| Previous changeset 19:333a6e13b622 (2021-11-30) Next changeset 21:914cfcba0ec8 (2022-10-31) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb |
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modified:
stringtie.xml stringtie_merge.xml test-data/stringtie_merge_out1.gtf test-data/stringtie_merge_out2.gtf test-data/stringtie_out10.gtf test-data/stringtie_out11.gtf test-data/stringtie_out12.gtf test-data/stringtie_out5.gtf test-data/stringtie_out6.gtf test-data/stringtie_out8.gtf test-data/stringtie_out9.gtf test-data/stringtie_out_coverage.gtf |
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added:
test-data/stringtie_out1_re.gtf test-data/stringtie_out2_re.gtf test-data/stringtie_out3_re.gtf test-data/stringtie_out4_re.gtf |
| b |
| diff -r 333a6e13b622 -r cef79931dda5 stringtie.xml --- a/stringtie.xml Tue Nov 30 11:01:34 2021 +0000 +++ b/stringtie.xml Wed Jul 27 09:28:15 2022 +0000 |
| [ |
| @@ -277,7 +277,7 @@ <param name="input_mode" value="short_reads"/> <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> </conditional> - <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" lines_diff="4" /> + <output name="output_gtf" file="stringtie_out1_re.gtf" ftype="gtf" compare="re_match" sort="true"/> </test> <!--Ensure fraction option works --> <test expect_num_outputs="1"> @@ -286,7 +286,7 @@ <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> </conditional> <param name="fraction" value="0.17" /> - <output name="output_gtf" file="stringtie_out2.gtf" ftype="gtf" lines_diff="4" /> + <output name="output_gtf" file="stringtie_out2_re.gtf" ftype="gtf" compare="re_match" sort="true"/> </test> <!--Ensure guide option works --> <test expect_num_outputs="1"> @@ -297,7 +297,7 @@ <param name="use_guide" value="yes" /> <param name="guide_gff_select" value="history" /> <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" /> - <output name="output_gtf" file="stringtie_out3.gtf" ftype="gtf" lines_diff="4" /> + <output name="output_gtf" file="stringtie_out3_re.gtf" ftype="gtf" compare="re_match" sort="true"/> </test> <!--Ensure guide with fraction works --> <test expect_num_outputs="1"> @@ -309,7 +309,7 @@ <param name="guide_gff_select" value="history" /> <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" /> <param name="fraction" value="0.17" /> - <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="4" /> + <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" compare="re_match" sort="true"/> </test> <!--Ensure coverage and output for Ballgown works --> <test expect_num_outputs="7"> @@ -327,8 +327,8 @@ <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular" /> <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular" /> <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular" /> - <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" lines_diff="4" /> - <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" /> + <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" compare="re_match" sort="true"/> + <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" compare="re_match" sort="true"/> </test> <!--Ensure output for edgeR works --> <test expect_num_outputs="5"> @@ -346,8 +346,8 @@ <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular" /> <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular" /> <output name="legend" file="legend.tsv" ftype="tabular" /> - <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" lines_diff="4" /> - <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" /> + <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" compare="re_match" sort="true"/> + <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" compare="re_match" sort="true"/> </test> <!--Ensure gene abundances output works --> <test expect_num_outputs="2"> @@ -360,7 +360,7 @@ <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" /> <param name="fraction" value="0.17" /> <param name="abundance_estimation" value="true" /> - <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="4" /> + <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" compare="re_match" sort="true"/> <output name="gene_abundance_estimation" file="stringtie_out7.tsv" ftype="tabular" lines_diff="2" /> </test> <!--Ensure another fraction value works --> @@ -373,7 +373,7 @@ <param name="guide_gff_select" value="history" /> <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" /> <param name="fraction" value="0.15" /> - <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="4" /> + <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" compare="re_match" sort="true"/> </test> <!--Ensure built-in GTFs work --> <test expect_num_outputs="1"> @@ -384,7 +384,7 @@ <param name="use_guide" value="yes" /> <param name="guide_gff_select" value="cached" /> <param name="fraction" value="0.15" /> - <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" lines_diff="4" /> + <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" compare="re_match" sort="true"/> </test> <!-- Test long reads input --> <test expect_num_outputs="1"> @@ -395,7 +395,7 @@ <param name="use_guide" value="yes" /> <param name="guide_gff_select" value="cached" /> <param name="fraction" value="0.15" /> - <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" lines_diff="4" /> + <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" compare="re_match" sort="true"/> </test> <!-- Test error splice option --> <test expect_num_outputs="1"> @@ -407,7 +407,7 @@ <param name="use_guide" value="yes" /> <param name="guide_gff_select" value="cached" /> <param name="fraction" value="0.15" /> - <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" lines_diff="4" /> + <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" compare="re_match" sort="true"/> </test> <!-- Test mixed reads input --> <test expect_num_outputs="1"> @@ -416,7 +416,7 @@ <param name="input_bam_short" ftype="bam" value="short_reads.bam" /> <param name="input_bam_long" ftype="bam" value="long_reads.bam" /> </conditional> - <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" lines_diff="4" /> + <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" compare="re_match" sort="true"/> </test> </tests> <help><![CDATA[ |
| b |
| diff -r 333a6e13b622 -r cef79931dda5 stringtie_merge.xml --- a/stringtie_merge.xml Tue Nov 30 11:01:34 2021 +0000 +++ b/stringtie_merge.xml Wed Jul 27 09:28:15 2022 +0000 |
| b |
| @@ -43,12 +43,12 @@ <test> <param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" /> <param name="guide_gff" ftype="gtf" value="stringtie_in.gtf" /> - <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="4" /> + <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" compare="re_match" sort="true" /> </test> <test> <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> <param name="guide_gff" ftype="gtf" value="stringtie_merge_in3.gtf" /> - <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="4" /> + <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" compare="re_match" sort="true" /> </test> <test> <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> |
| b |
| diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_merge_out1.gtf --- a/test-data/stringtie_merge_out1.gtf Tue Nov 30 11:01:34 2021 +0000 +++ b/test-data/stringtie_merge_out1.gtf Wed Jul 27 09:28:15 2022 +0000 |
| [ |
| @@ -1,6 +1,6 @@ -# stringtie --merge -p 1 -G /tmp/tmp9cgbzsli/files/f/8/0/dataset_f808ceaa-08fb-4e16-8d00-3af3bd707ede.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmp9cgbzsli/files/1/2/f/dataset_12ff3ea2-5306-479a-915b-9af32e1defa1.dat /tmp/tmp9cgbzsli/files/5/e/0/dataset_5e0ac785-035b-41ca-acb3-1276d358574d.dat /tmp/tmp9cgbzsli/files/b/3/1/dataset_b3195d2c-e25d-4c21-a9f8-14c79961b98b.dat /tmp/tmp9cgbzsli/files/a/5/f/dataset_a5f7edd6-3748-4854-bd0d-68c03c3ba68e.dat /tmp/tmp9cgbzsli/files/4/5/d/dataset_45d17dfd-c663-43fd-a2ef-e41dd94caa53.dat -# StringTie version 2.1.7 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; ref_gene_id "CUFF.1"; -test_chromosome StringTie exon 53 250 1000 + . gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "1"; ref_gene_id "CUFF.1"; -test_chromosome StringTie exon 351 400 1000 + . gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "2"; ref_gene_id "CUFF.1"; -test_chromosome StringTie exon 501 550 1000 + . gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "3"; ref_gene_id "CUFF.1"; +# StringTie version 2\.1\.7 +# stringtie --merge -p [0-9]+ -G /[-_/a-zA-Z0-9]+\.dat -m 50 -c 0 -F 1\.0 -T 1\.0 -f 0\.01 -g 250 -o /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat +test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+"; +test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+"; +test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+"; +test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; |
| b |
| diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_merge_out2.gtf --- a/test-data/stringtie_merge_out2.gtf Tue Nov 30 11:01:34 2021 +0000 +++ b/test-data/stringtie_merge_out2.gtf Wed Jul 27 09:28:15 2022 +0000 |
| [ |
| b'@@ -1,100 +1,100 @@\n-# stringtie --merge -p 1 -G /tmp/tmp9cgbzsli/files/d/3/d/dataset_d3debef6-0cc0-44aa-898c-086d4fa8adb0.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmp9cgbzsli/files/b/4/d/dataset_b4dd908f-5f52-428f-bc2c-ba62cd00a83e.dat /tmp/tmp9cgbzsli/files/8/1/a/dataset_81a6719e-2f36-40ca-9d63-325d6eadd1d3.dat /tmp/tmp9cgbzsli/files/2/2/f/dataset_22f857ec-0df8-40d8-ba00-28b709b98b03.dat\n-# StringTie version 2.1.7\n-chr1\tStringTie\ttranscript\t3189811\t3193042\t1000\t.\t.\tgene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; \n-chr1\tStringTie\texon\t3189811\t3193042\t1000\t.\t.\tgene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; \n-chr1\tStringTie\ttranscript\t3200023\t3200191\t1000\t.\t.\tgene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; \n-chr1\tStringTie\texon\t3200023\t3200191\t1000\t.\t.\tgene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "1"; \n-chr1\tStringTie\ttranscript\t3201078\t3201809\t1000\t.\t.\tgene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; \n-chr1\tStringTie\texon\t3201078\t3201809\t1000\t.\t.\tgene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "1"; \n-chr1\tStringTie\ttranscript\t3204563\t3661579\t1000\t-\t.\tgene_id "MSTRG.4"; transcript_id "Xkr4"; ref_gene_id "Xkr4"; \n-chr1\tStringTie\texon\t3204563\t3207049\t1000\t-\t.\tgene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "1"; ref_gene_id "Xkr4"; \n-chr1\tStringTie\texon\t3411783\t3411982\t1000\t-\t.\tgene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "2"; ref_gene_id "Xkr4"; \n-chr1\tStringTie\texon\t3660633\t3661579\t1000\t-\t.\tgene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "3"; ref_gene_id "Xkr4"; \n-chr1\tStringTie\ttranscript\t3212214\t3212439\t1000\t.\t.\tgene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; \n-chr1\tStringTie\texon\t3212214\t3212439\t1000\t.\t.\tgene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; exon_number "1"; \n-chr1\tStringTie\ttranscript\t3212718\t3212801\t1000\t.\t.\tgene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; \n-chr1\tStringTie\texon\t3212718\t3212801\t1000\t.\t.\tgene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; exon_number "1"; \n-chr1\tStringTie\ttranscript\t3213096\t3213242\t1000\t.\t.\tgene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; \n-chr1\tStringTie\texon\t3213096\t3213242\t1000\t.\t.\tgene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; exon_number "1"; \n-chr1\tStringTie\ttranscript\t3242634\t3243079\t1000\t.\t.\tgene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; \n-chr1\tStringTie\texon\t3242634\t3243079\t1000\t.\t.\tgene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; exon_number "1"; \n-chr1\tStringTie\ttranscript\t3243348\t3243401\t1000\t.\t.\tgene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; \n-chr1\tStringTie\texon\t3243348\t3243401\t1000\t.\t.\tgene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; exon_number "1"; \n-chr1\tStringTie\ttranscript\t3277914\t3278390\t1000\t.\t.\tgene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; \n-chr1\tStringTie\texon\t3277914\t3278390\t1000\t.\t.\tgene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; exon_number "1"; \n-chr1\tStringTie\ttranscript\t3280687\t3280741\t1000\t.\t.\tgene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; \n-chr1\tStringTie\texon\t3280687\t3280741\t1000\t.\t.\tgene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; exon_number "1"; \n-chr1\tStringTie\ttranscript\t3282761\t3282832\t1000\t.\t.\tgene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; \n-chr1\tStringTie\texon\t3282761\t3282832\t1000\t.\t.\tgene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; exon_number "1"; \n-chr1\tStringTie\ttranscript\t3290489\t3291273\t1000\t.\t.\tgene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; \n-chr1\tStringTie\texon\t3290489\t3291273\t1000\t.\t.\tgene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; exon_number "1"; \n-chr1\tStringTie\ttranscript\t3299444\t3299664\t1000\t.\t.\tgene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; \n-chr1\tStringTie\texon\t3299444\t3299664\t1000\t.\t.\tgene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; exon_number "1"; \n-chr1\tStringTie\ttranscript\t3319000\t3319051\t1000\t.\t.\tgene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; \n-chr1\tStringTie\texon\t3319000\t3319051\t1000\t.\t.\tgene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; exon_number "1"; \n-chr1\tStringTie\ttranscript\t3351241\t3351311\t1000\t.\t.\tgene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; \n-chr1\tStringTie\texon\t3351241'..b'4774032\\t4774186\\t\\.\\t-\\t\\.\\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4775654\\t4775807\\t\\.\\t-\\t\\.\\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4775654\\t4775807\\t\\.\\t-\\t\\.\\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4775654\\t4775807\\t\\.\\t-\\t\\.\\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4797974\\t4798063\\t\\.\\t\\+\\t\\.\\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4798536\\t4798567\\t\\.\\t\\+\\t\\.\\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4818665\\t4818730\\t\\.\\t\\+\\t\\.\\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4820349\\t4820396\\t\\.\\t\\+\\t\\.\\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4822392\\t4822462\\t\\.\\t\\+\\t\\.\\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4827082\\t4827155\\t\\.\\t\\+\\t\\.\\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4829468\\t4829569\\t\\.\\t\\+\\t\\.\\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4831037\\t4831213\\t\\.\\t\\+\\t\\.\\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4835044\\t4836816\\t\\.\\t\\+\\t\\.\\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4847775\\t4848057\\t\\.\\t\\+\\t\\.\\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4847775\\t4848057\\t\\.\\t\\+\\t\\.\\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4857551\\t4857613\\t\\.\\t\\+\\t\\.\\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4857551\\t4857613\\t\\.\\t\\+\\t\\.\\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4868108\\t4868213\\t\\.\\t\\+\\t\\.\\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4876825\\t4876912\\t\\.\\t\\+\\t\\.\\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4879538\\t4879683\\t\\.\\t\\+\\t\\.\\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4880821\\t4880877\\t\\.\\t\\+\\t\\.\\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4881996\\t4882150\\t\\.\\t\\+\\t\\.\\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4883498\\t4883644\\t\\.\\t\\+\\t\\.\\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4885015\\t4885086\\t\\.\\t\\+\\t\\.\\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\texon\\t4886437\\t4887987\\t\\.\\t\\+\\t\\.\\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";\n+chr1\\tmm9_refFlat\\ttranscript\\t4334224\\t4350473\\t\\.\\t-\\t\\.\\tgene_id "Rp1"; transcript_id "Rp1"; ref_gene_id "Rp1";\n+chr1\\tmm9_refFlat\\ttranscript\\t4481009\\t4486494\\t\\.\\t-\\t\\.\\tgene_id "Sox17"; transcript_id "Sox17"; ref_gene_id "Sox17";\n+chr1\\tmm9_refFlat\\ttranscript\\t4763279\\t4775807\\t\\.\\t-\\t\\.\\tgene_id "Mrpl15"; transcript_id "Mrpl15"; ref_gene_id "Mrpl15";\n+chr1\\tmm9_refFlat\\ttranscript\\t4763279\\t4775807\\t\\.\\t-\\t\\.\\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; ref_gene_id "Mrpl15";\n+chr1\\tmm9_refFlat\\ttranscript\\t4763279\\t4775807\\t\\.\\t-\\t\\.\\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; ref_gene_id "Mrpl15";\n+chr1\\tmm9_refFlat\\ttranscript\\t4797974\\t4836816\\t\\.\\t\\+\\t\\.\\tgene_id "Lypla1"; transcript_id "Lypla1"; ref_gene_id "Lypla1";\n+chr1\\tmm9_refFlat\\ttranscript\\t4847775\\t4857613\\t\\.\\t\\+\\t\\.\\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; ref_gene_id "Tcea1";\n+chr1\\tmm9_refFlat\\ttranscript\\t4847775\\t4887987\\t\\.\\t\\+\\t\\.\\tgene_id "Tcea1"; transcript_id "Tcea1"; ref_gene_id "Tcea1";\n\\ No newline at end of file\n' |
| b |
| diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out10.gtf --- a/test-data/stringtie_out10.gtf Tue Nov 30 11:01:34 2021 +0000 +++ b/test-data/stringtie_out10.gtf Wed Jul 27 09:28:15 2022 +0000 |
| [ |
| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpgqe071sy/files/8/8/6/dataset_886a7110-225b-4286-8de0-3e630fa369da.dat -L -E 25 -o /tmp/tmpgqe071sy/files/d/5/4/dataset_d54d1211-a9e6-4f03-b0b6-58182b101e8b.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 2.1.7 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.795303"; FPKM "3354967.250000"; TPM "1000000.000000"; -test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.777779"; -test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "54.160000"; -test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000"; +# StringTie version 2\.1\.7 +# stringtie /[-_/a-zA-Z0-9]+\.dat -L -E 25 -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95 +test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "54\.160000"; +test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000"; +test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.777779"; +test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.795303"; FPKM "3354967\.250000"; TPM "1000000\.000000"; |
| b |
| diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out11.gtf --- a/test-data/stringtie_out11.gtf Tue Nov 30 11:01:34 2021 +0000 +++ b/test-data/stringtie_out11.gtf Wed Jul 27 09:28:15 2022 +0000 |
| [ |
| b'@@ -1,58 +1,58 @@\n-# stringtie /tmp/tmpgqe071sy/files/5/f/e/dataset_5feb7af0-84a3-4590-975e-97b02b89c256.dat -L -E 30 -o /tmp/tmpgqe071sy/files/d/9/c/dataset_d9c60f6e-5062-4d09-a7e3-05b74adcebca.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95\n-# StringTie version 2.1.7\n-chr19\tStringTie\ttranscript\t567221\t571736\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; cov "5.617600"; FPKM "37220.644531"; TPM "77823.132812";\n-chr19\tStringTie\texon\t567221\t567648\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "5.815421";\n-chr19\tStringTie\texon\t571440\t571596\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "5.859873";\n-chr19\tStringTie\texon\t571697\t571736\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "2.550000";\n-chr19\tStringTie\ttranscript\t571310\t583493\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; cov "5.416068"; FPKM "35885.347656"; TPM "75031.218750";\n-chr19\tStringTie\texon\t571310\t571579\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "4.559259";\n-chr19\tStringTie\texon\t580379\t580461\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "2"; cov "5.556142";\n-chr19\tStringTie\texon\t580646\t580782\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "3"; cov "5.689962";\n-chr19\tStringTie\texon\t581315\t581610\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "4"; cov "5.556142";\n-chr19\tStringTie\texon\t582514\t582582\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "5"; cov "5.556142";\n-chr19\tStringTie\texon\t582750\t583493\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "6"; cov "5.592226";\n-chr19\tStringTie\ttranscript\t572567\t583493\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; cov "6.175826"; FPKM "40919.292969"; TPM "85556.492188";\n-chr19\tStringTie\texon\t572567\t572701\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "1"; cov "3.325926";\n-chr19\tStringTie\texon\t577774\t578121\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "2"; cov "6.436781";\n-chr19\tStringTie\texon\t579500\t579656\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "3"; cov "7.000000";\n-chr19\tStringTie\texon\t580379\t580461\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "4"; cov "7.443858";\n-chr19\tStringTie\texon\t580646\t580782\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "5"; cov "6.631207";\n-chr19\tStringTie\texon\t581315\t581610\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "6"; cov "6.443858";\n-chr19\tStringTie\texon\t582514\t582582\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "7"; cov "6.443858";\n-chr19\tStringTie\texon\t582750\t583493\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "8"; cov "6.040156";\n-chr19\tStringTie\ttranscript\t589891\t617159\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; cov "19.938414"; FPKM "132106.343750"; TPM "276215.781250";\n-chr19\tStringTie\texon\t589891\t590577\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "1"; cov "18.537119";\n-chr19\tStringTie\texon\t603544\t603967\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "2"; cov "21.000000";\n-chr19\tStringTie\texon\t605061\t605222\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "3"; cov "21.000000";\n-chr19\tStringTie\texon\t607964\t608182\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "4"; cov "21.000000";\n-chr19\tStringTie\texon\t610259\t610405\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "5"; cov "21.000000";\n-chr19\tStringTie\texon\t613248\t613488\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "6"; cov "21.000000";\n-chr19\tStringTie\texon\t613852\t614016\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "7"; cov "21.000000";\n-chr19\tStringTie\texon\t615795\t617159\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "8"; cov "19.587545";\n-chr19\tSt'..b'+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "30\\.891500";\n+chr19\\tStringTie\\texon\\t617777\\t617849\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "5\\.994817";\n+chr19\\tStringTie\\texon\\t618488\\t618586\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "5\\.525252";\n+chr19\\tStringTie\\texon\\t618705\\t618760\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "13\\.750000";\n+chr19\\tStringTie\\texon\\t618705\\t618760\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "6\\.875000";\n+chr19\\tStringTie\\texon\\t618997\\t619110\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "6\\.000000";\n+chr19\\tStringTie\\texon\\t619210\\t619296\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "6\\.000000";\n+chr19\\tStringTie\\texon\\t619586\\t619765\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "6\\.000000";\n+chr19\\tStringTie\\texon\\t619958\\t620080\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "7\\.000000";\n+chr19\\tStringTie\\texon\\t620365\\t620487\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "7\\.000000";\n+chr19\\tStringTie\\texon\\t621058\\t621846\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "6\\.751584";\n+chr19\\tStringTie\\texon\\t622149\\t622373\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "6\\.000000";\n+chr19\\tStringTie\\texon\\t622582\\t622752\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "6\\.000000";\n+chr19\\tStringTie\\texon\\t622821\\t622985\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "6\\.000000";\n+chr19\\tStringTie\\texon\\t623454\\t623603\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "6\\.000000";\n+chr19\\tStringTie\\texon\\t624719\\t624905\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "6\\.000000";\n+chr19\\tStringTie\\texon\\t625124\\t625254\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "6\\.000000";\n+chr19\\tStringTie\\texon\\t629540\\t630168\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "5\\.941176";\n+chr19\\tStringTie\\texon\\t632834\\t632938\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "5\\.000000";\n+chr19\\tStringTie\\texon\\t633425\\t633601\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "3\\.988701";\n+chr19\\tStringTie\\ttranscript\\t567221\\t571736\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; cov "5\\.617600"; FPKM "37220\\.644531"; TPM "77823\\.132812";\n+chr19\\tStringTie\\ttranscript\\t571310\\t583493\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; cov "5\\.416068"; FPKM "35885\\.347656"; TPM "75031\\.218750";\n+chr19\\tStringTie\\ttranscript\\t572567\\t583493\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; cov "6\\.175826"; FPKM "40919\\.292969"; TPM "85556\\.492188";\n+chr19\\tStringTie\\ttranscript\\t589891\\t617159\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; cov "19\\.938414"; FPKM "132106\\.343750"; TPM "276215\\.781250";\n+chr19\\tStringTie\\ttranscript\\t617224\\t618760\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; cov "29\\.150192"; FPKM "193141\\.000000"; TPM "403830\\.687500";\n+chr19\\tStringTie\\ttranscript\\t617224\\t633601\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; cov "5\\.886094"; FPKM "38999\\.609375"; TPM "81542\\.703125";\n' |
| b |
| diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out12.gtf --- a/test-data/stringtie_out12.gtf Tue Nov 30 11:01:34 2021 +0000 +++ b/test-data/stringtie_out12.gtf Wed Jul 27 09:28:15 2022 +0000 |
| [ |
| b'@@ -1,73 +1,73 @@\n-# stringtie short_sorted.sam long_sorted.sam -E 25 -o /tmp/tmpgqe071sy/files/9/5/b/dataset_95b1ec38-2151-43e7-8584-aa4aff72e957.dat -p 1 -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95\n-# StringTie version 2.1.7\n-chr19\tStringTie\ttranscript\t567221\t571736\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; cov "5.043160"; FPKM "15396.282227"; TPM "50141.804688";\n-chr19\tStringTie\texon\t567221\t567648\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "5.815421";\n-chr19\tStringTie\texon\t571440\t571596\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "3.573089";\n-chr19\tStringTie\texon\t571697\t571736\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "2.550000";\n-chr19\tStringTie\ttranscript\t571310\t583493\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; cov "4.701019"; FPKM "14351.757812"; TPM "46740.058594";\n-chr19\tStringTie\texon\t571310\t571579\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "5.888981";\n-chr19\tStringTie\texon\t580379\t580461\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "2"; cov "4.879346";\n-chr19\tStringTie\texon\t580646\t580782\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "3"; cov "4.616338";\n-chr19\tStringTie\texon\t581315\t581610\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "4"; cov "4.479919";\n-chr19\tStringTie\texon\t582514\t582582\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "5"; cov "4.504012";\n-chr19\tStringTie\texon\t582750\t583493\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "6"; cov "4.371838";\n-chr19\tStringTie\ttranscript\t572567\t583493\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; cov "6.933517"; FPKM "21167.359375"; TPM "68936.750000";\n-chr19\tStringTie\texon\t572567\t572701\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "1"; cov "3.325926";\n-chr19\tStringTie\texon\t577774\t578121\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "2"; cov "6.436781";\n-chr19\tStringTie\texon\t579500\t579656\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "3"; cov "7.000000";\n-chr19\tStringTie\texon\t580379\t580461\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "4"; cov "8.120653";\n-chr19\tStringTie\texon\t580646\t580782\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "5"; cov "7.682931";\n-chr19\tStringTie\texon\t581315\t581610\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "6"; cov "7.455892";\n-chr19\tStringTie\texon\t582514\t582582\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "7"; cov "7.495987";\n-chr19\tStringTie\texon\t582750\t583493\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "8"; cov "7.276011";\n-chr19\tStringTie\ttranscript\t589891\t617159\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; cov "19.937536"; FPKM "60867.378906"; TPM "198229.687500";\n-chr19\tStringTie\texon\t589891\t590577\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "1"; cov "18.537117";\n-chr19\tStringTie\texon\t603544\t603967\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "2"; cov "21.000000";\n-chr19\tStringTie\texon\t605061\t605222\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "3"; cov "20.981482";\n-chr19\tStringTie\texon\t607964\t608182\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "4"; cov "21.000000";\n-chr19\tStringTie\texon\t610259\t610405\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "5"; cov "21.000000";\n-chr19\tStringTie\texon\t613248\t613488\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "6"; cov "21.000000";\n-chr19\tStringTie\texon\t613852\t614016\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "7"; cov "21.000000";\n-chr19\tStringTie\texon\t615795\t617159\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "8"; cov "19.587545";\n-chr16\tStringTie\ttranscript\t784986\t788300\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.1"; cov "30.'..b'STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "3"; cov "2\\.550000";\n+chr19\\tStringTie\\texon\\t572567\\t572701\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "1"; cov "3\\.325926";\n+chr19\\tStringTie\\texon\\t577774\\t578121\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "2"; cov "6\\.436781";\n+chr19\\tStringTie\\texon\\t579500\\t579656\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "3"; cov "7\\.000000";\n+chr19\\tStringTie\\texon\\t580379\\t580461\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "2"; cov "4\\.879346";\n+chr19\\tStringTie\\texon\\t580379\\t580461\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "4"; cov "8\\.120653";\n+chr19\\tStringTie\\texon\\t580646\\t580782\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "3"; cov "4\\.616338";\n+chr19\\tStringTie\\texon\\t580646\\t580782\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "5"; cov "7\\.682931";\n+chr19\\tStringTie\\texon\\t581315\\t581610\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "4"; cov "4\\.479919";\n+chr19\\tStringTie\\texon\\t581315\\t581610\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "6"; cov "7\\.455892";\n+chr19\\tStringTie\\texon\\t582514\\t582582\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "5"; cov "4\\.504012";\n+chr19\\tStringTie\\texon\\t582514\\t582582\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "7"; cov "7\\.495987";\n+chr19\\tStringTie\\texon\\t582750\\t583493\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "6"; cov "4\\.371838";\n+chr19\\tStringTie\\texon\\t582750\\t583493\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "8"; cov "7\\.276011";\n+chr19\\tStringTie\\texon\\t589891\\t590577\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "1"; cov "18\\.537117";\n+chr19\\tStringTie\\texon\\t603544\\t603967\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "2"; cov "21\\.000000";\n+chr19\\tStringTie\\texon\\t605061\\t605222\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "3"; cov "20\\.981482";\n+chr19\\tStringTie\\texon\\t607964\\t608182\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "4"; cov "21\\.000000";\n+chr19\\tStringTie\\texon\\t610259\\t610405\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "5"; cov "21\\.000000";\n+chr19\\tStringTie\\texon\\t613248\\t613488\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "6"; cov "21\\.000000";\n+chr19\\tStringTie\\texon\\t613852\\t614016\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "7"; cov "21\\.000000";\n+chr19\\tStringTie\\texon\\t615795\\t617159\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; exon_number "8"; cov "19\\.587545";\n+chr19\\tStringTie\\ttranscript\\t567221\\t571736\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; cov "5\\.043160"; FPKM "15396\\.282227"; TPM "50141\\.804688";\n+chr19\\tStringTie\\ttranscript\\t571310\\t583493\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; cov "4\\.701019"; FPKM "14351\\.757812"; TPM "46740\\.058594";\n+chr19\\tStringTie\\ttranscript\\t572567\\t583493\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; cov "6\\.933517"; FPKM "21167\\.359375"; TPM "68936\\.750000";\n+chr19\\tStringTie\\ttranscript\\t589891\\t617159\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.[0-9+]"; cov "19\\.937536"; FPKM "60867\\.378906"; TPM "198229\\.687500";\n' |
| b |
| diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out1_re.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_out1_re.gtf Wed Jul 27 09:28:15 2022 +0000 |
| [ |
| @@ -0,0 +1,6 @@ +# StringTie version 2\.1\.7 +# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95 +test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004"; +test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000"; +test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "49\.237373"; +test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000"; |
| b |
| diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out2_re.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_out2_re.gtf Wed Jul 27 09:28:15 2022 +0000 |
| [ |
| @@ -0,0 +1,6 @@ +# StringTie version 2\.1\.7 +# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95 +test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004"; +test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000"; +test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "49\.237373"; +test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000"; |
| b |
| diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out3_re.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_out3_re.gtf Wed Jul 27 09:28:15 2022 +0000 |
| [ |
| @@ -0,0 +1,6 @@ +# StringTie version 2\.1\.7 +# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95 +test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004"; +test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000"; +test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373"; +test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000"; |
| b |
| diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out4_re.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_out4_re.gtf Wed Jul 27 09:28:15 2022 +0000 |
| [ |
| @@ -0,0 +1,6 @@ +# StringTie version 2\.1\.7 +# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95( -A /[-_/a-zA-Z0-9]+\.dat)? +test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004"; +test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000"; +test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373"; +test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000"; |
| b |
| diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out5.gtf --- a/test-data/stringtie_out5.gtf Tue Nov 30 11:01:34 2021 +0000 +++ b/test-data/stringtie_out5.gtf Wed Jul 27 09:28:15 2022 +0000 |
| [ |
| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpgqe071sy/files/0/e/1/dataset_0e10eba1-035e-4481-9311-22277f50cd38.dat -o /tmp/tmpgqe071sy/files/d/a/a/dataset_daa0c96d-9176-476d-82fc-e2b7ef2dcd8e.dat -p 1 -G guide.gff -C /tmp/tmpgqe071sy/files/9/6/1/dataset_9614085c-99c8-4957-9b89-2391d231ddb8.dat -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 2.1.7 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000"; -test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373"; -test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "53.000004"; -test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000"; +# StringTie version 2\.1\.7 +# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -C /[-_/a-zA-Z0-9]+\.dat -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95 +test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004"; +test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000"; +test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373"; +test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000"; |
| b |
| diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out6.gtf --- a/test-data/stringtie_out6.gtf Tue Nov 30 11:01:34 2021 +0000 +++ b/test-data/stringtie_out6.gtf Wed Jul 27 09:28:15 2022 +0000 |
| [ |
| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpgqe071sy/files/a/7/3/dataset_a739b50f-5870-4fab-becb-e667dfdfd00e.dat -o /tmp/tmpgqe071sy/files/8/3/6/dataset_8365f524-36d5-4bce-89dd-0c362b90be45.dat -p 1 -G guide.gff -C /tmp/tmpgqe071sy/files/3/9/6/dataset_39649d2b-5fe0-4cbe-8d5a-cd4c8b2663c9.dat -e -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 2.1.7 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000"; -test_chromosome StringTie exon 53 250 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; cov "49.237373"; -test_chromosome StringTie exon 351 400 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; cov "53.000004"; -test_chromosome StringTie exon 501 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; cov "21.660000"; +# StringTie version 2\.1\.7 +# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -C /[-_/a-zA-Z0-9]+\.dat -e -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95 +test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004"; +test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000"; +test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "49\.237373"; +test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000"; |
| b |
| diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out8.gtf --- a/test-data/stringtie_out8.gtf Tue Nov 30 11:01:34 2021 +0000 +++ b/test-data/stringtie_out8.gtf Wed Jul 27 09:28:15 2022 +0000 |
| [ |
| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpgqe071sy/files/d/e/8/dataset_de884427-d510-47bf-acb3-4375c0ce2337.dat -o /tmp/tmpgqe071sy/files/2/7/e/dataset_27e677d1-ed55-49db-bfb2-a38c2c6bf911.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 2.1.7 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000"; -test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373"; -test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "53.000004"; -test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000"; +# StringTie version 2\.1\.7 +# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95 +test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004"; +test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000"; +test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373"; +test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000"; |
| b |
| diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out9.gtf --- a/test-data/stringtie_out9.gtf Tue Nov 30 11:01:34 2021 +0000 +++ b/test-data/stringtie_out9.gtf Wed Jul 27 09:28:15 2022 +0000 |
| [ |
| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpgqe071sy/files/a/3/b/dataset_a3ba39e7-c812-41eb-a15c-e039ad42a33a.dat -o /tmp/tmpgqe071sy/files/7/4/7/dataset_74713e40-e879-4efa-b57e-f3d95a82284f.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 2.1.7 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000"; -test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.237373"; -test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "53.000004"; -test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.660000"; +# StringTie version 2\.1\.7 +# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0\.95 +test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004"; +test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000"; +test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373"; +test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000"; |
| b |
| diff -r 333a6e13b622 -r cef79931dda5 test-data/stringtie_out_coverage.gtf --- a/test-data/stringtie_out_coverage.gtf Tue Nov 30 11:01:34 2021 +0000 +++ b/test-data/stringtie_out_coverage.gtf Wed Jul 27 09:28:15 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -test_chromosome Cufflinks transcript 53 550 1000 + . ID=CUFF.1.1;geneID=CUFF.1;coverage=60.97 -test_chromosome Cufflinks exon 53 250 1000 + . Parent=CUFF.1.1 -test_chromosome Cufflinks exon 351 400 1000 + . Parent=CUFF.1.1 -test_chromosome Cufflinks exon 501 550 1000 + . Parent=CUFF.1.1 +test_chromosome\tCufflinks\texon\t351\t400\t1000\t\+\t\.\tParent=CUFF\.[0-9]+\.1 +test_chromosome\tCufflinks\texon\t501\t550\t1000\t\+\t\.\tParent=CUFF\.[0-9]+\.1 +test_chromosome\tCufflinks\texon\t53\t250\t1000\t\+\t\.\tParent=CUFF\.[0-9]+\.1 +test_chromosome\tCufflinks\ttranscript\t53\t550\t1000\t\+\t\.\tID=CUFF\.[0-9]+\.1;geneID=CUFF\.[0-9]+;coverage=60\.97 |