Mercurial > repos > iuc > stringtie
diff test-data/stringtie_out11.gtf @ 20:cef79931dda5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb
| author | iuc |
|---|---|
| date | Wed, 27 Jul 2022 09:28:15 +0000 |
| parents | 258d696dbd7e |
| children | 914cfcba0ec8 |
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--- 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 @@ -1,58 +1,58 @@ -# 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 -# StringTie version 2.1.7 -chr19 StringTie transcript 567221 571736 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "5.617600"; FPKM "37220.644531"; TPM "77823.132812"; -chr19 StringTie exon 567221 567648 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "5.815421"; -chr19 StringTie exon 571440 571596 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "5.859873"; -chr19 StringTie exon 571697 571736 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "2.550000"; -chr19 StringTie transcript 571310 583493 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.1"; cov "5.416068"; FPKM "35885.347656"; TPM "75031.218750"; -chr19 StringTie exon 571310 571579 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "4.559259"; -chr19 StringTie exon 580379 580461 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "2"; cov "5.556142"; -chr19 StringTie exon 580646 580782 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "3"; cov "5.689962"; -chr19 StringTie exon 581315 581610 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "4"; cov "5.556142"; -chr19 StringTie exon 582514 582582 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "5"; cov "5.556142"; -chr19 StringTie exon 582750 583493 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "6"; cov "5.592226"; -chr19 StringTie transcript 572567 583493 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; cov "6.175826"; FPKM "40919.292969"; TPM "85556.492188"; -chr19 StringTie exon 572567 572701 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "1"; cov "3.325926"; -chr19 StringTie exon 577774 578121 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "2"; cov "6.436781"; -chr19 StringTie exon 579500 579656 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "3"; cov "7.000000"; -chr19 StringTie exon 580379 580461 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "4"; cov "7.443858"; -chr19 StringTie exon 580646 580782 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "5"; cov "6.631207"; -chr19 StringTie exon 581315 581610 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "6"; cov "6.443858"; -chr19 StringTie exon 582514 582582 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "7"; cov "6.443858"; -chr19 StringTie exon 582750 583493 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "8"; cov "6.040156"; -chr19 StringTie transcript 589891 617159 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; cov "19.938414"; FPKM "132106.343750"; TPM "276215.781250"; -chr19 StringTie exon 589891 590577 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "1"; cov "18.537119"; -chr19 StringTie exon 603544 603967 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "2"; cov "21.000000"; -chr19 StringTie exon 605061 605222 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "3"; cov "21.000000"; -chr19 StringTie exon 607964 608182 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "4"; cov "21.000000"; -chr19 StringTie exon 610259 610405 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "5"; cov "21.000000"; -chr19 StringTie exon 613248 613488 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "6"; cov "21.000000"; -chr19 StringTie exon 613852 614016 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "7"; cov "21.000000"; -chr19 StringTie exon 615795 617159 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "8"; cov "19.587545"; -chr19 StringTie transcript 617224 618760 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; cov "29.150192"; FPKM "193141.000000"; TPM "403830.687500"; -chr19 StringTie exon 617224 617323 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "1"; cov "20.289286"; -chr19 StringTie exon 617419 617480 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "2"; cov "28.788761"; -chr19 StringTie exon 617570 618586 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "3"; cov "30.891500"; -chr19 StringTie exon 618705 618760 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "4"; cov "13.750000"; -chr19 StringTie transcript 617224 633601 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; cov "5.886094"; FPKM "38999.609375"; TPM "81542.703125"; -chr19 StringTie exon 617224 617323 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "1"; cov "1.560714"; -chr19 StringTie exon 617419 617480 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "2"; cov "1.985432"; -chr19 StringTie exon 617570 617655 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "3"; cov "4.996770"; -chr19 StringTie exon 617777 617849 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "4"; cov "5.994817"; -chr19 StringTie exon 618488 618586 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "5"; cov "5.525252"; -chr19 StringTie exon 618705 618760 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "6"; cov "6.875000"; -chr19 StringTie exon 618997 619110 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "7"; cov "6.000000"; -chr19 StringTie exon 619210 619296 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "8"; cov "6.000000"; -chr19 StringTie exon 619586 619765 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "9"; cov "6.000000"; -chr19 StringTie exon 619958 620080 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "10"; cov "7.000000"; -chr19 StringTie exon 620365 620487 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "11"; cov "7.000000"; -chr19 StringTie exon 621058 621846 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "12"; cov "6.751584"; -chr19 StringTie exon 622149 622373 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "13"; cov "6.000000"; -chr19 StringTie exon 622582 622752 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "14"; cov "6.000000"; -chr19 StringTie exon 622821 622985 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "15"; cov "6.000000"; -chr19 StringTie exon 623454 623603 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "16"; cov "6.000000"; -chr19 StringTie exon 624719 624905 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "17"; cov "6.000000"; -chr19 StringTie exon 625124 625254 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "18"; cov "6.000000"; -chr19 StringTie exon 629540 630168 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "19"; cov "5.941176"; -chr19 StringTie exon 632834 632938 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "20"; cov "5.000000"; -chr19 StringTie exon 633425 633601 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "21"; cov "3.988701"; +# StringTie version 2\.1\.7 +# stringtie /[-_/a-zA-Z0-9]+\.dat -L -E 30 -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 +chr19\tStringTie\texon\t567221\t567648\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.815421"; +chr19\tStringTie\texon\t571310\t571579\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "4\.559259"; +chr19\tStringTie\texon\t571440\t571596\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.859873"; +chr19\tStringTie\texon\t571697\t571736\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "2\.550000"; +chr19\tStringTie\texon\t572567\t572701\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "3\.325926"; +chr19\tStringTie\texon\t577774\t578121\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.436781"; +chr19\tStringTie\texon\t579500\t579656\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "7\.000000"; +chr19\tStringTie\texon\t580379\t580461\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.556142"; +chr19\tStringTie\texon\t580379\t580461\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "7\.443858"; +chr19\tStringTie\texon\t580646\t580782\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.689962"; +chr19\tStringTie\texon\t580646\t580782\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.631207"; +chr19\tStringTie\texon\t581315\t581610\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.556142"; +chr19\tStringTie\texon\t581315\t581610\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.443858"; +chr19\tStringTie\texon\t582514\t582582\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.556142"; +chr19\tStringTie\texon\t582514\t582582\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.443858"; +chr19\tStringTie\texon\t582750\t583493\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "5\.592226"; +chr19\tStringTie\texon\t582750\t583493\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.040156"; +chr19\tStringTie\texon\t589891\t590577\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "18\.537119"; +chr19\tStringTie\texon\t603544\t603967\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000"; +chr19\tStringTie\texon\t605061\t605222\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000"; +chr19\tStringTie\texon\t607964\t608182\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000"; +chr19\tStringTie\texon\t610259\t610405\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000"; +chr19\tStringTie\texon\t613248\t613488\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000"; +chr19\tStringTie\texon\t613852\t614016\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.000000"; +chr19\tStringTie\texon\t615795\t617159\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "19\.587545"; +chr19\tStringTie\texon\t617224\t617323\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "20\.289286"; +chr19\tStringTie\texon\t617224\t617323\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "1\.560714"; +chr19\tStringTie\texon\t617419\t617480\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "28\.788761"; +chr19\tStringTie\texon\t617419\t617480\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "1\.985432"; +chr19\tStringTie\texon\t617570\t617655\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "4\.996770"; +chr19\tStringTie\texon\t617570\t618586\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "30\.891500"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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"; +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";