Mercurial > repos > devteam > picard
changeset 22:f6ced08779c4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
| author | iuc |
|---|---|
| date | Fri, 29 Mar 2019 08:34:36 -0400 |
| parents | 6f9c0884a3e7 |
| children | 1cd1cf786389 |
| files | picard_CollectRnaSeqMetrics.xml read_group_macros.xml test-data/picard_CollectRnaSeqMetrics.gtf test-data/picard_CollectRnaSeqMetrics_test2.tab |
| diffstat | 4 files changed, 252 insertions(+), 28 deletions(-) [+] |
line wrap: on
line diff
--- a/picard_CollectRnaSeqMetrics.xml Tue Oct 16 11:49:10 2018 -0400 +++ b/picard_CollectRnaSeqMetrics.xml Fri Mar 29 08:34:36 2019 -0400 @@ -23,7 +23,7 @@ #if str($gene_reference_source.gene_reference_source_selector) == "gtf" #if $gene_reference_source.refFlat.ext != 'gff3' - gtfToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw && + gtfToGenePred -genePredExt '${gene_reference_source.refFlat}' refFlat.tab.raw && #else gff3ToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw && #end if
--- a/read_group_macros.xml Tue Oct 16 11:49:10 2018 -0400 +++ b/read_group_macros.xml Fri Mar 29 08:34:36 2019 -0400 @@ -242,7 +242,7 @@ <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" /> </xml> <xml name="read_group_pu_required_param"> - <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" /> + <param name="PU" type="text" value="run" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" /> </xml> <!-- Only ID is required - all groups available --> <xml name="read_group_inputs_spec">
--- a/test-data/picard_CollectRnaSeqMetrics.gtf Tue Oct 16 11:49:10 2018 -0400 +++ b/test-data/picard_CollectRnaSeqMetrics.gtf Fri Mar 29 08:34:36 2019 -0400 @@ -1,23 +1,144 @@ -chrM hg19_knownGene exon 236 368 0.000000 - . gene_id "uc004coq.4"; transcript_id "uc004coq.4"; -chrM hg19_knownGene exon 651 674 0.000000 + . gene_id "uc022bqo.2"; transcript_id "uc022bqo.2"; -chrM hg19_knownGene exon 1604 1634 0.000000 + . gene_id "uc004cor.1"; transcript_id "uc004cor.1"; -chrM hg19_knownGene exon 1844 4264 0.000000 + . gene_id "uc004cos.5"; transcript_id "uc004cos.5"; -chrM hg19_knownGene exon 5544 5566 0.000000 - . gene_id "uc022bqp.1"; transcript_id "uc022bqp.1"; -chrM hg19_knownGene exon 5586 5606 0.000000 - . gene_id "uc022bqq.1"; transcript_id "uc022bqq.1"; -chrM hg19_knownGene exon 5691 5714 0.000000 - . gene_id "uc022bqr.1"; transcript_id "uc022bqr.1"; -chrM hg19_knownGene exon 5905 7439 0.000000 + . gene_id "uc031tga.1"; transcript_id "uc031tga.1"; -chrM hg19_knownGene exon 7587 7982 0.000000 - . gene_id "uc022bqs.1"; transcript_id "uc022bqs.1"; -chrM hg19_knownGene exon 15504 15888 0.000000 - . gene_id "uc022bqs.1"; transcript_id "uc022bqs.1"; -chrM hg19_knownGene exon 7587 9208 0.000000 + . gene_id "uc011mfi.2"; transcript_id "uc011mfi.2"; -chrM hg19_knownGene exon 8367 8472 0.000000 - . gene_id "uc022bqt.1"; transcript_id "uc022bqt.1"; -chrM hg19_knownGene exon 13450 14149 0.000000 - . gene_id "uc022bqt.1"; transcript_id "uc022bqt.1"; -chrM hg19_knownGene exon 10060 10404 0.000000 + . gene_id "uc022bqu.2"; transcript_id "uc022bqu.2"; -chrM hg19_knownGene exon 10471 12138 0.000000 + . gene_id "uc004cov.5"; transcript_id "uc004cov.5"; -chrM hg19_knownGene exon 10761 11231 0.000000 - . gene_id "uc031tgb.1"; transcript_id "uc031tgb.1"; -chrM hg19_knownGene exon 13979 14149 0.000000 - . gene_id "uc031tgb.1"; transcript_id "uc031tgb.1"; -chrM hg19_knownGene exon 12208 12264 0.000000 + . gene_id "uc004cow.2"; transcript_id "uc004cow.2"; -chrM hg19_knownGene exon 12908 14149 0.000000 + . gene_id "uc004cox.4"; transcript_id "uc004cox.4"; -chrM hg19_knownGene exon 14675 14698 0.000000 - . gene_id "uc022bqv.1"; transcript_id "uc022bqv.1"; -chrM hg19_knownGene exon 14857 15888 0.000000 + . gene_id "uc022bqw.1"; transcript_id "uc022bqw.1"; -chrM hg19_knownGene exon 15960 16024 0.000000 - . gene_id "uc022bqx.1"; transcript_id "uc022bqx.1"; -chrM hg19_knownGene exon 15999 16571 0.000000 + . gene_id "uc004coz.1"; transcript_id "uc004coz.1"; \ No newline at end of file +chrM insdc gene 577 647 . + . gene_id "ENSG00000210049"; gene_version "1"; gene_name "MT-TF"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 577 647 . + . gene_id "ENSG00000210049"; gene_version "1"; transcript_id "ENST00000387314"; transcript_version "1"; gene_name "MT-TF"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TF-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 577 647 . + . gene_id "ENSG00000210049"; gene_version "1"; transcript_id "ENST00000387314"; transcript_version "1"; exon_number "1"; gene_name "MT-TF"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TF-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544501"; exon_version "1"; tag "basic"; +chrM insdc gene 648 1601 . + . gene_id "ENSG00000211459"; gene_version "2"; gene_name "MT-RNR1"; gene_source "insdc"; gene_biotype "Mt_rRNA"; +chrM insdc transcript 648 1601 . + . gene_id "ENSG00000211459"; gene_version "2"; transcript_id "ENST00000389680"; transcript_version "2"; gene_name "MT-RNR1"; gene_source "insdc"; gene_biotype "Mt_rRNA"; transcript_name "MT-RNR1-201"; transcript_source "insdc"; transcript_biotype "Mt_rRNA"; tag "basic"; +chrM insdc exon 648 1601 . + . gene_id "ENSG00000211459"; gene_version "2"; transcript_id "ENST00000389680"; transcript_version "2"; exon_number "1"; gene_name "MT-RNR1"; gene_source "insdc"; gene_biotype "Mt_rRNA"; transcript_name "MT-RNR1-201"; transcript_source "insdc"; transcript_biotype "Mt_rRNA"; exon_id "ENSE00001544499"; exon_version "2"; tag "basic"; +chrM insdc gene 1602 1670 . + . gene_id "ENSG00000210077"; gene_version "1"; gene_name "MT-TV"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 1602 1670 . + . gene_id "ENSG00000210077"; gene_version "1"; transcript_id "ENST00000387342"; transcript_version "1"; gene_name "MT-TV"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TV-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 1602 1670 . + . gene_id "ENSG00000210077"; gene_version "1"; transcript_id "ENST00000387342"; transcript_version "1"; exon_number "1"; gene_name "MT-TV"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TV-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544498"; exon_version "1"; tag "basic"; +chrM insdc gene 1671 3229 . + . gene_id "ENSG00000210082"; gene_version "2"; gene_name "MT-RNR2"; gene_source "insdc"; gene_biotype "Mt_rRNA"; +chrM insdc transcript 1671 3229 . + . gene_id "ENSG00000210082"; gene_version "2"; transcript_id "ENST00000387347"; transcript_version "2"; gene_name "MT-RNR2"; gene_source "insdc"; gene_biotype "Mt_rRNA"; transcript_name "MT-RNR2-201"; transcript_source "insdc"; transcript_biotype "Mt_rRNA"; tag "basic"; +chrM insdc exon 1671 3229 . + . gene_id "ENSG00000210082"; gene_version "2"; transcript_id "ENST00000387347"; transcript_version "2"; exon_number "1"; gene_name "MT-RNR2"; gene_source "insdc"; gene_biotype "Mt_rRNA"; transcript_name "MT-RNR2-201"; transcript_source "insdc"; transcript_biotype "Mt_rRNA"; exon_id "ENSE00001544497"; exon_version "2"; tag "basic"; +chrM insdc gene 3230 3304 . + . gene_id "ENSG00000209082"; gene_version "1"; gene_name "MT-TL1"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 3230 3304 . + . gene_id "ENSG00000209082"; gene_version "1"; transcript_id "ENST00000386347"; transcript_version "1"; gene_name "MT-TL1"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TL1-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 3230 3304 . + . gene_id "ENSG00000209082"; gene_version "1"; transcript_id "ENST00000386347"; transcript_version "1"; exon_number "1"; gene_name "MT-TL1"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TL1-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00002006242"; exon_version "1"; tag "basic"; +chrM insdc gene 3307 4262 . + . gene_id "ENSG00000198888"; gene_version "2"; gene_name "MT-ND1"; gene_source "insdc"; gene_biotype "protein_coding"; +chrM insdc transcript 3307 4262 . + . gene_id "ENSG00000198888"; gene_version "2"; transcript_id "ENST00000361390"; transcript_version "2"; gene_name "MT-ND1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc exon 3307 4262 . + . gene_id "ENSG00000198888"; gene_version "2"; transcript_id "ENST00000361390"; transcript_version "2"; exon_number "1"; gene_name "MT-ND1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001435714"; exon_version "2"; tag "basic"; +chrM insdc CDS 3307 4262 . + 0 gene_id "ENSG00000198888"; gene_version "2"; transcript_id "ENST00000361390"; transcript_version "2"; exon_number "1"; gene_name "MT-ND1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354687"; protein_version "2"; tag "basic"; +chrM insdc start_codon 3307 3309 . + 0 gene_id "ENSG00000198888"; gene_version "2"; transcript_id "ENST00000361390"; transcript_version "2"; exon_number "1"; gene_name "MT-ND1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc gene 4263 4331 . + . gene_id "ENSG00000210100"; gene_version "1"; gene_name "MT-TI"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 4263 4331 . + . gene_id "ENSG00000210100"; gene_version "1"; transcript_id "ENST00000387365"; transcript_version "1"; gene_name "MT-TI"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TI-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 4263 4331 . + . gene_id "ENSG00000210100"; gene_version "1"; transcript_id "ENST00000387365"; transcript_version "1"; exon_number "1"; gene_name "MT-TI"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TI-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001993597"; exon_version "1"; tag "basic"; +chrM insdc gene 4329 4400 . - . gene_id "ENSG00000210107"; gene_version "1"; gene_name "MT-TQ"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 4329 4400 . - . gene_id "ENSG00000210107"; gene_version "1"; transcript_id "ENST00000387372"; transcript_version "1"; gene_name "MT-TQ"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TQ-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 4329 4400 . - . gene_id "ENSG00000210107"; gene_version "1"; transcript_id "ENST00000387372"; transcript_version "1"; exon_number "1"; gene_name "MT-TQ"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TQ-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544494"; exon_version "1"; tag "basic"; +chrM insdc gene 4402 4469 . + . gene_id "ENSG00000210112"; gene_version "1"; gene_name "MT-TM"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 4402 4469 . + . gene_id "ENSG00000210112"; gene_version "1"; transcript_id "ENST00000387377"; transcript_version "1"; gene_name "MT-TM"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TM-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 4402 4469 . + . gene_id "ENSG00000210112"; gene_version "1"; transcript_id "ENST00000387377"; transcript_version "1"; exon_number "1"; gene_name "MT-TM"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TM-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544493"; exon_version "1"; tag "basic"; +chrM insdc gene 4470 5511 . + . gene_id "ENSG00000198763"; gene_version "3"; gene_name "MT-ND2"; gene_source "insdc"; gene_biotype "protein_coding"; +chrM insdc transcript 4470 5511 . + . gene_id "ENSG00000198763"; gene_version "3"; transcript_id "ENST00000361453"; transcript_version "3"; gene_name "MT-ND2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc exon 4470 5511 . + . gene_id "ENSG00000198763"; gene_version "3"; transcript_id "ENST00000361453"; transcript_version "3"; exon_number "1"; gene_name "MT-ND2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001435686"; exon_version "3"; tag "basic"; +chrM insdc CDS 4470 5511 . + 0 gene_id "ENSG00000198763"; gene_version "3"; transcript_id "ENST00000361453"; transcript_version "3"; exon_number "1"; gene_name "MT-ND2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000355046"; protein_version "4"; tag "basic"; +chrM insdc start_codon 4470 4472 . + 0 gene_id "ENSG00000198763"; gene_version "3"; transcript_id "ENST00000361453"; transcript_version "3"; exon_number "1"; gene_name "MT-ND2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc gene 5512 5579 . + . gene_id "ENSG00000210117"; gene_version "1"; gene_name "MT-TW"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 5512 5579 . + . gene_id "ENSG00000210117"; gene_version "1"; transcript_id "ENST00000387382"; transcript_version "1"; gene_name "MT-TW"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TW-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 5512 5579 . + . gene_id "ENSG00000210117"; gene_version "1"; transcript_id "ENST00000387382"; transcript_version "1"; exon_number "1"; gene_name "MT-TW"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TW-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544492"; exon_version "1"; tag "basic"; +chrM insdc gene 5587 5655 . - . gene_id "ENSG00000210127"; gene_version "1"; gene_name "MT-TA"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 5587 5655 . - . gene_id "ENSG00000210127"; gene_version "1"; transcript_id "ENST00000387392"; transcript_version "1"; gene_name "MT-TA"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TA-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 5587 5655 . - . gene_id "ENSG00000210127"; gene_version "1"; transcript_id "ENST00000387392"; transcript_version "1"; exon_number "1"; gene_name "MT-TA"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TA-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544491"; exon_version "1"; tag "basic"; +chrM insdc gene 5657 5729 . - . gene_id "ENSG00000210135"; gene_version "1"; gene_name "MT-TN"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 5657 5729 . - . gene_id "ENSG00000210135"; gene_version "1"; transcript_id "ENST00000387400"; transcript_version "1"; gene_name "MT-TN"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TN-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 5657 5729 . - . gene_id "ENSG00000210135"; gene_version "1"; transcript_id "ENST00000387400"; transcript_version "1"; exon_number "1"; gene_name "MT-TN"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TN-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544490"; exon_version "1"; tag "basic"; +chrM insdc gene 5761 5826 . - . gene_id "ENSG00000210140"; gene_version "1"; gene_name "MT-TC"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 5761 5826 . - . gene_id "ENSG00000210140"; gene_version "1"; transcript_id "ENST00000387405"; transcript_version "1"; gene_name "MT-TC"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TC-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 5761 5826 . - . gene_id "ENSG00000210140"; gene_version "1"; transcript_id "ENST00000387405"; transcript_version "1"; exon_number "1"; gene_name "MT-TC"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TC-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544489"; exon_version "1"; tag "basic"; +chrM insdc gene 5826 5891 . - . gene_id "ENSG00000210144"; gene_version "1"; gene_name "MT-TY"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 5826 5891 . - . gene_id "ENSG00000210144"; gene_version "1"; transcript_id "ENST00000387409"; transcript_version "1"; gene_name "MT-TY"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TY-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 5826 5891 . - . gene_id "ENSG00000210144"; gene_version "1"; transcript_id "ENST00000387409"; transcript_version "1"; exon_number "1"; gene_name "MT-TY"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TY-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544488"; exon_version "1"; tag "basic"; +chrM insdc gene 5904 7445 . + . gene_id "ENSG00000198804"; gene_version "2"; gene_name "MT-CO1"; gene_source "insdc"; gene_biotype "protein_coding"; +chrM insdc transcript 5904 7445 . + . gene_id "ENSG00000198804"; gene_version "2"; transcript_id "ENST00000361624"; transcript_version "2"; gene_name "MT-CO1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc exon 5904 7445 . + . gene_id "ENSG00000198804"; gene_version "2"; transcript_id "ENST00000361624"; transcript_version "2"; exon_number "1"; gene_name "MT-CO1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001435647"; exon_version "2"; tag "basic"; +chrM insdc CDS 5904 7442 . + 0 gene_id "ENSG00000198804"; gene_version "2"; transcript_id "ENST00000361624"; transcript_version "2"; exon_number "1"; gene_name "MT-CO1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354499"; protein_version "2"; tag "basic"; +chrM insdc start_codon 5904 5906 . + 0 gene_id "ENSG00000198804"; gene_version "2"; transcript_id "ENST00000361624"; transcript_version "2"; exon_number "1"; gene_name "MT-CO1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc stop_codon 7443 7445 . + 0 gene_id "ENSG00000198804"; gene_version "2"; transcript_id "ENST00000361624"; transcript_version "2"; exon_number "1"; gene_name "MT-CO1"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO1-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc gene 7446 7514 . - . gene_id "ENSG00000210151"; gene_version "2"; gene_name "MT-TS1"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 7446 7514 . - . gene_id "ENSG00000210151"; gene_version "2"; transcript_id "ENST00000387416"; transcript_version "2"; gene_name "MT-TS1"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TS1-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 7446 7514 . - . gene_id "ENSG00000210151"; gene_version "2"; transcript_id "ENST00000387416"; transcript_version "2"; exon_number "1"; gene_name "MT-TS1"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TS1-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544487"; exon_version "2"; tag "basic"; +chrM insdc gene 7518 7585 . + . gene_id "ENSG00000210154"; gene_version "1"; gene_name "MT-TD"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 7518 7585 . + . gene_id "ENSG00000210154"; gene_version "1"; transcript_id "ENST00000387419"; transcript_version "1"; gene_name "MT-TD"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TD-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 7518 7585 . + . gene_id "ENSG00000210154"; gene_version "1"; transcript_id "ENST00000387419"; transcript_version "1"; exon_number "1"; gene_name "MT-TD"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TD-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544486"; exon_version "1"; tag "basic"; +chrM insdc gene 7586 8269 . + . gene_id "ENSG00000198712"; gene_version "1"; gene_name "MT-CO2"; gene_source "insdc"; gene_biotype "protein_coding"; +chrM insdc transcript 7586 8269 . + . gene_id "ENSG00000198712"; gene_version "1"; transcript_id "ENST00000361739"; transcript_version "1"; gene_name "MT-CO2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc exon 7586 8269 . + . gene_id "ENSG00000198712"; gene_version "1"; transcript_id "ENST00000361739"; transcript_version "1"; exon_number "1"; gene_name "MT-CO2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001435613"; exon_version "1"; tag "basic"; +chrM insdc CDS 7586 8266 . + 0 gene_id "ENSG00000198712"; gene_version "1"; transcript_id "ENST00000361739"; transcript_version "1"; exon_number "1"; gene_name "MT-CO2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354876"; protein_version "1"; tag "basic"; +chrM insdc start_codon 7586 7588 . + 0 gene_id "ENSG00000198712"; gene_version "1"; transcript_id "ENST00000361739"; transcript_version "1"; exon_number "1"; gene_name "MT-CO2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc stop_codon 8267 8269 . + 0 gene_id "ENSG00000198712"; gene_version "1"; transcript_id "ENST00000361739"; transcript_version "1"; exon_number "1"; gene_name "MT-CO2"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO2-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc gene 8295 8364 . + . gene_id "ENSG00000210156"; gene_version "1"; gene_name "MT-TK"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 8295 8364 . + . gene_id "ENSG00000210156"; gene_version "1"; transcript_id "ENST00000387421"; transcript_version "1"; gene_name "MT-TK"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TK-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 8295 8364 . + . gene_id "ENSG00000210156"; gene_version "1"; transcript_id "ENST00000387421"; transcript_version "1"; exon_number "1"; gene_name "MT-TK"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TK-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544484"; exon_version "1"; tag "basic"; +chrM insdc gene 8366 8572 . + . gene_id "ENSG00000228253"; gene_version "1"; gene_name "MT-ATP8"; gene_source "insdc"; gene_biotype "protein_coding"; +chrM insdc transcript 8366 8572 . + . gene_id "ENSG00000228253"; gene_version "1"; transcript_id "ENST00000361851"; transcript_version "1"; gene_name "MT-ATP8"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP8-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc exon 8366 8572 . + . gene_id "ENSG00000228253"; gene_version "1"; transcript_id "ENST00000361851"; transcript_version "1"; exon_number "1"; gene_name "MT-ATP8"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP8-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001435286"; exon_version "1"; tag "basic"; +chrM insdc CDS 8366 8569 . + 0 gene_id "ENSG00000228253"; gene_version "1"; transcript_id "ENST00000361851"; transcript_version "1"; exon_number "1"; gene_name "MT-ATP8"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP8-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000355265"; protein_version "1"; tag "basic"; +chrM insdc start_codon 8366 8368 . + 0 gene_id "ENSG00000228253"; gene_version "1"; transcript_id "ENST00000361851"; transcript_version "1"; exon_number "1"; gene_name "MT-ATP8"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP8-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc stop_codon 8570 8572 . + 0 gene_id "ENSG00000228253"; gene_version "1"; transcript_id "ENST00000361851"; transcript_version "1"; exon_number "1"; gene_name "MT-ATP8"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP8-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc gene 8527 9207 . + . gene_id "ENSG00000198899"; gene_version "2"; gene_name "MT-ATP6"; gene_source "insdc"; gene_biotype "protein_coding"; +chrM insdc transcript 8527 9207 . + . gene_id "ENSG00000198899"; gene_version "2"; transcript_id "ENST00000361899"; transcript_version "2"; gene_name "MT-ATP6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc exon 8527 9207 . + . gene_id "ENSG00000198899"; gene_version "2"; transcript_id "ENST00000361899"; transcript_version "2"; exon_number "1"; gene_name "MT-ATP6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001727012"; exon_version "2"; tag "basic"; +chrM insdc CDS 8527 9204 . + 0 gene_id "ENSG00000198899"; gene_version "2"; transcript_id "ENST00000361899"; transcript_version "2"; exon_number "1"; gene_name "MT-ATP6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354632"; protein_version "2"; tag "basic"; +chrM insdc start_codon 8527 8529 . + 0 gene_id "ENSG00000198899"; gene_version "2"; transcript_id "ENST00000361899"; transcript_version "2"; exon_number "1"; gene_name "MT-ATP6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc stop_codon 9205 9207 . + 0 gene_id "ENSG00000198899"; gene_version "2"; transcript_id "ENST00000361899"; transcript_version "2"; exon_number "1"; gene_name "MT-ATP6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ATP6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc gene 9207 9990 . + . gene_id "ENSG00000198938"; gene_version "2"; gene_name "MT-CO3"; gene_source "insdc"; gene_biotype "protein_coding"; +chrM insdc transcript 9207 9990 . + . gene_id "ENSG00000198938"; gene_version "2"; transcript_id "ENST00000362079"; transcript_version "2"; gene_name "MT-CO3"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO3-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc exon 9207 9990 . + . gene_id "ENSG00000198938"; gene_version "2"; transcript_id "ENST00000362079"; transcript_version "2"; exon_number "1"; gene_name "MT-CO3"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO3-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001608952"; exon_version "2"; tag "basic"; +chrM insdc CDS 9207 9990 . + 0 gene_id "ENSG00000198938"; gene_version "2"; transcript_id "ENST00000362079"; transcript_version "2"; exon_number "1"; gene_name "MT-CO3"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO3-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354982"; protein_version "2"; tag "basic"; +chrM insdc start_codon 9207 9209 . + 0 gene_id "ENSG00000198938"; gene_version "2"; transcript_id "ENST00000362079"; transcript_version "2"; exon_number "1"; gene_name "MT-CO3"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CO3-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc gene 9991 10058 . + . gene_id "ENSG00000210164"; gene_version "1"; gene_name "MT-TG"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 9991 10058 . + . gene_id "ENSG00000210164"; gene_version "1"; transcript_id "ENST00000387429"; transcript_version "1"; gene_name "MT-TG"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TG-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 9991 10058 . + . gene_id "ENSG00000210164"; gene_version "1"; transcript_id "ENST00000387429"; transcript_version "1"; exon_number "1"; gene_name "MT-TG"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TG-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544483"; exon_version "1"; tag "basic"; +chrM insdc gene 10059 10404 . + . gene_id "ENSG00000198840"; gene_version "2"; gene_name "MT-ND3"; gene_source "insdc"; gene_biotype "protein_coding"; +chrM insdc transcript 10059 10404 . + . gene_id "ENSG00000198840"; gene_version "2"; transcript_id "ENST00000361227"; transcript_version "2"; gene_name "MT-ND3"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND3-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc exon 10059 10404 . + . gene_id "ENSG00000198840"; gene_version "2"; transcript_id "ENST00000361227"; transcript_version "2"; exon_number "1"; gene_name "MT-ND3"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND3-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001435444"; exon_version "2"; tag "basic"; +chrM insdc CDS 10059 10404 . + 0 gene_id "ENSG00000198840"; gene_version "2"; transcript_id "ENST00000361227"; transcript_version "2"; exon_number "1"; gene_name "MT-ND3"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND3-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000355206"; protein_version "2"; tag "basic"; +chrM insdc start_codon 10059 10061 . + 0 gene_id "ENSG00000198840"; gene_version "2"; transcript_id "ENST00000361227"; transcript_version "2"; exon_number "1"; gene_name "MT-ND3"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND3-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc gene 10405 10469 . + . gene_id "ENSG00000210174"; gene_version "1"; gene_name "MT-TR"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 10405 10469 . + . gene_id "ENSG00000210174"; gene_version "1"; transcript_id "ENST00000387439"; transcript_version "1"; gene_name "MT-TR"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TR-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 10405 10469 . + . gene_id "ENSG00000210174"; gene_version "1"; transcript_id "ENST00000387439"; transcript_version "1"; exon_number "1"; gene_name "MT-TR"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TR-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544482"; exon_version "1"; tag "basic"; +chrM insdc gene 10470 10766 . + . gene_id "ENSG00000212907"; gene_version "2"; gene_name "MT-ND4L"; gene_source "insdc"; gene_biotype "protein_coding"; +chrM insdc transcript 10470 10766 . + . gene_id "ENSG00000212907"; gene_version "2"; transcript_id "ENST00000361335"; transcript_version "1"; gene_name "MT-ND4L"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4L-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc exon 10470 10766 . + . gene_id "ENSG00000212907"; gene_version "2"; transcript_id "ENST00000361335"; transcript_version "1"; exon_number "1"; gene_name "MT-ND4L"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4L-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001596097"; exon_version "1"; tag "basic"; +chrM insdc CDS 10470 10763 . + 0 gene_id "ENSG00000212907"; gene_version "2"; transcript_id "ENST00000361335"; transcript_version "1"; exon_number "1"; gene_name "MT-ND4L"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4L-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354728"; protein_version "1"; tag "basic"; +chrM insdc start_codon 10470 10472 . + 0 gene_id "ENSG00000212907"; gene_version "2"; transcript_id "ENST00000361335"; transcript_version "1"; exon_number "1"; gene_name "MT-ND4L"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4L-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc stop_codon 10764 10766 . + 0 gene_id "ENSG00000212907"; gene_version "2"; transcript_id "ENST00000361335"; transcript_version "1"; exon_number "1"; gene_name "MT-ND4L"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4L-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc gene 10760 12137 . + . gene_id "ENSG00000198886"; gene_version "2"; gene_name "MT-ND4"; gene_source "insdc"; gene_biotype "protein_coding"; +chrM insdc transcript 10760 12137 . + . gene_id "ENSG00000198886"; gene_version "2"; transcript_id "ENST00000361381"; transcript_version "2"; gene_name "MT-ND4"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc exon 10760 12137 . + . gene_id "ENSG00000198886"; gene_version "2"; transcript_id "ENST00000361381"; transcript_version "2"; exon_number "1"; gene_name "MT-ND4"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001666004"; exon_version "2"; tag "basic"; +chrM insdc CDS 10760 12137 . + 0 gene_id "ENSG00000198886"; gene_version "2"; transcript_id "ENST00000361381"; transcript_version "2"; exon_number "1"; gene_name "MT-ND4"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354961"; protein_version "2"; tag "basic"; +chrM insdc start_codon 10760 10762 . + 0 gene_id "ENSG00000198886"; gene_version "2"; transcript_id "ENST00000361381"; transcript_version "2"; exon_number "1"; gene_name "MT-ND4"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND4-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc gene 12138 12206 . + . gene_id "ENSG00000210176"; gene_version "1"; gene_name "MT-TH"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 12138 12206 . + . gene_id "ENSG00000210176"; gene_version "1"; transcript_id "ENST00000387441"; transcript_version "1"; gene_name "MT-TH"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TH-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 12138 12206 . + . gene_id "ENSG00000210176"; gene_version "1"; transcript_id "ENST00000387441"; transcript_version "1"; exon_number "1"; gene_name "MT-TH"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TH-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544480"; exon_version "1"; tag "basic"; +chrM insdc gene 12207 12265 . + . gene_id "ENSG00000210184"; gene_version "1"; gene_name "MT-TS2"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 12207 12265 . + . gene_id "ENSG00000210184"; gene_version "1"; transcript_id "ENST00000387449"; transcript_version "1"; gene_name "MT-TS2"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TS2-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 12207 12265 . + . gene_id "ENSG00000210184"; gene_version "1"; transcript_id "ENST00000387449"; transcript_version "1"; exon_number "1"; gene_name "MT-TS2"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TS2-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544479"; exon_version "1"; tag "basic"; +chrM insdc gene 12266 12336 . + . gene_id "ENSG00000210191"; gene_version "1"; gene_name "MT-TL2"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 12266 12336 . + . gene_id "ENSG00000210191"; gene_version "1"; transcript_id "ENST00000387456"; transcript_version "1"; gene_name "MT-TL2"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TL2-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 12266 12336 . + . gene_id "ENSG00000210191"; gene_version "1"; transcript_id "ENST00000387456"; transcript_version "1"; exon_number "1"; gene_name "MT-TL2"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TL2-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544478"; exon_version "1"; tag "basic"; +chrM insdc gene 12337 14148 . + . gene_id "ENSG00000198786"; gene_version "2"; gene_name "MT-ND5"; gene_source "insdc"; gene_biotype "protein_coding"; +chrM insdc transcript 12337 14148 . + . gene_id "ENSG00000198786"; gene_version "2"; transcript_id "ENST00000361567"; transcript_version "2"; gene_name "MT-ND5"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND5-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc exon 12337 14148 . + . gene_id "ENSG00000198786"; gene_version "2"; transcript_id "ENST00000361567"; transcript_version "2"; exon_number "1"; gene_name "MT-ND5"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND5-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001435330"; exon_version "2"; tag "basic"; +chrM insdc CDS 12337 14145 . + 0 gene_id "ENSG00000198786"; gene_version "2"; transcript_id "ENST00000361567"; transcript_version "2"; exon_number "1"; gene_name "MT-ND5"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND5-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354813"; protein_version "2"; tag "basic"; +chrM insdc start_codon 12337 12339 . + 0 gene_id "ENSG00000198786"; gene_version "2"; transcript_id "ENST00000361567"; transcript_version "2"; exon_number "1"; gene_name "MT-ND5"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND5-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc stop_codon 14146 14148 . + 0 gene_id "ENSG00000198786"; gene_version "2"; transcript_id "ENST00000361567"; transcript_version "2"; exon_number "1"; gene_name "MT-ND5"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND5-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc gene 14149 14673 . - . gene_id "ENSG00000198695"; gene_version "2"; gene_name "MT-ND6"; gene_source "insdc"; gene_biotype "protein_coding"; +chrM insdc transcript 14149 14673 . - . gene_id "ENSG00000198695"; gene_version "2"; transcript_id "ENST00000361681"; transcript_version "2"; gene_name "MT-ND6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc exon 14149 14673 . - . gene_id "ENSG00000198695"; gene_version "2"; transcript_id "ENST00000361681"; transcript_version "2"; exon_number "1"; gene_name "MT-ND6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001434974"; exon_version "2"; tag "basic"; +chrM insdc CDS 14152 14673 . - 0 gene_id "ENSG00000198695"; gene_version "2"; transcript_id "ENST00000361681"; transcript_version "2"; exon_number "1"; gene_name "MT-ND6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354665"; protein_version "2"; tag "basic"; +chrM insdc start_codon 14671 14673 . - 0 gene_id "ENSG00000198695"; gene_version "2"; transcript_id "ENST00000361681"; transcript_version "2"; exon_number "1"; gene_name "MT-ND6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc stop_codon 14149 14151 . - 0 gene_id "ENSG00000198695"; gene_version "2"; transcript_id "ENST00000361681"; transcript_version "2"; exon_number "1"; gene_name "MT-ND6"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-ND6-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc gene 14674 14742 . - . gene_id "ENSG00000210194"; gene_version "1"; gene_name "MT-TE"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 14674 14742 . - . gene_id "ENSG00000210194"; gene_version "1"; transcript_id "ENST00000387459"; transcript_version "1"; gene_name "MT-TE"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TE-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 14674 14742 . - . gene_id "ENSG00000210194"; gene_version "1"; transcript_id "ENST00000387459"; transcript_version "1"; exon_number "1"; gene_name "MT-TE"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TE-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544476"; exon_version "1"; tag "basic"; +chrM insdc gene 14747 15887 . + . gene_id "ENSG00000198727"; gene_version "2"; gene_name "MT-CYB"; gene_source "insdc"; gene_biotype "protein_coding"; +chrM insdc transcript 14747 15887 . + . gene_id "ENSG00000198727"; gene_version "2"; transcript_id "ENST00000361789"; transcript_version "2"; gene_name "MT-CYB"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CYB-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc exon 14747 15887 . + . gene_id "ENSG00000198727"; gene_version "2"; transcript_id "ENST00000361789"; transcript_version "2"; exon_number "1"; gene_name "MT-CYB"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CYB-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; exon_id "ENSE00001436074"; exon_version "2"; tag "basic"; +chrM insdc CDS 14747 15887 . + 0 gene_id "ENSG00000198727"; gene_version "2"; transcript_id "ENST00000361789"; transcript_version "2"; exon_number "1"; gene_name "MT-CYB"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CYB-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; protein_id "ENSP00000354554"; protein_version "2"; tag "basic"; +chrM insdc start_codon 14747 14749 . + 0 gene_id "ENSG00000198727"; gene_version "2"; transcript_id "ENST00000361789"; transcript_version "2"; exon_number "1"; gene_name "MT-CYB"; gene_source "insdc"; gene_biotype "protein_coding"; transcript_name "MT-CYB-201"; transcript_source "insdc"; transcript_biotype "protein_coding"; tag "basic"; +chrM insdc gene 15888 15953 . + . gene_id "ENSG00000210195"; gene_version "2"; gene_name "MT-TT"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 15888 15953 . + . gene_id "ENSG00000210195"; gene_version "2"; transcript_id "ENST00000387460"; transcript_version "2"; gene_name "MT-TT"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TT-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 15888 15953 . + . gene_id "ENSG00000210195"; gene_version "2"; transcript_id "ENST00000387460"; transcript_version "2"; exon_number "1"; gene_name "MT-TT"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TT-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544475"; exon_version "2"; tag "basic"; +chrM insdc gene 15956 16023 . - . gene_id "ENSG00000210196"; gene_version "2"; gene_name "MT-TP"; gene_source "insdc"; gene_biotype "Mt_tRNA"; +chrM insdc transcript 15956 16023 . - . gene_id "ENSG00000210196"; gene_version "2"; transcript_id "ENST00000387461"; transcript_version "2"; gene_name "MT-TP"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TP-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; tag "basic"; +chrM insdc exon 15956 16023 . - . gene_id "ENSG00000210196"; gene_version "2"; transcript_id "ENST00000387461"; transcript_version "2"; exon_number "1"; gene_name "MT-TP"; gene_source "insdc"; gene_biotype "Mt_tRNA"; transcript_name "MT-TP-201"; transcript_source "insdc"; transcript_biotype "Mt_tRNA"; exon_id "ENSE00001544473"; exon_version "2"; tag "basic";
--- a/test-data/picard_CollectRnaSeqMetrics_test2.tab Tue Oct 16 11:49:10 2018 -0400 +++ b/test-data/picard_CollectRnaSeqMetrics_test2.tab Fri Mar 29 08:34:36 2019 -0400 @@ -1,10 +1,113 @@ ## htsjdk.samtools.metrics.StringHeader -# CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_34.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpYRm8q4/files/000/dataset_35.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false +# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/opt/galaxy/galaxy/database/files/033/dataset_33778.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/opt/galaxy/galaxy/database/files/033/dataset_33779.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json ## htsjdk.samtools.metrics.StringHeader -# Started on: Sat Apr 14 09:30:06 CEST 2018 +# Started on: Thu Jan 31 11:57:28 GMT 2019 ## METRICS CLASS picard.analysis.RnaSeqMetrics PF_BASES PF_ALIGNED_BASES RIBOSOMAL_BASES CODING_BASES UTR_BASES INTRONIC_BASES INTERGENIC_BASES IGNORED_READS CORRECT_STRAND_READS INCORRECT_STRAND_READS NUM_R1_TRANSCRIPT_STRAND_READS NUM_R2_TRANSCRIPT_STRAND_READS NUM_UNEXPLAINED_READS PCT_R1_TRANSCRIPT_STRAND_READS PCT_R2_TRANSCRIPT_STRAND_READS PCT_RIBOSOMAL_BASES PCT_CODING_BASES PCT_UTR_BASES PCT_INTRONIC_BASES PCT_INTERGENIC_BASES PCT_MRNA_BASES PCT_USABLE_BASES PCT_CORRECT_STRAND_READS MEDIAN_CV_COVERAGE MEDIAN_5PRIME_BIAS MEDIAN_3PRIME_BIAS MEDIAN_5PRIME_TO_3PRIME_BIAS SAMPLE LIBRARY READ_GROUP -48870 48712 0 0 0 48712 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 +48870 48712 40205 8172 0 335 0 0 0 118 141 5 0.455598 0.544402 0.825361 0.167762 0 0.006877 0.993123 0.989912 0 0.801606 0.364744 0.224119 0.579618 +## HISTOGRAM java.lang.Integer +normalized_position All_Reads.normalized_coverage +0 0.228841 +1 0.251223 +2 0.223738 +3 0.233838 +4 0.256581 +5 0.266966 +6 0.271332 +7 0.265645 +8 0.260346 +9 0.231289 +10 0.269298 +11 0.326408 +12 0.373618 +13 0.473463 +14 0.54793 +15 0.577498 +16 0.542569 +17 0.558467 +18 0.650338 +19 0.635229 +20 0.574853 +21 0.588563 +22 0.650078 +23 0.686162 +24 0.634014 +25 0.644335 +26 0.631052 +27 0.639668 +28 0.705101 +29 0.778048 +30 0.736876 +31 0.70567 +32 0.707551 +33 0.76318 +34 0.852513 +35 0.873038 +36 0.943469 +37 1.040668 +38 1.070803 +39 1.117516 +40 1.166565 +41 1.178104 +42 1.151426 +43 1.209844 +44 1.198299 +45 1.132792 +46 1.149512 +47 1.21306 +48 1.345953 +49 1.32854 +50 1.309067 +51 1.296104 +52 1.346535 +53 1.450902 +54 1.475516 +55 1.548883 +56 1.628424 +57 1.665228 +58 1.612393 +59 1.653451 +60 1.599084 +61 1.674705 +62 1.670767 +63 1.759351 +64 1.771555 +65 1.653379 +66 1.634736 +67 1.642939 +68 1.587437 +69 1.558905 +70 1.571999 +71 1.620224 +72 1.57181 +73 1.545141 +74 1.433348 +75 1.497304 +76 1.693651 +77 1.728257 +78 1.754671 +79 1.731652 +80 1.713865 +81 1.641332 +82 1.515711 +83 1.413569 +84 1.441502 +85 1.330984 +86 1.269559 +87 1.225153 +88 1.133803 +89 0.956795 +90 0.793511 +91 0.692324 +92 0.542889 +93 0.499087 +94 0.422605 +95 0.338219 +96 0.272388 +97 0.207126 +98 0.152439 +99 0.095696 +100 0.069183