[galaxy-commits] galaxy-dist commit 121be69ca306: Make Cuffdiff wrapper compatible with v0.9.1 of Cufflinks tool suite and add full functional test.

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks@emory.edu> # Date 1288197699 14400 # Node ID 121be69ca30675593dc9fc247a4b10a118fed227 # Parent 243d80d9905af9121452f1a0955b2b49c076d66e Make Cuffdiff wrapper compatible with v0.9.1 of Cufflinks tool suite and add full functional test. --- /dev/null +++ b/test-data/cuffdiff_out8.txt @@ -0,0 +1,1 @@ +tracking_id class_code nearest_ref_id gene_short_name tss_id locus --- /dev/null +++ b/test-data/cuffdiff_out9.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant --- /dev/null +++ b/test-data/cuffdiff_out11.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant --- /dev/null +++ b/test-data/cuffdiff_out6.txt @@ -0,0 +1,88 @@ +tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi +XLOC_000001 - - - - chr1:3204754-3204833 0 0 0 0 0 0 +XLOC_000002 - - - - chr1:3111449-3111490 0 0 0 0 0 0 +XLOC_000003 - - - - chr1:3111545-3111576 0 0 0 0 0 0 +XLOC_000004 - - - - chr1:3174765-3174792 0 0 0 0 0 0 +XLOC_000005 - - - - chr1:3187401-3187428 0 0 0 0 0 0 +XLOC_000006 - - - - chr1:3188521-3188548 0 0 0 0 0 0 +XLOC_000007 - - - - chr1:3189810-3190789 343500 342328 344672 947555 680603 1.21451e+06 +XLOC_000008 - - - - chr1:3190858-3191434 328433 327286 329579 254485 253476 255494 +XLOC_000009 - - - - chr1:3191512-3192077 345096 343921 346271 1.07827e+06 822433 1.33412e+06 +XLOC_000010 - - - - chr1:3192250-3192336 0 0 0 0 0 0 +XLOC_000011 - - - - chr1:3192441-3192494 0 0 0 0 0 0 +XLOC_000012 - - - - chr1:3192550-3192629 0 0 0 0 0 0 +XLOC_000013 - - - - chr1:3192649-3192676 0 0 0 0 0 0 +XLOC_000014 - - - - chr1:3192731-3192811 0 0 0 0 0 0 +XLOC_000015 - - - - chr1:3192940-3193042 0 0 0 0 0 0 +XLOC_000016 - - - - chr1:3194185-3194226 0 0 0 0 0 0 +XLOC_000017 - - - - chr1:3194302-3194329 0 0 0 0 0 0 +XLOC_000018 - - - - chr1:3194706-3194733 0 0 0 0 0 0 +XLOC_000019 - - - - chr1:3195083-3195110 0 0 0 0 0 0 +XLOC_000020 - - - - chr1:3195450-3195477 0 0 0 0 0 0 +XLOC_000021 - - - - chr1:3197089-3197116 0 0 0 0 0 0 +XLOC_000022 - - - - chr1:3197246-3197273 0 0 0 0 0 0 +XLOC_000023 - - - - chr1:3197346-3197373 0 0 0 0 0 0 +XLOC_000024 - - - - chr1:3197425-3197452 0 0 0 0 0 0 +XLOC_000025 - - - - chr1:3200022-3200191 0 0 0 0 0 0 +XLOC_000026 - - - - chr1:3200325-3200352 0 0 0 0 0 0 +XLOC_000027 - - - - chr1:3200430-3200457 0 0 0 0 0 0 +XLOC_000028 - - - - chr1:3201007-3201039 0 0 0 0 0 0 +XLOC_000029 - - - - chr1:3201077-3201481 0 0 0 155328 154540 156116 +XLOC_000030 - - - - chr1:3201596-3201666 0 0 0 0 0 0 +XLOC_000031 - - - - chr1:3201672-3201699 0 0 0 0 0 0 +XLOC_000032 - - - - chr1:3201725-3201809 0 0 0 0 0 0 +XLOC_000033 - - - - chr1:3211521-3211561 0 0 0 0 0 0 +XLOC_000034 - - - - chr1:3212213-3212292 0 0 0 0 0 0 +XLOC_000035 - - - - chr1:3212367-3212439 0 0 0 0 0 0 +XLOC_000036 - - - - chr1:3212717-3212801 0 0 0 0 0 0 +XLOC_000037 - - - - chr1:3213095-3213192 0 0 0 0 0 0 +XLOC_000038 - - - - chr1:3240606-3240633 0 0 0 0 0 0 +XLOC_000039 - - - - chr1:3242479-3242512 0 0 0 0 0 0 +XLOC_000040 - - - - chr1:3242633-3242923 0 0 0 0 0 0 +XLOC_000041 - - - - chr1:3242924-3243005 0 0 0 0 0 0 +XLOC_000042 - - - - chr1:3243018-3243079 0 0 0 0 0 0 +XLOC_000043 - - - - chr1:3243108-3243154 0 0 0 0 0 0 +XLOC_000044 - - - - chr1:3243347-3243401 0 0 0 0 0 0 +XLOC_000045 - - - - chr1:3254079-3254106 0 0 0 0 0 0 +XLOC_000046 - - - - chr1:3256974-3257011 0 0 0 0 0 0 +XLOC_000047 - - - - chr1:3277155-3277182 0 0 0 0 0 0 +XLOC_000048 - - - - chr1:3277190-3277218 0 0 0 0 0 0 +XLOC_000049 - - - - chr1:3277913-3278390 165459 164646 166273 0 0 0 +XLOC_000050 - - - - chr1:3280117-3280144 0 0 0 0 0 0 +XLOC_000051 - - - - chr1:3280498-3280525 0 0 0 0 0 0 +XLOC_000052 - - - - chr1:3280686-3280741 0 0 0 0 0 0 +XLOC_000053 - - - - chr1:3282504-3282531 0 0 0 0 0 0 +XLOC_000054 - - - - chr1:3282650-3282677 0 0 0 0 0 0 +XLOC_000055 - - - - chr1:3282760-3282832 0 0 0 0 0 0 +XLOC_000056 - - - - chr1:3284966-3284993 0 0 0 0 0 0 +XLOC_000057 - - - - chr1:3290488-3290553 0 0 0 0 0 0 +XLOC_000058 - - - - chr1:3290798-3290859 0 0 0 0 0 0 +XLOC_000059 - - - - chr1:3290919-3291273 163613 162804 164422 0 0 0 +XLOC_000060 - - - - chr1:3299443-3299664 0 0 0 0 0 0 +XLOC_000061 - - - - chr1:3299691-3299733 0 0 0 0 0 0 +XLOC_000062 - - - - chr1:3300051-3300078 0 0 0 0 0 0 +XLOC_000063 - - - - chr1:3307748-3307775 0 0 0 0 0 0 +XLOC_000064 - - - - chr1:3318620-3318647 0 0 0 0 0 0 +XLOC_000065 - - - - chr1:3318999-3319051 0 0 0 0 0 0 +XLOC_000066 - - - - chr1:3330527-3330554 0 0 0 0 0 0 +XLOC_000067 - - - - chr1:3351240-3351311 0 0 0 0 0 0 +XLOC_000068 - - - - chr1:3355887-3356119 0 0 0 0 0 0 +XLOC_000069 - - - - chr1:3356180-3356225 0 0 0 0 0 0 +XLOC_000070 - - - - chr1:3363076-3363176 0 0 0 0 0 0 +XLOC_000071 - - - - chr1:3363214-3363278 0 0 0 0 0 0 +XLOC_000072 - - - - chr1:3363387-3363446 0 0 0 0 0 0 +XLOC_000073 - - - - chr1:3363753-3363849 0 0 0 0 0 0 +XLOC_000074 - - - - chr1:3364871-3364919 0 0 0 0 0 0 +XLOC_000075 - - - - chr1:3367135-3367162 0 0 0 0 0 0 +XLOC_000076 - - - - chr1:3367210-3367237 0 0 0 0 0 0 +XLOC_000077 - - - - chr1:3367333-3367382 0 0 0 0 0 0 +XLOC_000078 - - - - chr1:3369580-3369607 0 0 0 0 0 0 +XLOC_000079 - - - - chr1:3375001-3375028 0 0 0 0 0 0 +XLOC_000080 - - - - chr1:3377211-3377262 0 0 0 0 0 0 +XLOC_000081 - - - - chr1:3379888-3379915 0 0 0 0 0 0 +XLOC_000082 - - - - chr1:3386739-3386836 0 0 0 0 0 0 +XLOC_000083 - - - - chr1:3391325-3391352 0 0 0 0 0 0 +XLOC_000084 - - - - chr1:3435841-3435880 0 0 0 0 0 0 +XLOC_000085 - - - - chr1:3447761-3447788 0 0 0 0 0 0 +XLOC_000086 - - - - chr1:3450906-3450965 0 0 0 0 0 0 +XLOC_000087 - - - - chr1:3451051-3451109 0 0 0 0 0 0 --- /dev/null +++ b/test-data/cuffdiff_out10.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant --- /dev/null +++ b/test-data/cuffdiff_out7.txt @@ -0,0 +1,1 @@ +tracking_id class_code nearest_ref_id gene_short_name tss_id locus --- /dev/null +++ b/test-data/cuffdiff_out1.txt @@ -0,0 +1,99 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant +TCONS_00000001 - chr1:3204754-3204833 q1 q2 OK 0 0 0 0 1 no +TCONS_00000002 - chr1:3111449-3111490 q1 q2 OK 0 0 0 0 1 no +TCONS_00000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 no +TCONS_00000004 - chr1:3189810-3190789 q1 q2 OK 0 645918 6.95322e-310 1.79769e+308 0 yes +TCONS_00000005 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 no +TCONS_00000006 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 no +TCONS_00000007 - chr1:3191512-3192077 q1 q2 OK 0 704881 6.95322e-310 1.79769e+308 0 yes +TCONS_00000008 - chr1:3191512-3192077 q1 q2 OK 0 0 0 0 1 no +TCONS_00000009 - chr1:3192441-3192494 q1 q2 OK 0 0 0 0 1 no +TCONS_00000010 - chr1:3192550-3192629 q1 q2 OK 0 0 0 0 1 no +TCONS_00000011 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 no +TCONS_00000012 - chr1:3192940-3193042 q1 q2 OK 0 0 0 0 1 no +TCONS_00000013 - chr1:3194185-3194226 q1 q2 OK 0 0 0 0 1 no +TCONS_00000014 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 no +TCONS_00000015 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 no +TCONS_00000016 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 no +TCONS_00000017 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 no +TCONS_00000018 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 no +TCONS_00000019 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 no +TCONS_00000020 - chr1:3200022-3200191 q1 q2 OK 0 0 0 0 1 no +TCONS_00000021 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 no +TCONS_00000022 - chr1:3201077-3201481 q1 q2 OK 0 155328 0 1.79769e+308 0 yes +TCONS_00000023 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 no +TCONS_00000024 - chr1:3212213-3212292 q1 q2 OK 0 0 0 0 1 no +TCONS_00000025 - chr1:3212367-3212439 q1 q2 OK 0 0 0 0 1 no +TCONS_00000026 - chr1:3213095-3213192 q1 q2 OK 0 0 0 0 1 no +TCONS_00000027 - chr1:3242633-3242923 q1 q2 OK 0 0 0 0 1 no +TCONS_00000028 - chr1:3243018-3243079 q1 q2 OK 0 0 0 0 1 no +TCONS_00000029 - chr1:3243347-3243401 q1 q2 OK 0 0 0 0 1 no +TCONS_00000030 - chr1:3256974-3257011 q1 q2 OK 0 0 0 0 1 no +TCONS_00000031 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 no +TCONS_00000032 - chr1:3277913-3278390 q1 q2 OK 0 0 0 0 1 no +TCONS_00000033 - chr1:3280686-3280741 q1 q2 OK 0 0 0 0 1 no +TCONS_00000034 - chr1:3290488-3290553 q1 q2 OK 0 0 0 0 1 no +TCONS_00000035 - chr1:3290919-3291273 q1 q2 OK 0 0 0 0 1 no +TCONS_00000036 - chr1:3290919-3291273 q1 q2 OK 0 0 0 0 1 no +TCONS_00000037 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no +TCONS_00000038 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 no +TCONS_00000039 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 no +TCONS_00000040 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no +TCONS_00000041 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 no +TCONS_00000042 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 no +TCONS_00000043 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 no +TCONS_00000044 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 no +TCONS_00000045 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 no +TCONS_00000046 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 no +TCONS_00000047 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 no +TCONS_00000048 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 no +TCONS_00000049 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 no +TCONS_00000050 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 no +TCONS_00000051 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 no +TCONS_00000052 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 no +TCONS_00000053 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 no +TCONS_00000054 - chr1:3189810-3190789 q1 q2 OK 343500 303241 -0.124659 2.28891 0.0220846 no +TCONS_00000055 - chr1:3190858-3191434 q1 q2 OK 328433 254485 -0.255089 96.5921 0 yes +TCONS_00000056 - chr1:3191512-3192077 q1 q2 OK 345096 376320 0.0866161 -1.17079 0.241685 no +TCONS_00000057 - chr1:3192250-3192336 q1 q2 OK 0 0 0 0 1 no +TCONS_00000058 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 no +TCONS_00000059 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 no +TCONS_00000060 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 no +TCONS_00000061 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 no +TCONS_00000062 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 no +TCONS_00000063 - chr1:3201077-3201481 q1 q2 OK 0 0 0 0 1 no +TCONS_00000064 - chr1:3201596-3201666 q1 q2 OK 0 0 0 0 1 no +TCONS_00000065 - chr1:3201725-3201809 q1 q2 OK 0 0 0 0 1 no +TCONS_00000066 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 no +TCONS_00000067 - chr1:3212717-3212801 q1 q2 OK 0 0 0 0 1 no +TCONS_00000068 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 no +TCONS_00000069 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 no +TCONS_00000070 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 no +TCONS_00000071 - chr1:3243108-3243154 q1 q2 OK 0 0 0 0 1 no +TCONS_00000072 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 no +TCONS_00000073 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 no +TCONS_00000074 - chr1:3277913-3278390 q1 q2 OK 165459 0 0 2.22507e-308 0 yes +TCONS_00000075 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 no +TCONS_00000076 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 no +TCONS_00000077 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 no +TCONS_00000078 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 no +TCONS_00000079 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 no +TCONS_00000080 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 no +TCONS_00000081 - chr1:3290798-3290859 q1 q2 OK 0 0 0 0 1 no +TCONS_00000082 - chr1:3290919-3291273 q1 q2 OK 163613 0 0 2.22507e-308 0 yes +TCONS_00000083 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no +TCONS_00000084 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 no +TCONS_00000085 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 no +TCONS_00000086 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 no +TCONS_00000087 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 no +TCONS_00000088 - chr1:3351240-3351311 q1 q2 OK 0 0 0 0 1 no +TCONS_00000089 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no +TCONS_00000090 - chr1:3356180-3356225 q1 q2 OK 0 0 0 0 1 no +TCONS_00000091 - chr1:3363076-3363176 q1 q2 OK 0 0 0 0 1 no +TCONS_00000092 - chr1:3363387-3363446 q1 q2 OK 0 0 0 0 1 no +TCONS_00000093 - chr1:3364871-3364919 q1 q2 OK 0 0 0 0 1 no +TCONS_00000094 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 no +TCONS_00000095 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 no +TCONS_00000096 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 no +TCONS_00000097 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 no +TCONS_00000098 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 no --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -73,11 +73,21 @@ <param name="min_mapqual" value="0" ftype="sam" /><param name="min_alignment_count" value="0" ftype="sam" /><param name="sPaired" value="single" ftype="sam" /> - - <!-- This won't pass until the test harness is updated to handle outputs better. --> - <!-- - <output name="XXXX" file="cuffdiff_out5.tracking" /> + <!-- + Line diffs are needed because cuffdiff does not produce deterministic output. + TODO: can we find datasets that lead to deterministic behavior? --> + <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="8"/> + <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="4"/> + <output name="tss_groups_exp" file="cuffdiff_out3.txt"/> + <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/> + <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="8"/> + <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="4"/> + <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/> + <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/> + <output name="splicing_diff" file="cuffdiff_out9.txt"/> + <output name="promoters_diff" file="cuffdiff_out10.txt"/> + <output name="cds_diff" file="cuffdiff_out11.txt"/></test></tests> --- a/tools/ngs_rna/cuffdiff_wrapper.py +++ b/tools/ngs_rna/cuffdiff_wrapper.py @@ -111,13 +111,13 @@ def __main__(): shutil.copyfile( os.path.join( tmp_output_dir, "genes.fpkm_tracking" ), options.genes_fpkm_tracking_output ) shutil.copyfile( os.path.join( tmp_output_dir, "cds.fpkm_tracking" ), options.cds_fpkm_tracking_output ) shutil.copyfile( os.path.join( tmp_output_dir, "tss_groups.fpkm_tracking" ), options.tss_groups_fpkm_tracking_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_isoform_exp.diff" ), options.isoforms_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_gene_exp.diff" ), options.genes_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_tss_group_exp.diff" ), options.tss_groups_exp_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_splicing.diff" ), options.splicing_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_cds.diff" ), options.cds_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_cds_exp.diff" ), options.cds_diff_output ) - shutil.copyfile( os.path.join( tmp_output_dir, "0_1_promoters.diff" ), options.promoters_diff_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "isoform_exp.diff" ), options.isoforms_exp_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "gene_exp.diff" ), options.genes_exp_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "tss_group_exp.diff" ), options.tss_groups_exp_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "splicing.diff" ), options.splicing_diff_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "cds.diff" ), options.cds_diff_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "cds_exp.diff" ), options.cds_exp_fpkm_tracking_output ) + shutil.copyfile( os.path.join( tmp_output_dir, "promoters.diff" ), options.promoters_diff_output ) except Exception, e: stop_err( 'Error in cuffdiff:\n' + str( e ) ) finally: --- /dev/null +++ b/test-data/cuffdiff_out5.txt @@ -0,0 +1,99 @@ +tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi +TCONS_00000001 c Xkr4 - - chr1:3204754-3204833 0 0 0 0 0 0 +TCONS_00000002 - - - - chr1:3111449-3111490 0 0 0 0 0 0 +TCONS_00000003 - - - - chr1:3111545-3111576 0 0 0 0 0 0 +TCONS_00000004 - - - - chr1:3189810-3190789 0 0 0 645918 357201 934636 +TCONS_00000005 - - - - chr1:3189810-3190789 0 0 0 0 0 0 +TCONS_00000006 - - - - chr1:3189810-3190789 0 0 0 0 0 0 +TCONS_00000007 - - - - chr1:3191512-3192077 0 0 0 704881 400219 1.00954e+06 +TCONS_00000008 - - - - chr1:3191512-3192077 0 0 0 0 0 0 +TCONS_00000009 - - - - chr1:3192441-3192494 0 0 0 0 0 0 +TCONS_00000010 - - - - chr1:3192550-3192629 0 0 0 0 0 0 +TCONS_00000011 - - - - chr1:3192731-3192811 0 0 0 0 0 0 +TCONS_00000012 - - - - chr1:3192940-3193042 0 0 0 0 0 0 +TCONS_00000013 - - - - chr1:3194185-3194226 0 0 0 0 0 0 +TCONS_00000014 - - - - chr1:3194302-3194329 0 0 0 0 0 0 +TCONS_00000015 - - - - chr1:3195083-3195110 0 0 0 0 0 0 +TCONS_00000016 - - - - chr1:3195450-3195477 0 0 0 0 0 0 +TCONS_00000017 - - - - chr1:3197089-3197116 0 0 0 0 0 0 +TCONS_00000018 - - - - chr1:3197246-3197273 0 0 0 0 0 0 +TCONS_00000019 - - - - chr1:3197346-3197373 0 0 0 0 0 0 +TCONS_00000020 - - - - chr1:3200022-3200191 0 0 0 0 0 0 +TCONS_00000021 - - - - chr1:3200325-3200352 0 0 0 0 0 0 +TCONS_00000022 - - - - chr1:3201077-3201481 0 0 0 155328 154540 156116 +TCONS_00000023 - - - - chr1:3201672-3201699 0 0 0 0 0 0 +TCONS_00000024 i Xkr4 - - chr1:3212213-3212292 0 0 0 0 0 0 +TCONS_00000025 i Xkr4 - - chr1:3212367-3212439 0 0 0 0 0 0 +TCONS_00000026 i Xkr4 - - chr1:3213095-3213192 0 0 0 0 0 0 +TCONS_00000027 i Xkr4 - - chr1:3242633-3242923 0 0 0 0 0 0 +TCONS_00000028 i Xkr4 - - chr1:3243018-3243079 0 0 0 0 0 0 +TCONS_00000029 i Xkr4 - - chr1:3243347-3243401 0 0 0 0 0 0 +TCONS_00000030 i Xkr4 - - chr1:3256974-3257011 0 0 0 0 0 0 +TCONS_00000031 i Xkr4 - - chr1:3277190-3277218 0 0 0 0 0 0 +TCONS_00000032 i Xkr4 - - chr1:3277913-3278390 0 0 0 0 0 0 +TCONS_00000033 i Xkr4 - - chr1:3280686-3280741 0 0 0 0 0 0 +TCONS_00000034 i Xkr4 - - chr1:3290488-3290553 0 0 0 0 0 0 +TCONS_00000035 i Xkr4 - - chr1:3290919-3291273 0 0 0 0 0 0 +TCONS_00000036 i Xkr4 - - chr1:3290919-3291273 0 0 0 0 0 0 +TCONS_00000037 i Xkr4 - - chr1:3299443-3299664 0 0 0 0 0 0 +TCONS_00000038 i Xkr4 - - chr1:3300051-3300078 0 0 0 0 0 0 +TCONS_00000039 i Xkr4 - - chr1:3318999-3319051 0 0 0 0 0 0 +TCONS_00000040 i Xkr4 - - chr1:3355887-3356119 0 0 0 0 0 0 +TCONS_00000041 i Xkr4 - - chr1:3363214-3363278 0 0 0 0 0 0 +TCONS_00000042 i Xkr4 - - chr1:3363753-3363849 0 0 0 0 0 0 +TCONS_00000043 i Xkr4 - - chr1:3367135-3367162 0 0 0 0 0 0 +TCONS_00000044 i Xkr4 - - chr1:3367333-3367382 0 0 0 0 0 0 +TCONS_00000045 i Xkr4 - - chr1:3377211-3377262 0 0 0 0 0 0 +TCONS_00000046 i Xkr4 - - chr1:3391325-3391352 0 0 0 0 0 0 +TCONS_00000047 i Xkr4 - - chr1:3435841-3435880 0 0 0 0 0 0 +TCONS_00000048 i Xkr4 - - chr1:3447761-3447788 0 0 0 0 0 0 +TCONS_00000049 i Xkr4 - - chr1:3450906-3450965 0 0 0 0 0 0 +TCONS_00000050 i Xkr4 - - chr1:3451051-3451109 0 0 0 0 0 0 +TCONS_00000051 - - - - chr1:3174765-3174792 0 0 0 0 0 0 +TCONS_00000052 - - - - chr1:3187401-3187428 0 0 0 0 0 0 +TCONS_00000053 - - - - chr1:3188521-3188548 0 0 0 0 0 0 +TCONS_00000054 - - - - chr1:3189810-3190789 343500 342328 344672 303241 270227 336255 +TCONS_00000055 - - - - chr1:3190858-3191434 328433 327286 329579 254485 253476 255494 +TCONS_00000056 - - - - chr1:3191512-3192077 345096 343921 346271 376320 320653 431986 +TCONS_00000057 - - - - chr1:3192250-3192336 0 0 0 0 0 0 +TCONS_00000058 - - - - chr1:3192649-3192676 0 0 0 0 0 0 +TCONS_00000059 - - - - chr1:3194706-3194733 0 0 0 0 0 0 +TCONS_00000060 - - - - chr1:3197425-3197452 0 0 0 0 0 0 +TCONS_00000061 - - - - chr1:3200430-3200457 0 0 0 0 0 0 +TCONS_00000062 - - - - chr1:3201007-3201039 0 0 0 0 0 0 +TCONS_00000063 - - - - chr1:3201077-3201481 0 0 0 0 0 0 +TCONS_00000064 - - - - chr1:3201596-3201666 0 0 0 0 0 0 +TCONS_00000065 - - - - chr1:3201725-3201809 0 0 0 0 0 0 +TCONS_00000066 i Xkr4 - - chr1:3211521-3211561 0 0 0 0 0 0 +TCONS_00000067 i Xkr4 - - chr1:3212717-3212801 0 0 0 0 0 0 +TCONS_00000068 i Xkr4 - - chr1:3240606-3240633 0 0 0 0 0 0 +TCONS_00000069 i Xkr4 - - chr1:3242479-3242512 0 0 0 0 0 0 +TCONS_00000070 i Xkr4 - - chr1:3242924-3243005 0 0 0 0 0 0 +TCONS_00000071 i Xkr4 - - chr1:3243108-3243154 0 0 0 0 0 0 +TCONS_00000072 i Xkr4 - - chr1:3254079-3254106 0 0 0 0 0 0 +TCONS_00000073 i Xkr4 - - chr1:3277155-3277182 0 0 0 0 0 0 +TCONS_00000074 i Xkr4 - - chr1:3277913-3278390 165459 164646 166273 0 0 0 +TCONS_00000075 i Xkr4 - - chr1:3280117-3280144 0 0 0 0 0 0 +TCONS_00000076 i Xkr4 - - chr1:3280498-3280525 0 0 0 0 0 0 +TCONS_00000077 i Xkr4 - - chr1:3282504-3282531 0 0 0 0 0 0 +TCONS_00000078 i Xkr4 - - chr1:3282650-3282677 0 0 0 0 0 0 +TCONS_00000079 i Xkr4 - - chr1:3282760-3282832 0 0 0 0 0 0 +TCONS_00000080 i Xkr4 - - chr1:3284966-3284993 0 0 0 0 0 0 +TCONS_00000081 i Xkr4 - - chr1:3290798-3290859 0 0 0 0 0 0 +TCONS_00000082 i Xkr4 - - chr1:3290919-3291273 163613 162804 164422 0 0 0 +TCONS_00000083 i Xkr4 - - chr1:3299443-3299664 0 0 0 0 0 0 +TCONS_00000084 i Xkr4 - - chr1:3299691-3299733 0 0 0 0 0 0 +TCONS_00000085 i Xkr4 - - chr1:3307748-3307775 0 0 0 0 0 0 +TCONS_00000086 i Xkr4 - - chr1:3318620-3318647 0 0 0 0 0 0 +TCONS_00000087 i Xkr4 - - chr1:3330527-3330554 0 0 0 0 0 0 +TCONS_00000088 i Xkr4 - - chr1:3351240-3351311 0 0 0 0 0 0 +TCONS_00000089 i Xkr4 - - chr1:3355887-3356119 0 0 0 0 0 0 +TCONS_00000090 i Xkr4 - - chr1:3356180-3356225 0 0 0 0 0 0 +TCONS_00000091 i Xkr4 - - chr1:3363076-3363176 0 0 0 0 0 0 +TCONS_00000092 i Xkr4 - - chr1:3363387-3363446 0 0 0 0 0 0 +TCONS_00000093 i Xkr4 - - chr1:3364871-3364919 0 0 0 0 0 0 +TCONS_00000094 i Xkr4 - - chr1:3367210-3367237 0 0 0 0 0 0 +TCONS_00000095 i Xkr4 - - chr1:3369580-3369607 0 0 0 0 0 0 +TCONS_00000096 i Xkr4 - - chr1:3375001-3375028 0 0 0 0 0 0 +TCONS_00000097 i Xkr4 - - chr1:3379888-3379915 0 0 0 0 0 0 +TCONS_00000098 i Xkr4 - - chr1:3386739-3386836 0 0 0 0 0 0 --- a/test-data/cuffdiff_out5.tracking +++ /dev/null @@ -1,2 +0,0 @@ -tracking_id class_code nearest_ref_id gene_short_name tss_id locus q0_FPKM q0_conf_lo q0_conf_hi q1_FPKM q1_conf_lo q1_conf_hi -TCONS_00000001 c Xkr4 - - chr1:3204754-3204833 0 0 0 67745 0 163551 --- /dev/null +++ b/test-data/cuffdiff_out2.txt @@ -0,0 +1,88 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant +XLOC_000001 - chr1:3204754-3204833 q1 q2 OK 0 0 0 0 1 no +XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 0 0 0 1 no +XLOC_000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 no +XLOC_000004 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 no +XLOC_000005 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 no +XLOC_000006 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 no +XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 343500 949159 1.01639 -7.54436 4.55191e-14 yes +XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 328433 254485 -0.255089 96.5921 0 yes +XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 345096 1.0812e+06 1.142 -9.91597 0 yes +XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 0 0 0 0 1 no +XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 0 0 0 1 no +XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 0 0 0 1 no +XLOC_000013 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 no +XLOC_000014 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 no +XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 0 0 0 1 no +XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 0 0 0 1 no +XLOC_000017 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 no +XLOC_000018 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 no +XLOC_000019 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 no +XLOC_000020 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 no +XLOC_000021 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 no +XLOC_000022 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 no +XLOC_000023 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 no +XLOC_000024 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 no +XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 0 0 0 0 1 no +XLOC_000026 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 no +XLOC_000027 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 no +XLOC_000028 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 no +XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 0 155328 6.95322e-310 1.79769e+308 0 yes +XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 0 0 0 0 1 no +XLOC_000031 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 no +XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 0 0 0 0 1 no +XLOC_000033 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 no +XLOC_000034 - chr1:3212213-3212292 q1 q2 OK 0 0 0 0 1 no +XLOC_000035 - chr1:3212367-3212439 q1 q2 OK 0 0 0 0 1 no +XLOC_000036 - chr1:3212717-3212801 q1 q2 OK 0 0 0 0 1 no +XLOC_000037 - chr1:3213095-3213192 q1 q2 OK 0 0 0 0 1 no +XLOC_000038 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 no +XLOC_000039 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 no +XLOC_000040 - chr1:3242633-3242923 q1 q2 OK 0 0 0 0 1 no +XLOC_000041 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 no +XLOC_000042 - chr1:3243018-3243079 q1 q2 OK 0 0 0 0 1 no +XLOC_000043 - chr1:3243108-3243154 q1 q2 OK 0 0 0 0 1 no +XLOC_000044 - chr1:3243347-3243401 q1 q2 OK 0 0 0 0 1 no +XLOC_000045 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 no +XLOC_000046 - chr1:3256974-3257011 q1 q2 OK 0 0 0 0 1 no +XLOC_000047 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 no +XLOC_000048 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 no +XLOC_000049 - chr1:3277913-3278390 q1 q2 OK 165459 0 6.95322e-310 2.22507e-308 0 yes +XLOC_000050 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 no +XLOC_000051 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 no +XLOC_000052 - chr1:3280686-3280741 q1 q2 OK 0 0 0 0 1 no +XLOC_000053 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 no +XLOC_000054 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 no +XLOC_000055 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 no +XLOC_000056 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 no +XLOC_000057 - chr1:3290488-3290553 q1 q2 OK 0 0 0 0 1 no +XLOC_000058 - chr1:3290798-3290859 q1 q2 OK 0 0 0 0 1 no +XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 163613 0 6.95322e-310 2.22507e-308 0 yes +XLOC_000060 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no +XLOC_000061 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 no +XLOC_000062 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 no +XLOC_000063 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 no +XLOC_000064 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 no +XLOC_000065 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 no +XLOC_000066 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 no +XLOC_000067 - chr1:3351240-3351311 q1 q2 OK 0 0 0 0 1 no +XLOC_000068 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no +XLOC_000069 - chr1:3356180-3356225 q1 q2 OK 0 0 0 0 1 no +XLOC_000070 - chr1:3363076-3363176 q1 q2 OK 0 0 0 0 1 no +XLOC_000071 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 no +XLOC_000072 - chr1:3363387-3363446 q1 q2 OK 0 0 0 0 1 no +XLOC_000073 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 no +XLOC_000074 - chr1:3364871-3364919 q1 q2 OK 0 0 0 0 1 no +XLOC_000075 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 no +XLOC_000076 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 no +XLOC_000077 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 no +XLOC_000078 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 no +XLOC_000079 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 no +XLOC_000080 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 no +XLOC_000081 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 no +XLOC_000082 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 no +XLOC_000083 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 no +XLOC_000084 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 no +XLOC_000085 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 no +XLOC_000086 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 no +XLOC_000087 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 no --- /dev/null +++ b/test-data/cuffdiff_out3.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant --- /dev/null +++ b/test-data/cuffdiff_out4.txt @@ -0,0 +1,1 @@ +test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant