTGTGCT ++ +#$(4%$########$#$###$$$# +@1378_51_1671/1 +TGGGTAGGTGCGGCTCTTGCGGTC ++ +##$#$%###%%#%#$##$$##### +@1378_56_324/1 +AGGCTTGGATTGTTGCGCTGACCT ++ +/+#**###%%##%#####$$$#$# +@1378_56_773/1 +TGTCGTGAGGTCACTTATCCCCAT ++ +&%#%##%%#####&#$%##$%##$ +@1378_62_2027/1 +CTTCCACGATCTGCTCGCTGTGGT ++ +(#&&$##$$#$%#%$$$#$###'# +@1378_62_2029/1 +TCTGGGCTGTCTTCGGGTCGGTGT ++ +$%$$####$##$$#)##%%#$### +@1378_67_1795/1 +TAGTGGGCTAGTCCGGGATCTACC ++ +B@C2@@?;-@@1>'A@@91@.@1' +@1378_68_466/1 +GTGATCGTCGGTGCCAGTCCCTGT ++ +#(%)+##$#$#%#+$%##$##### +@1378_68_1692/1 +GGTCTTCTGGGCACGGGCCAAGTT ++ +###)%'&%##$###%#######$# +@1378_80_664/1 +CTGCTTTGATCCCCGGTGGAGCAC ++ +7#%###$$6#######$##$$$## +@1378_85_1786/1 +ATACTATGTCGATCTGTAAAAAAA ++ +)&.)#3%(a)$&%-,2#&+.-%0&./ +@1378_86_1011/1 +CTACGTTATTGCTCTGTTTGTCCT ++ +######$%##$$$%###%#$#### +@1378_86_1789/1 +CGAATATCCCCTGGTTTAGAAGTA ++ +61?1;@/>@<=/(.7'(<5@=%$= +@1378_91_1596/1 +TTAGCGGTTGACTATCTGCTGACA ++ +*&+'#9'(%*'#//,&<),/)'*# +@1378_94_1595/1 +CGTGCGACAGCCCATGTTTTCAGA ++ +-=..5,3826&*+.+#+#%%6;%# +@1378_95_1039/1 +CGGCGTCCATCTTCGCCTTGAGAT ++ +$##.#$##$$#%$#$%%$###$)$ +@1378_95_1767/1 +ACACGCACCATCTGGCGGCTAACC ++ +86<65<4<C27/$5+#;-$+#2%$ +@1378_96_1037/1 +ATCCCCCAAGATGCCTGTTGATTG ++ +$#$'##$$$#%$$#%###+##$#$ +@1378_96_1764/1 +TACACCGGAACCTTGCACTAAAGC ++ +6-9'<#+81?+*<8-=69&6;*3) +@1378_98_1574/1 +GTTCTGCCGGTGTCTGTGGCGGGC ++ +$$#+&$$####%$$$###$%#%%# +@1378_107_1647/1 +AGGCCTACTACGCGTCATTGATAG ++ +&#$$#$(.#%#$$####&$%##($ +@1378_111_829/1 +TGCGGCACTTGCTTCTTCGTATTT ++ +%#%##%#$%#$#%###$$##&#$$ +@1378_111_1900/1 +TCCCCTCGCTCGGCTCTGTGCTGT ++ +$&%*$#(#)##$#'##%(##$#$% +@1378_112_1483/1 +TGTCCAGCTATGCGGCTTCCTCCT ++ +%#$+#%#&#$#####%####%$## +@1378_125_1287/1 +TGTCTCTGGGGGGCCTGGTTAGGT ++ +$##13$'%#$###$$###$$$#&# +@1378_126_468/1 +TCTCCTGATTAGACATATCTCCGT ++ +7>@318?=,=8@49579?..7,7) +@1378_127_664/1 +AGAGGTTGGTGTCTTGTCGCAGCT ++ +##'#$######$$%######$$$# +@1378_129_463/1 +CCTGTGGGCCAAGCCCAATGAAAG ++ +8),,<6(--)<()5&.&/8+;.2+ +@1378_129_875/1 +TTTCTATGGCTTACGCTGTCTGCC ++ +#$($##%####%$#$#####$### +@1378_140_1251/1 +ATCCTAGCGCGGTGTCTTGGGGAC ++ +#$%1#$$$##$##$#$#$##$%$$ +@1378_141_809/1 +TGTCCTCCAGTGTCTGTTGGGTGT ++ +%&,-##$$#(%###$#$$'###'# +@1378_144_983/1 +AGCGCCCGGTTGGTGCGGCTCGTC ++ +-$(&%*$#*#))#$$$#%%$#$## +@1378_153_270/1 +AGTCCTTGTCCCCTGGGTTTTCCC ++ ++''$#&%$%#$##&$$($#&#$$# +@1378_155_1689/1 +TTGGGAGGGAGAGAGACTAGACCG ++ +?4@@4<<??<?-@4@=4<5<?:/> +@1378_157_1580/1 +TGGGCCTCGGTGCCCTTGGTCTGT ++ +#%)$##'#$$$&#####%#$#$## +@1378_161_317/1 +TTGGCCGGCAACCCCGGTACCTAA ++ +7<,<'@)@>.)2@/')'&(?/-<( +@1378_177_735/1 +AGTACGCCATGTATTTGCGACCAG ++ +=?@?C<88@=>:7>@55/.,416, +@1378_181_1684/1 +CGACTCCCGCATTCACGGTCAAGT ++ +&*#,##$#&$*$$#$#$$$#%$## +@1378_187_1407/1 +TGGCGTCCACTCGTGGGTCTATCG ++ +$#$'%#$%$%&$%#####$#$#%# +@1378_203_721/1 +CCTAAATAACCCAGGGTAAAAGAT ++ +9<1+2+1@=259@+;2.71&@+2& +@1378_206_2039/1 +CCCCCCCCCCCCCCCCCCCCCCCC ++ +9@?8>;>>><<994;=895895-8 diff -r dd1b55dd3c22 -r 0d5182c4870b test-data/s2fq_out3.tabular --- a/test-data/s2fq_out3.tabular Tue Aug 04 12:05:12 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,192 +0,0 @@ -@1378_11_329/1 -AGACCGGGCGGGGTGGCGTTCGGT -+ -%##+'#######%###$#$##$(# -@1378_17_1788/1 -TGCCGTGTCTTGCTAACGCCGATT -+ -#'#$$#$###%%##$$$$###### -@1378_25_2035/1 -CTGCGTGTTGGTGTCTACTGGGGT -+ -#%#'##$#$##&%#%$$$%#%#'# -@1378_28_770/1 -CTGCTATGCCGGCCGCCTGCCCCT -+ -%##(#$$#%$#$%###$%%$##$# -@1378_33_1945/1 -GGGGGGGGGGGGGGGGGGGGGGGG -+ -+9;64287788752796/576352 -@1378_34_789/1 -ATGGTGGCTGACGCGTTTGACTGT -+ -#$##%#$##$&$#%##$##$###$ -@1378_35_263/1 -GGGCGGGGGGCGGCGGGGGGGGGG -+ -),,#%'$)'-(%&%'%',%%&&(& -@1378_43_186/1 -ATACTAGTTGGGACGCGTTGTGCT -+ -#$(4%$########$#$###$$$# -@1378_51_1671/1 -TGGGTAGGTGCGGCTCTTGCGGTC -+ -##$#$%###%%#%#$##$$##### -@1378_56_324/1 -AGGCTTGGATTGTTGCGCTGACCT -+ -/+#**###%%##%#####$$$#$# -@1378_56_773/1 -TGTCGTGAGGTCACTTATCCCCAT -+ -&%#%##%%#####&#$%##$%##$ -@1378_62_2027/1 -CTTCCACGATCTGCTCGCTGTGGT -+ -(#&&$##$$#$%#%$$$#$###'# -@1378_62_2029/1 -TCTGGGCTGTCTTCGGGTCGGTGT -+ -$%$$####$##$$#)##%%#$### -@1378_67_1795/1 -TAGTGGGCTAGTCCGGGATCTACC -+ -B@C2@@?;-@@1>'A@@91@.@1' -@1378_68_466/1 -GTGATCGTCGGTGCCAGTCCCTGT -+ -#(%)+##$#$#%#+$%##$##### -@1378_68_1692/1 -GGTCTTCTGGGCACGGGCCAAGTT -+ -###)%'&%##$###%#######$# -@1378_80_664/1 -CTGCTTTGATCCCCGGTGGAGCAC -+ -7#%###$$6#######$##$$$## -@1378_85_1786/1 -ATACTATGTCGATCTGTAAAAAAA -+ -)&.)#3%(a)$&%-,2#&+.-%0&./ -@1378_86_1011/1 -CTACGTTATTGCTCTGTTTGTCCT -+ -######$%##$$$%###%#$#### -@1378_86_1789/1 -CGAATATCCCCTGGTTTAGAAGTA -+ -61?1;@/>@<=/(.7'(<5@=%$= -@1378_91_1596/1 -TTAGCGGTTGACTATCTGCTGACA -+ -*&+'#9'(%*'#//,&<),/)'*# -@1378_94_1595/1 -CGTGCGACAGCCCATGTTTTCAGA -+ --=..5,3826&*+.+#+#%%6;%# -@1378_95_1039/1 -CGGCGTCCATCTTCGCCTTGAGAT -+ -$##.#$##$$#%$#$%%$###$)$ -@1378_95_1767/1 -ACACGCACCATCTGGCGGCTAACC -+ -86<65<4<C27/$5+#;-$+#2%$ -@1378_96_1037/1 -ATCCCCCAAGATGCCTGTTGATTG -+ -$#$'##$$$#%$$#%###+##$#$ -@1378_96_1764/1 -TACACCGGAACCTTGCACTAAAGC -+ -6-9'<#+81?+*<8-=69&6;*3) -@1378_98_1574/1 -GTTCTGCCGGTGTCTGTGGCGGGC -+ -$$#+&$$####%$$$###$%#%%# -@1378_107_1647/1 -AGGCCTACTACGCGTCATTGATAG -+ -&#$$#$(.#%#$$####&$%##($ -@1378_111_829/1 -TGCGGCACTTGCTTCTTCGTATTT -+ -%#%##%#$%#$#%###$$##&#$$ -@1378_111_1900/1 -TCCCCTCGCTCGGCTCTGTGCTGT -+ -$&%*$#(#)##$#'##%(##$#$% -@1378_112_1483/1 -TGTCCAGCTATGCGGCTTCCTCCT -+ -%#$+#%#&#$#####%####%$## -@1378_125_1287/1 -TGTCTCTGGGGGGCCTGGTTAGGT -+ -$##13$'%#$###$$###$$$#&# -@1378_126_468/1 -TCTCCTGATTAGACATATCTCCGT -+ -7>@318?=,=8@49579?..7,7) -@1378_127_664/1 -AGAGGTTGGTGTCTTGTCGCAGCT -+ -##'#$######$$%######$$$# -@1378_129_463/1 -CCTGTGGGCCAAGCCCAATGAAAG -+ -8),,<6(--)<()5&.&/8+;.2+ -@1378_129_875/1 -TTTCTATGGCTTACGCTGTCTGCC -+ -#$($##%####%$#$#####$### -@1378_140_1251/1 -ATCCTAGCGCGGTGTCTTGGGGAC -+ -#$%1#$$$##$##$#$#$##$%$$ -@1378_141_809/1 -TGTCCTCCAGTGTCTGTTGGGTGT -+ -%&,-##$$#(%###$#$$'###'# -@1378_144_983/1 -AGCGCCCGGTTGGTGCGGCTCGTC -+ --$(&%*$#*#))#$$$#%%$#$## -@1378_153_270/1 -AGTCCTTGTCCCCTGGGTTTTCCC -+ -+''$#&%$%#$##&$$($#&#$$# -@1378_155_1689/1 -TTGGGAGGGAGAGAGACTAGACCG -+ -?4@@4<<??<?-@4@=4<5<?:/> -@1378_157_1580/1 -TGGGCCTCGGTGCCCTTGGTCTGT -+ -#%)$##'#$$$&#####%#$#$## -@1378_161_317/1 -TTGGCCGGCAACCCCGGTACCTAA -+ -7<,<'@)@>.)2@/')'&(?/-<( -@1378_177_735/1 -AGTACGCCATGTATTTGCGACCAG -+ -=?@?C<88@=>:7>@55/.,416, -@1378_181_1684/1 -CGACTCCCGCATTCACGGTCAAGT -+ -&*#,##$#&$*$$#$#$$$#%$## -@1378_187_1407/1 -TGGCGTCCACTCGTGGGTCTATCG -+ -$#$'%#$%$%&$%#####$#$#%# -@1378_203_721/1 -CCTAAATAACCCAGGGTAAAAGAT -+ -9<1+2+1@=259@+;2.71&@+2& -@1378_206_2039/1 -CCCCCCCCCCCCCCCCCCCCCCCC -+ -9@?8>;>>><<994;=895895-8 diff -r dd1b55dd3c22 -r 0d5182c4870b tools/next_gen_conversion/solid_to_fastq.xml --- a/tools/next_gen_conversion/solid_to_fastq.xml Tue Aug 04 12:05:12 2009 -0400 +++ b/tools/next_gen_conversion/solid_to_fastq.xml Tue Aug 04 16:32:57 2009 -0400 @@ -38,17 +38,18 @@ </inputs> <outputs>  - <data name="output1" format="tabular"/> - <data name="output2" format="tabular"> + <data name="output1" format="fastqsanger"/> + <data name="output2" format="fastqsanger"> <filter>paired['pairedSingle'] == 'paired'</filter> </data> </outputs> <tests> -  </tests>

1 0

[hg] galaxy 2533: Bugfix in process_css.py
by Greg Von Kuster 06 Aug '09

06 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ab5bf78270af changeset: 2533:ab5bf78270af user: James Taylor <james(a)jamestaylor.org> date: Wed Aug 05 10:44:57 2009 -0400 description: Bugfix in process_css.py 1 file(s) affected in this change: static/june_2007_style/process_css.py diffs (21 lines): diff -r f0978599ba8d -r ab5bf78270af static/june_2007_style/process_css.py --- a/static/june_2007_style/process_css.py Wed Aug 05 08:58:23 2009 -0400 +++ b/static/june_2007_style/process_css.py Wed Aug 05 10:44:57 2009 -0400 @@ -139,7 +139,7 @@ pad = 10 - class SpriteGroup(): + class SpriteGroup( object ): def __init__( self, name ): self.name = name self.offset = 0 @@ -152,7 +152,7 @@ self.offset += sprite.image.size[1] + pad return sprite - class Sprite(): + class Sprite( object ): def __init__( self, fname, offset ): self.fname = fname self.image = Image.open( os.path.join( image_dir, fname ) )

1 0

[hg] galaxy 2532: Allow nested groupings in testing framework.
by Greg Von Kuster 06 Aug '09

06 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f0978599ba8d changeset: 2532:f0978599ba8d user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Aug 05 08:58:23 2009 -0400 description: Allow nested groupings in testing framework. 3 file(s) affected in this change: test-data/joiner_out3.bed test/functional/test_toolbox.py tools/filters/joiner.xml diffs (171 lines): diff -r 0d5182c4870b -r f0978599ba8d test-data/joiner_out3.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/joiner_out3.bed Wed Aug 05 08:58:23 2009 -0400 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + X X X X X X +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + X X X X X X +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - X X X X X X +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + X X X X X X +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - X X X X X X +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - X X X X X X +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + X X X X X X +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - X X X X X X +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + X X X X X X +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + X X X X X X +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - X X X X X X +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + X X X X X X +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - X X X X X X +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - X X X X X X +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + X X X X X X +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - X X X X X X +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 - diff -r 0d5182c4870b -r f0978599ba8d test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Tue Aug 04 16:32:57 2009 -0400 +++ b/test/functional/test_toolbox.py Wed Aug 05 08:58:23 2009 -0400 @@ -65,52 +65,39 @@ def shortDescription( self ): return self.name - def __expand_grouping( self, tool_inputs, declared_inputs, repeat_index=0, repeat_sep='' ): + def __expand_grouping( self, tool_inputs, declared_inputs, prefix='' ): expanded_inputs = {} for key, value in tool_inputs.items(): - if isinstance(value, grouping.Conditional): - for i, case in enumerate(value.cases): - if declared_inputs[value.test_param.name] == case.value: + if isinstance( value, grouping.Conditional ): + if prefix: + new_prefix = "%s|%s" % ( prefix, value.name ) + else: + new_prefix = value.name + for i, case in enumerate( value.cases ): + if declared_inputs[ value.test_param.name ] == case.value: if isinstance(case.value, str): - if repeat_sep: - cond_sep = "%s%s" % ( repeat_sep, value.test_param.name ) - else: - cond_sep = "%s|%s" % ( value.name, value.test_param.name ) - expanded_inputs[ cond_sep ] = case.value.split( "," ) + expanded_inputs[ "%s|%s" % ( new_prefix, value.test_param.name ) ] = case.value.split( "," ) else: - if repeat_sep: - cond_sep = "%s%s" % ( repeat_sep, value.test_param.name ) - else: - cond_sep = "%s|%s" % ( value.name, value.test_param.name ) - expanded_inputs[ cond_sep ] = case.value + expanded_inputs[ "%s|%s" % ( new_prefix, value.test_param.name ) ] = case.value for input_name, input_value in case.inputs.items(): - if isinstance(input_value, grouping.Conditional): - expanded_inputs.update( self.__expand_grouping( { input_name:input_value }, declared_inputs, repeat_index=repeat_index, repeat_sep=repeat_sep ) ) - elif isinstance(declared_inputs[input_name], str): - if repeat_sep: - cond_sep = "%s%s" % ( repeat_sep, input_name ) - else: - cond_sep = "%s|%s" % ( value.name, input_name ) - expanded_inputs.update( { cond_sep : declared_inputs[ input_name ].split( "," ) } ) - else: - if repeat_sep: - cond_sep = "%s%s" % ( repeat_sep, input_name ) - else: - cond_sep = "%s|%s" % ( value.name, input_name ) - expanded_inputs.update( { cond_sep : declared_inputs[ input_name ] } ) + expanded_inputs.update( self.__expand_grouping( { input_name:input_value }, declared_inputs, prefix = new_prefix ) ) elif isinstance( value, grouping.Repeat ): - for r_name, r_value in value.inputs.items(): - repeat_sep = "%s_%d|%s" % ( value.name, repeat_index, r_name ) - if isinstance( r_value, grouping.Conditional ): - cond_sep = repeat_sep + "|" - expanded_inputs.update( self.__expand_grouping( { r_name:r_value }, declared_inputs, repeat_index=repeat_index, repeat_sep=cond_sep ) ) - else: - expanded_inputs.update( { repeat_sep : [ declared_inputs[ r_name ] ] } ) - repeat_index += 1 + for repeat_index in xrange( 0, 1 ): #need to allow for and figure out how many repeats we have + for r_name, r_value in value.inputs.iteritems(): + new_prefix = "%s_%d" % ( value.name, repeat_index ) + if prefix: + new_prefix = "%s|%s" % ( prefix, new_prefix ) + expanded_inputs.update( self.__expand_grouping( { new_prefix : r_value }, declared_inputs, prefix = new_prefix ) ) elif isinstance(declared_inputs[value.name], str): - expanded_inputs[value.name] = declared_inputs[value.name].split(",") + if prefix: + expanded_inputs["%s|%s" % ( prefix, value.name ) ] = declared_inputs[value.name].split(",") + else: + expanded_inputs[value.name] = declared_inputs[value.name].split(",") else: - expanded_inputs[value.name] = declared_inputs[value.name] + if prefix: + expanded_inputs["%s|%s" % ( prefix, value.name ) ] = declared_inputs[value.name] + else: + expanded_inputs[value.name] = declared_inputs[value.name] return expanded_inputs def get_testcase( testdef, name ): diff -r 0d5182c4870b -r f0978599ba8d tools/filters/joiner.xml --- a/tools/filters/joiner.xml Tue Aug 04 16:32:57 2009 -0400 +++ b/tools/filters/joiner.xml Wed Aug 05 08:58:23 2009 -0400 @@ -98,7 +98,7 @@ <param name="fill_empty_columns_switch" value="no_fill"/> <output name="out_file1" file="joiner_out2.bed"/> </test> - + </test> </tests> <help>

1 0

[hg] galaxy 2535: Fixed the issue which was causing the 'Lab' ta...
by Greg Von Kuster 06 Aug '09

06 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/93d502caec2a changeset: 2535:93d502caec2a user: rc date: Wed Aug 05 11:19:46 2009 -0400 description: Fixed the issue which was causing the 'Lab' tab in the masthead to appear automatically. Now, this tab is visible only when request types have been created by the admin. 1 file(s) affected in this change: templates/base_panels.mako diffs (30 lines): diff -r 80e1c1772ed5 -r 93d502caec2a templates/base_panels.mako --- a/templates/base_panels.mako Wed Aug 05 11:02:53 2009 -0400 +++ b/templates/base_panels.mako Wed Aug 05 11:19:46 2009 -0400 @@ -149,15 +149,17 @@ ${tab( "workflow", "Workflow", h.url_for( controller='workflow', action='index' ))} ${tab( "libraries", "Libraries", h.url_for( controller='library', action='index' ))} - - <td class="tab"> - <a>Lab</a> - <div class="submenu"> - <ul> - <li><a target="requests" href="${h.url_for( controller='requests', action='index' )}">Sequencing Requests</a></li> - </ul> - </div> - </td> + + %if trans.request_types(): + <td class="tab"> + <a>Lab</a> + <div class="submenu"> + <ul> + <li><a target="requests" href="${h.url_for( controller='requests', action='index' )}">Sequencing Requests</a></li> + </ul> + </div> + </td> + %endif %if app.config.get_bool( 'enable_tracks', False ): <td class="tab">

1 0

[hg] galaxy 2534: Remove last cheetah templates (dataset errors ...
by Greg Von Kuster 06 Aug '09

06 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/80e1c1772ed5 changeset: 2534:80e1c1772ed5 user: James Taylor <james(a)jamestaylor.org> date: Wed Aug 05 11:02:53 2009 -0400 description: Remove last cheetah templates (dataset errors and validation). Fix errors template to use correct form styles. Resolves #18 5 file(s) affected in this change: lib/galaxy/web/controllers/dataset.py lib/galaxy/web/controllers/root.py templates/dataset/errors.mako templates/dataset/errors.tmpl templates/dataset/validation.tmpl diffs (266 lines): diff -r ab5bf78270af -r 80e1c1772ed5 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Wed Aug 05 10:44:57 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Wed Aug 05 11:02:53 2009 -0400 @@ -44,7 +44,7 @@ @web.expose def errors( self, trans, id ): dataset = model.HistoryDatasetAssociation.get( id ) - return trans.fill_template( "dataset/errors.tmpl", dataset=dataset ) + return trans.fill_template( "dataset/errors.mako", dataset=dataset ) @web.expose def stderr( self, trans, id ): diff -r ab5bf78270af -r 80e1c1772ed5 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Wed Aug 05 10:44:57 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Wed Aug 05 11:02:53 2009 -0400 @@ -547,29 +547,29 @@ # return trans.fill_template( "/root/masthead.mako", brand=brand, wiki_url=wiki_url, # blog_url=blog_url,bugs_email=bugs_email, screencasts_url=screencasts_url, admin_user=admin_user, active_view=active_view ) - @web.expose - def dataset_errors( self, trans, id=None, **kwd ): - """View/fix errors associated with dataset""" - data = trans.app.model.HistoryDatasetAssociation.get( id ) - p = kwd - if p.get("fix_errors", None): - # launch tool to create new, (hopefully) error free dataset - tool_params = {} - tool_params["tool_id"] = 'fix_errors' - tool_params["runtool_btn"] = 'T' - tool_params["input"] = id - tool_params["ext"] = data.ext - # send methods selected - repair_methods = data.datatype.repair_methods( data ) - methods = [] - for method, description in repair_methods: - if method in p: methods.append(method) - tool_params["methods"] = ",".join(methods) - url = "/tool_runner/index?" + urllib.urlencode(tool_params) - trans.response.send_redirect(url) - else: - history = trans.app.model.History.get( data.history_id ) - return trans.fill_template('dataset/validation.tmpl', data=data, history=history) + # @web.expose + # def dataset_errors( self, trans, id=None, **kwd ): + # """View/fix errors associated with dataset""" + # data = trans.app.model.HistoryDatasetAssociation.get( id ) + # p = kwd + # if p.get("fix_errors", None): + # # launch tool to create new, (hopefully) error free dataset + # tool_params = {} + # tool_params["tool_id"] = 'fix_errors' + # tool_params["runtool_btn"] = 'T' + # tool_params["input"] = id + # tool_params["ext"] = data.ext + # # send methods selected + # repair_methods = data.datatype.repair_methods( data ) + # methods = [] + # for method, description in repair_methods: + # if method in p: methods.append(method) + # tool_params["methods"] = ",".join(methods) + # url = "/tool_runner/index?" + urllib.urlencode(tool_params) + # trans.response.send_redirect(url) + # else: + # history = trans.app.model.History.get( data.history_id ) + # return trans.fill_template('dataset/validation.tmpl', data=data, history=history) # ---- Debug methods ---------------------------------------------------- diff -r ab5bf78270af -r 80e1c1772ed5 templates/dataset/errors.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/dataset/errors.mako Wed Aug 05 11:02:53 2009 -0400 @@ -0,0 +1,72 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> +<html> + <head> + <title>Dataset generation errors</title> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <link href="/static/style/base.css" rel="stylesheet" type="text/css" /> + <style> + pre + { + background: white; + color: black; + border: dotted black 1px; + overflow: auto; + padding: 10px; + } + </style> + </head> + + <body> + <h2>Dataset generation errors</h2> + <p><b>Dataset ${dataset.hid}: ${dataset.display_name()}</b></p> + + %if dataset.creating_job_associations: + <% job = dataset.creating_job_associations[0].job %> + %if job.traceback: + The Galaxy framework encountered the following error while attempting to run the tool: + <pre>${job.traceback}</pre> + %endif + %if job.stderr or job.info: + Tool execution generated the following error message: + %if job.stderr: + <pre>${job.stderr}</pre> + %elif job.info: + <pre>${job.info}</pre> + %endif + %else: + Tool execution did not generate any error messages. + %endif + %if job.stdout: + The tool produced the following additional output: + <pre>${job.stdout}</pre> + %endif + %else: + The tool did not create any additional job / error info. + %endif + + <h2>Report this error to the Galaxy Team</h2> + <p> + The Galaxy team regularly reviews errors that occur in the application. + However, if you would like to provide additional information (such as + what you were trying to do when the error occurred) and a contact e-mail + address, we will be better able to investigate your problem and get back + to you. + </p> + <div class="toolForm"> + <div class="toolFormTitle">Error Report</div> + <div class="toolFormBody"> + <form name="report_error" action="${h.url_for( action='report_error')}" method="post" > + <input type="hidden" name="id" value="${dataset.id}" /> + <div class="form-row"> + <label>Your email</label> + <input type="text" name="email" size="40" /> + </div> + <div class="form-row"> + <label>Message</label> + <textarea name="message", rows="10" cols="40" /> + </div> + </form> + </div> + </div> + </body> +</html> diff -r ab5bf78270af -r 80e1c1772ed5 templates/dataset/errors.tmpl --- a/templates/dataset/errors.tmpl Wed Aug 05 10:44:57 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,69 +0,0 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> -<html> - <head> - <title>Dataset generation errors</title> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <link href="/static/style/base.css" rel="stylesheet" type="text/css" /> - <style> - pre - { - background: white; - color: black; - border: dotted black 1px; - overflow: auto; - padding: 10px; - } - </style> - </head> - - <body> - <h2>Dataset generation errors</h2> - <p><b>Dataset $dataset.hid: $dataset.display_name</b></p> - - #if $dataset.creating_job_associations - #set job = $dataset.creating_job_associations[0].job - #if job.traceback - The Galaxy framework encountered the following error while attempting to run the tool: - <pre>${job.traceback}</pre> - #end if - #if $job.stderr or $job.info - Tool execution generated the following error message: - #if $job.stderr - <pre>${job.stderr}</pre> - #elif $job.info - <pre>${job.info}</pre> - #end if - #else - Tool execution did not generate any error messages. - #end if - #if $job.stdout - The tool produced the following additional output: - <pre>${job.stdout}</pre> - #end if - #else - The tool did not create any additional job / error info. - #end if - - <h2>Report this error to the Galaxy Team</h2> - <p> - The Galaxy team regularly reviews errors that occur in the application. - However, if you would like to provide additional information (such as - what you were trying to do when the error occurred) and a contact e-mail - address, we will be better able to investigate your problem and get back - to you. - </p> - <div class="toolForm"> - <div class="toolFormTitle">Error Report</div> - <div class="toolFormBody"> - <form name="report_error" action="${h.url_for( action='report_error')}" method="post" > - <input type="hidden" name="id" value="$dataset.id" /> - <table> - <tr valign="top"><td>Your Email:</td><td><input type="text" name="email" size="40" /></td></tr> - <tr valign="top"><td>Message:</td><td><textarea name="message", rows="10" cols="40" /></textarea></td></tr> - <tr><td></td><td><input type="submit" value="Report"> - </table> - </form> - </div> - </div> - </body> -</html> diff -r ab5bf78270af -r 80e1c1772ed5 templates/dataset/validation.tmpl --- a/templates/dataset/validation.tmpl Wed Aug 05 10:44:57 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> -<html> - -<head> -<title>Galaxy</title> -<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<link href="/static/style/base.css" rel="stylesheet" type="text/css" /> -<script type="text/javascript" src="/static/universe.js">var dummy1=0;</script> -</head> - -<body onLoad="frame_dw();"> - -<div class="toolForm"> - <div class="toolFormTitle">Dataset Errors: $data.name</div> - <div class="toolFormBody"> - <form action="/dataset_errors" method="post" > - - <table> - <tr><td>Name:</td><td>$data.name</td></tr> - <tr><td>Info:</td><td>$data.info<input type="hidden" name="id" value="$data.id"></td></tr> - <tr><td>Errors:</td><td>$len($data.validation_errors)</td></tr> - </table> - #if len($data.validation_errors) > 0: - <table> - <tr><td>Displaying the first 10 errors:</td></tr> - #for count in range(min(len($data.validation_errors),10)): - <tr><td>$data.validation_errors[count].message</td></tr> - #end for - #if $data.datatype.repair_methods($data): - #for $option, $description in $data.datatype.repair_methods($data): - <tr><td><input type="checkbox" name="$option" value="true" />$description</td></tr> - #end for - <tr><td><input type="submit" name="fix_errors" value="Submit"></td></tr> - #end if - </table> - #end if - </form> - </div> -</div> - - -</body> - -</html> \ No newline at end of file

1 0

[hg] galaxy 2530: Changes to browse_library UI, removed nested t...
by Greg Von Kuster 06 Aug '09

06 Aug '09

details: http://www.bx.psu.edu/hg/galaxy/rev/dd1b55dd3c22 changeset: 2530:dd1b55dd3c22 user: James Taylor <james(a)jamestaylor.org> date: Tue Aug 04 12:05:12 2009 -0400 description: Changes to browse_library UI, removed nested tables so widths can be variable. Cleaned up some styles (more grid-like) 3 file(s) affected in this change: static/june_2007_style/blue/library.css static/june_2007_style/library.css.tmpl templates/library/browse_library.mako diffs (568 lines): diff -r 5003b7d10ff5 -r dd1b55dd3c22 static/june_2007_style/blue/library.css --- a/static/june_2007_style/blue/library.css Mon Aug 03 17:35:44 2009 -0400 +++ b/static/june_2007_style/blue/library.css Tue Aug 04 12:05:12 2009 -0400 @@ -12,4 +12,6 @@ pre.peek{background:white;color:black;width:100%;overflow:auto;} pre.peek th{color:white;background:#023858;} a.expandLink{text-decoration:none;} -span.expandLink{width:100%;height:100%;display:block;} +span.expandLink{width:16px;height:16px;display:inline-block;vertical-align:middle;background:url(../images/silk/resultset_next.png);} +.folderRow.expanded span.expandLink{background:url(../images/silk/resultset_bottom.png);} +.folderRow span.rowIcon{width:16px;height:16px;display:inline-block;vertical-align:middle;background:url(../images/silk/folder.png);} diff -r 5003b7d10ff5 -r dd1b55dd3c22 static/june_2007_style/library.css.tmpl --- a/static/june_2007_style/library.css.tmpl Mon Aug 03 17:35:44 2009 -0400 +++ b/static/june_2007_style/library.css.tmpl Tue Aug 04 12:05:12 2009 -0400 @@ -69,7 +69,22 @@ } span.expandLink { - width: 100%; - height: 100%; - display: block; + width: 16px; + height: 16px; + display: inline-block; + vertical-align: middle; + background: url(../images/silk/resultset_next.png); } + +.folderRow.expanded span.expandLink { + background: url(../images/silk/resultset_bottom.png); +} + +.folderRow span.rowIcon { + width: 16px; + height: 16px; + display: inline-block; + vertical-align: middle; + background: url(../images/silk/folder.png); +} + diff -r 5003b7d10ff5 -r dd1b55dd3c22 templates/library/browse_library.mako --- a/templates/library/browse_library.mako Mon Aug 03 17:35:44 2009 -0400 +++ b/templates/library/browse_library.mako Tue Aug 04 12:05:12 2009 -0400 @@ -1,5 +1,5 @@ <%inherit file="/base.mako"/> -<%namespace file="common.mako" import="render_dataset" /> +## <%namespace file="common.mako" import="render_dataset" /> <%namespace file="/message.mako" import="render_msg" /> <% from galaxy import util %> @@ -10,102 +10,144 @@ </%def> <% + def name_sorted( l ): return sorted( l, lambda a, b: cmp( a.name.lower(), b.name.lower() ) ) + +class RowCounter( object ): + def __init__( self ): + self.count = 0 + def increment( self ): + self.count += 1 + def __str__( self ): + return str( self.count ) + %> <script type="text/javascript"> $( document ).ready( function () { - // Check/uncheck boxes in subfolders. - $("input.folderCheckbox").click( function() { - if ( $(this).is(":checked") ) { - //$(this).parent().children().find("input[type=checkbox]").each( function() { this.checked = true; }); - $(this).parent().next("ul").find("input[type=checkbox]").each( function() { this.checked = true; }); - } else { - //$(this).parent().children().find("input[type=checkbox]").each( function() { this.checked = false; }); - $(this).parent().next("ul").find("input[type=checkbox]").each( function() { this.checked = false; }); - } - }); - // If you uncheck a lower level checkbox, uncheck the boxes above it - // (since deselecting a child means the parent is not fully selected any - // more). - $("input[type=checkbox]").click( function() { - if ( ! $(this).is(":checked") ) { - //var folder_rows = $(this).parents("ul").next("li.folderRow"); - //var folder_rows = $(this).parents("ul").children("li.folderRow"); - var folder_rows = $(this).parents("ul").prev("li.folderRow"); - //$(folder_rows).children("input[type=checkbox]").not(this).each( function() { - $(folder_rows).find("input[type=checkbox]").each( function() { - this.checked = false; + $("#library-grid").each( function() { + // Recursively fill in children and descendents of each row + var process_row = function( q, parents ) { + // Find my index + var index = $(q).parent().children().index( $(q) ); + // Find my immediate children + var children = $(q).siblings().filter( "[parent='" + index + "']" ); + // Recursively handle them + var descendents = children; + children.each( function() { + child_descendents = process_row( $(this), parents.add( q ) ); + descendents = descendents.add( child_descendents ); }); - } - }); - // Handle the hide/show triangles - $("span.expandLink").wrap( "<a href='#' class='expandLink'></a>" ).click( function() { - var contents = $(this).parents("li:first").next("ul"); - if ( this.id == "libraryRow" ) { - var icon_open = "${h.url_for( '/static/images/silk/book_open.png' )}"; - var icon_closed = "${h.url_for( '/static/images/silk/book.png' )}"; - } else { - var icon_open = "${h.url_for( '/static/images/silk/folder_page.png' )}"; - var icon_closed = "${h.url_for( '/static/images/silk/folder.png' )}"; - } - if ( contents.is(":visible") ) { - contents.slideUp("fast"); - $(this).find("img.expanderIcon").each( function() { this.src = "${h.url_for( '/static/images/silk/resultset_next.png' )}"; }); - $(this).find("img.rowIcon").each( function() { this.src = icon_closed; }); - } else { - contents.slideDown("fast"); - $(this).find("img.expanderIcon").each( function() { this.src = "${h.url_for( '/static/images/silk/resultset_bottom.png' )}"; }); - $(this).find("img.rowIcon").each( function() { this.src = icon_open; }); - } - }); - // Hide all dataset bodies - $("div.historyItemBody").hide(); - // Handle the dataset body hide/show link. - $("div.historyItemWrapper").each( function() { - var id = this.id; - var li = $(this).parent(); - var body = $(this).children( "div.historyItemBody" ); - var peek = body.find( "pre.peek" ) - $(this).children( ".historyItemTitleBar" ).find( ".historyItemTitle" ).wrap( "<a href='#'></a>" ).click( function() { - if ( body.is(":visible") ) { - if ( $.browser.mozilla ) { peek.css( "overflow", "hidden" ) } - body.slideUp( "fast" ); - li.removeClass( "datasetHighlighted" ); - } - else { - body.slideDown( "fast", function() { - if ( $.browser.mozilla ) { peek.css( "overflow", "auto" ); } - }); - li.addClass( "datasetHighlighted" ); - } - return false; - }); + // Set up expand / hide link + $(q).find( "span.expandLink").wrap( "<a href='#' class='expandLink'></a>" ).click( function() { + if ( children.is( ":visible" ) ) { + descendents.hide(); + descendents.removeClass( "expanded" ); + q.removeClass( "expanded" ); + // expanded = false; + } else { + children.show(); + q.addClass( "expanded" ); + // expanded = true; + } + }); + // Check/uncheck boxes in subfolders. + q.children( "td" ).children( "input[type=checkbox]" ).click( function() { + if ( $(this).is(":checked") ) { + descendents.find( "input[type=checkbox]").attr( 'checked', true ); + } else { + descendents.find( "input[type=checkbox]").attr( 'checked', false ); + // If you uncheck a lower level checkbox, uncheck the boxes above it + // (since deselecting a child means the parent is not fully selected any + // more). + parents.children( "td" ).children( "input[type=checkbox]" ).attr( "checked", false ); + } + }); + // return descendents for use by parent + return descendents; + } + $(this).find( "tbody tr" ).not( "[parent]").each( function() { + descendents = process_row( $(this), $([]) ); + descendents.hide(); + }); }); }); </script> -<![if gte IE 7]> -<script type="text/javascript"> - $( document ).ready( function() { - // Add rollover effect to any image with a 'rollover' attribute - preload_images = {} - $( "img[rollover]" ).each( function() { - var r = $(this).attr('rollover'); - var s = $(this).attr('src'); - preload_images[r] = true; - $(this).hover( - function() { $(this).attr( 'src', r ) }, - function() { $(this).attr( 'src', s ) } - ) - }) - for ( r in preload_images ) { $( "<img>" ).attr( "src", r ) } - }) -</script> -<![endif]> +<%def name="render_dataset( library_dataset, selected, library, pad, parent, row_conter )"> + <% + ## The received data must always be a LibraryDataset object, but the object id passed to methods from the drop down menu + ## should be the underlying ldda id to prevent id collision ( which could happen when displaying children, which are always + ## lddas ). We also need to make sure we're displaying the latest version of this library_dataset, so we display the attributes + ## from the ldda. + ldda = library_dataset.library_dataset_dataset_association + if ldda.user: + uploaded_by = ldda.user.email + else: + uploaded_by = 'anonymous' + if ldda == ldda.library_dataset.library_dataset_dataset_association: + current_version = True + else: + current_version = False + %> -<%def name="render_folder( folder, folder_pad, created_ldda_ids, library_id )"> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + style="display: none;" + %endif + > + <td style="padding-left: ${pad+20}px;"> + + + %if selected: + <input type="checkbox" name="ldda_ids" value="${ldda.id}" checked/> + %else: + <input type="checkbox" name="ldda_ids" value="${ldda.id}"/> + %endif + + <a href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, info=True )}"><b>${ldda.name[:60]}</b></a> + <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> + + <div popupmenu="dataset-${ldda.id}-popup"> + %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ): + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> + %else: + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, information=True )}">View this dataset's information</a> + %endif + ## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use + ##%if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=ldda.library_dataset ): + ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, library_dataset_id=library_dataset.id, new_template=True )}">Add an information template to this dataset</a> + ##%endif + %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset=ldda.dataset ) and trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=ldda.library_dataset ): + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> + %if current_version and trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=ldda.library_dataset ): + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library_dataset.folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a> + %endif + %endif + %if ldda.has_data: + <a class="action-button" href="${h.url_for( controller='library', action='datasets', library_id=library.id, ldda_ids=str( ldda.id ), do_action='add' )}">Import this dataset into your current history</a> + <a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', id=ldda.id, library_id=library.id )}">Download this dataset</a> + %endif + </div> + + </td> + <td>${ldda.message}</td> + <td>${uploaded_by}</td> + <td>${ldda.create_time.strftime( "%Y-%m-%d" )}</td> + </tr> + + <% + my_row = row_counter.count + row_counter.increment() + %> + + +</%def> + + +<%def name="render_folder( folder, folder_pad, created_ldda_ids, library_id, parent=None, row_counter=None )"> <% def show_folder(): if trans.app.security_agent.check_folder_contents( trans.user, folder ) or trans.app.security_agent.show_library_item( trans.user, folder ): @@ -119,27 +161,36 @@ else: pad = folder_pad + 20 if folder_pad == 0: - expander = "/static/images/silk/resultset_bottom.png" - folder_img = "/static/images/silk/folder_page.png" subfolder = False else: - expander = "/static/images/silk/resultset_next.png" - folder_img = "/static/images/silk/folder.png" subfolder = True created_ldda_id_list = util.listify( created_ldda_ids ) if created_ldda_id_list: created_ldda_ids = [ int( ldda_id ) for ldda_id in created_ldda_id_list ] + my_row = None %> %if not root_folder: - <li class="folderRow libraryOrFolderRow" style="padding-left: ${pad}px;"> - <input type="checkbox" class="folderCheckbox" style="float: left;"/> - <div class="rowTitle"> - <span class="expandLink"><img src="${h.url_for( expander )}" class="expanderIcon"/><img src="${h.url_for( folder_img )}" class="rowIcon"/> + <tr class="folderRow libraryOrFolderRow" + %if parent is not None: + parent="${parent}" + style="display: none;" + %endif + > + <td style="padding-left: ${folder_pad}px;"> + + <span class="expandLink"></span> + + <input type="checkbox" class="folderCheckbox"/> + + <span class="rowIcon"></span> + ${folder.name} %if folder.description: <i>- ${folder.description}</i> %endif + <a id="folder_img-${folder.id}-popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="folder_img-${folder.id}-popup"> %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=folder ): <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder.id )}">Add datasets to this folder</a> @@ -167,125 +218,135 @@ %endif </div> </div> - </li> + <td colspan="3"></td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> %endif - %if subfolder: - <ul id="subFolder" style="display: none;"> - %else: - <ul> - %endif - %for child_folder in name_sorted( folder.active_folders ): - ${render_folder( child_folder, pad, created_ldda_ids, library_id )} - %endfor - %for library_dataset in name_sorted( folder.active_datasets ): - <% - selected = created_ldda_ids and library_dataset.library_dataset_dataset_association.id in created_ldda_ids - %> - %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.DATASET_ACCESS, dataset=library_dataset.library_dataset_dataset_association.dataset ): - <li class="datasetRow" style="padding-left: ${pad + 20}px;">${render_dataset( library_dataset, selected, library )}</li> - %endif - %endfor - </ul> + + %for child_folder in name_sorted( folder.active_folders ): + ${render_folder( child_folder, pad, created_ldda_ids, library_id, my_row, row_counter )} + %endfor + %for library_dataset in name_sorted( folder.active_datasets ): + <% + selected = created_ldda_ids and library_dataset.library_dataset_dataset_association.id in created_ldda_ids + %> + %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.DATASET_ACCESS, dataset=library_dataset.library_dataset_dataset_association.dataset ): + ${render_dataset( library_dataset, selected, library, pad, my_row, row_counter )} + %endif + %endfor </%def> -<h2>Library '${library.name}'</h2> +<h2>Library “${library.name}”</h2> -%if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ): - <ul class="manage-table-actions"> - %if not deleted: - <li> - <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this library</span></a> - </li> - <li> - <a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, id=library.root_folder.id, library_id=library.id )}">Add a folder to this library</a> - </li> - %endif - </ul> -%endif +<ul class="manage-table-actions"> + + %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ): + %if not deleted: + <li> + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this library</span></a> + </li> + <li> + <a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, id=library.root_folder.id, library_id=library.id )}">Add a folder to this library</a> + </li> + %endif + %endif + + %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library ): + <li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">Edit this library's information</a></li> + %else: + <li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">View this library's information</a></li> + %endif + ## TODO: temporarily eliminating templates until we have the new forms features done + ##%if library.library_info_template_associations: + ## <% template = library.get_library_item_info_templates( template_list=[], restrict=False )[0] %> + ## %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=template ): + ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this library's information template</a> + ## %endif + ##%else: + ## %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ): + ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, new_template=True )}">Add an information template to this library</a> + ## %endif + ##%endif + %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library ): + <li><a class="action-button" href="${h.url_for( controller='library', action='library', permissions=True, id=library.id )}">Edit this library's permissions</a></li> + %endif + +</ul> %if msg: ${render_msg( msg, messagetype )} %endif <form name="import_from_library" action="${h.url_for( controller='library', action='datasets', library_id=library.id )}" method="post"> - <ul> - <li class="libraryRow libraryOrFolderRow"> - <div class="rowTitle"> - <% - library_item_ids = {} - library_item_ids[ 'library' ] = library.id - %> - <table cellspacing="0" cellpadding="0" border="0" width="100%" class="libraryTitle"> - <tr> - <th width="*"> - <span class="expandLink" id="libraryRow"><img src="${h.url_for( '/static/images/silk/resultset_bottom.png' )}" class="expanderIcon"/><img src="${h.url_for( '/static/images/silk/book_open.png' )}" class="rowIcon"/> - ${library.name} - %if library.description: - <i>- ${library.description}</i> - %endif - <a id="library-${library.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="library-${library.id}-popup"> - %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=library ): - <a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">Edit this library's information</a> - %else: - <a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">View this library's information</a> - %endif - ## TODO: temporarily eliminating templates until we have the new forms features done - ##%if library.library_info_template_associations: - ## <% template = library.get_library_item_info_templates( template_list=[], restrict=False )[0] %> - ## %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=template ): - ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this library's information template</a> - ## %endif - ##%else: - ## %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ): - ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, new_template=True )}">Add an information template to this library</a> - ## %endif - ##%endif - %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library ): - <a class="action-button" href="${h.url_for( controller='library', action='library', permissions=True, id=library.id )}">Edit this library's permissions</a> - %endif - </div> - </span> - </th> - <th width="500">Information</th> - <th width="150">Uploaded By</th> - <th width="60">Date</th> - </tr> - </table> - </div> - </li> - <ul> - ${render_folder( library.root_folder, 0, created_ldda_ids, library.id )} - </ul> - <br/> - </ul> - <select name="do_action" id="action_on_datasets_select"> - %if default_action == 'add': - <option value="add" selected>Import selected datasets into your current history</option> - %else: - <option value="add">Import selected datasets into your current history</option> - %endif - %if default_action == 'manage_permissions': - <option value="manage_permissions" selected>Edit selected datasets' permissions</option> - # This condition should not contain an else clause because the user is not authorized - # to manage dataset permissions unless the default action is 'manage_permissions' - %endif - %if 'bz2' in comptypes: - <option value="tbz" - %if default_action == 'download': - selected - %endif> - >Download selected datasets as a .tar.bz2 file</option> - %endif - %if 'gz' in comptypes: - <option value="tgz">Download selected datasets as a .tar.gz file</option> - %endif - %if 'zip' in comptypes: - <option value="zip">Download selected datasets as a .zip file</option> - %endif - </select> - <input type="submit" class="primary-button" name="action_on_datasets_button" id="action_on_datasets_button" value="Go"/> + + <% + library_item_ids = {} + library_item_ids[ 'library' ] = library.id + %> + + <table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid"> + <thead> + + <tr class="libraryTitle"> + <th style="padding-left: 42px;">Name</th> + <th>Information</th> + <th>Uploaded By</th> + <th>Date</th> + </thead> + </tr> + + <% row_counter = RowCounter() %> + + ${render_folder( library.root_folder, 0, created_ldda_ids, library.id, Nonw, row_counter )} + + <tfoot> + + <tr> + <td colspan="4" style="padding-left: 42px;"> + + For selected items: + + <select name="do_action" id="action_on_datasets_select"> + %if default_action == 'add': + <option value="add" selected>Import into your current history</option> + %else: + <option value="add">Import into your current history</option> + %endif + %if default_action == 'manage_permissions': + <option value="manage_permissions" selected>Edit permissions</option> + # This condition should not contain an else clause because the user is not authorized + # to manage dataset permissions unless the default action is 'manage_permissions' + %endif + %if 'bz2' in comptypes: + <option value="tbz" + %if default_action == 'download': + selected + %endif> + >Download as a .tar.bz2 file</option> + %endif + %if 'gz' in comptypes: + <option value="tgz">Download as a .tar.gz file</option> + %endif + %if 'zip' in comptypes: + <option value="zip">Download as a .zip file</option> + %endif + </select> + <input type="submit" class="primary-button" name="action_on_datasets_button" id="action_on_datasets_button" value="Go"/> + + </td> + + </tr> + + </tfoot> + + </table> + </form> + +## Help about compression types %if len( comptypes ) > 1: <div>

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Re: [galaxy-dev] manage_db: MySQL error 1059
by Nate Coraor 05 Aug '09

05 Aug '09

Hi Pieter, I moved this over to the galaxy-dev list since it's related to a local installation. Pieter Neerincx wrote: > Hi, > > I upgraded today from a Galaxy release from about a month ago and got > this error when I ran the manage_db script: > > 7 -> 8... done > 8 -> 9... done > 9 -> 10... > done > 10 -> 11... done > > This is with MySQL 5.0.45-7.el5 (on CentOS 5.3). Manual inspection > shows that despite the error the table was created: > and I have the following indices on this table: > I guess that the ix_hdadaa_history_dataset_association_id is the > abbreviated name for > ix_history_dataset_association_display_at_authorization_update_time... > or not? The question is can I safely ignore the update error or do I > have a problem? Database version 11 was created to fix the problem in 10. MySQL has a name length limit and thus the index has to be manually created. You can safely ignore these errors. --nate

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