Mercurial > repos > vipints > fml_gff3togtf
diff test-data/gencode_ens_hav.gtf @ 9:7d67331368f3
fixing the new version upload manually
| author | vipints <vipin@cbio.mskcc.org> |
|---|---|
| date | Thu, 23 Apr 2015 17:57:49 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gencode_ens_hav.gtf Thu Apr 23 17:57:49 2015 -0400 @@ -0,0 +1,50 @@ +1 HAVANA gene 69091 70008 . + . gene_id "ENSG00000186092.4"; transcript_id "ENSG00000186092.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5"; level 2; havana_gene "OTTHUMG00000001094.1"; +1 HAVANA transcript 69091 70008 . + . gene_id "ENSG00000186092.4"; transcript_id "ENST00000335137.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.1"; havana_transcript "OTTHUMT00000003223.1"; +1 HAVANA exon 69091 70008 . + . gene_id "ENSG00000186092.4"; transcript_id "ENST00000335137.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5-001"; exon_number 1; exon_id "ENSE00002319515.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.1"; havana_transcript "OTTHUMT00000003223.1"; +1 HAVANA CDS 69091 70005 . + 0 gene_id "ENSG00000186092.4"; transcript_id "ENST00000335137.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5-001"; exon_number 1; exon_id "ENSE00002319515.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.1"; havana_transcript "OTTHUMT00000003223.1"; +1 HAVANA start_codon 69091 69093 . + 0 gene_id "ENSG00000186092.4"; transcript_id "ENST00000335137.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5-001"; exon_number 1; exon_id "ENSE00002319515.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.1"; havana_transcript "OTTHUMT00000003223.1"; +1 HAVANA stop_codon 70006 70008 . + 0 gene_id "ENSG00000186092.4"; transcript_id "ENST00000335137.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5-001"; exon_number 1; exon_id "ENSE00002319515.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.1"; havana_transcript "OTTHUMT00000003223.1"; +1 HAVANA UTR 70006 70008 . + . gene_id "ENSG00000186092.4"; transcript_id "ENST00000335137.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.1"; havana_transcript "OTTHUMT00000003223.1"; +1 ENSEMBL gene 134901 139379 . - . gene_id "ENSG00000237683.5"; transcript_id "ENSG00000237683.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1"; level 3; +1 ENSEMBL transcript 134901 139379 . - . gene_id "ENSG00000237683.5"; transcript_id "ENST00000423372.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1-201"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL exon 137621 139379 . - . gene_id "ENSG00000237683.5"; transcript_id "ENST00000423372.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1-201"; exon_number 1; exon_id "ENSE00002221580.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL CDS 138533 139309 . - 0 gene_id "ENSG00000237683.5"; transcript_id "ENST00000423372.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1-201"; exon_number 1; exon_id "ENSE00002221580.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL stop_codon 138530 138532 . - 0 gene_id "ENSG00000237683.5"; transcript_id "ENST00000423372.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1-201"; exon_number 1; exon_id "ENSE00002221580.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL exon 134901 135802 . - . gene_id "ENSG00000237683.5"; transcript_id "ENST00000423372.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1-201"; exon_number 2; exon_id "ENSE00002314092.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL UTR 137621 138532 . - . gene_id "ENSG00000237683.5"; transcript_id "ENST00000423372.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1-201"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL UTR 139310 139379 . - . gene_id "ENSG00000237683.5"; transcript_id "ENST00000423372.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1-201"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL UTR 134901 135802 . - . gene_id "ENSG00000237683.5"; transcript_id "ENST00000423372.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1-201"; level 3; tag "basic"; tag "appris_principal"; +1 HAVANA gene 367640 368634 . + . gene_id "ENSG00000235249.1"; transcript_id "ENSG00000235249.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F29"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F29"; level 2; havana_gene "OTTHUMG00000002860.1"; +1 HAVANA transcript 367640 368634 . + . gene_id "ENSG00000235249.1"; transcript_id "ENST00000426406.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F29"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F29-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS41220.1"; havana_gene "OTTHUMG00000002860.1"; havana_transcript "OTTHUMT00000007999.1"; +1 HAVANA exon 367640 368634 . + . gene_id "ENSG00000235249.1"; transcript_id "ENST00000426406.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F29"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F29-001"; exon_number 1; exon_id "ENSE00002316283.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS41220.1"; havana_gene "OTTHUMG00000002860.1"; havana_transcript "OTTHUMT00000007999.1"; +1 HAVANA CDS 367659 368594 . + 0 gene_id "ENSG00000235249.1"; transcript_id "ENST00000426406.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F29"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F29-001"; exon_number 1; exon_id "ENSE00002316283.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS41220.1"; havana_gene "OTTHUMG00000002860.1"; havana_transcript "OTTHUMT00000007999.1"; +1 HAVANA start_codon 367659 367661 . + 0 gene_id "ENSG00000235249.1"; transcript_id "ENST00000426406.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F29"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F29-001"; exon_number 1; exon_id "ENSE00002316283.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS41220.1"; havana_gene "OTTHUMG00000002860.1"; havana_transcript "OTTHUMT00000007999.1"; +1 HAVANA stop_codon 368595 368597 . + 0 gene_id "ENSG00000235249.1"; transcript_id "ENST00000426406.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F29"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F29-001"; exon_number 1; exon_id "ENSE00002316283.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS41220.1"; havana_gene "OTTHUMG00000002860.1"; havana_transcript "OTTHUMT00000007999.1"; +1 HAVANA UTR 367640 367658 . + . gene_id "ENSG00000235249.1"; transcript_id "ENST00000426406.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F29"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F29-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS41220.1"; havana_gene "OTTHUMG00000002860.1"; havana_transcript "OTTHUMT00000007999.1"; +1 HAVANA UTR 368595 368634 . + . gene_id "ENSG00000235249.1"; transcript_id "ENST00000426406.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F29"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F29-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS41220.1"; havana_gene "OTTHUMG00000002860.1"; havana_transcript "OTTHUMT00000007999.1"; +1 HAVANA gene 621059 622053 . - . gene_id "ENSG00000185097.2"; transcript_id "ENSG00000185097.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F16"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F16"; level 2; havana_gene "OTTHUMG00000002581.1"; +1 HAVANA transcript 621059 622053 . - . gene_id "ENSG00000185097.2"; transcript_id "ENST00000332831.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F16"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F16-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS41221.1"; havana_gene "OTTHUMG00000002581.1"; havana_transcript "OTTHUMT00000007334.1"; +1 HAVANA exon 621059 622053 . - . gene_id "ENSG00000185097.2"; transcript_id "ENST00000332831.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F16"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F16-001"; exon_number 1; exon_id "ENSE00002324228.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS41221.1"; havana_gene "OTTHUMG00000002581.1"; havana_transcript "OTTHUMT00000007334.1"; +1 HAVANA CDS 621099 622034 . - 0 gene_id "ENSG00000185097.2"; transcript_id "ENST00000332831.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F16"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F16-001"; exon_number 1; exon_id "ENSE00002324228.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS41221.1"; havana_gene "OTTHUMG00000002581.1"; havana_transcript "OTTHUMT00000007334.1"; +1 HAVANA start_codon 622032 622034 . - 0 gene_id "ENSG00000185097.2"; transcript_id "ENST00000332831.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F16"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F16-001"; exon_number 1; exon_id "ENSE00002324228.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS41221.1"; havana_gene "OTTHUMG00000002581.1"; havana_transcript "OTTHUMT00000007334.1"; +1 HAVANA stop_codon 621096 621098 . - 0 gene_id "ENSG00000185097.2"; transcript_id "ENST00000332831.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F16"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F16-001"; exon_number 1; exon_id "ENSE00002324228.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS41221.1"; havana_gene "OTTHUMG00000002581.1"; havana_transcript "OTTHUMT00000007334.1"; +1 HAVANA UTR 621059 621098 . - . gene_id "ENSG00000185097.2"; transcript_id "ENST00000332831.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F16"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F16-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS41221.1"; havana_gene "OTTHUMG00000002581.1"; havana_transcript "OTTHUMT00000007334.1"; +1 HAVANA UTR 622035 622053 . - . gene_id "ENSG00000185097.2"; transcript_id "ENST00000332831.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F16"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F16-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS41221.1"; havana_gene "OTTHUMG00000002581.1"; havana_transcript "OTTHUMT00000007334.1"; +1 ENSEMBL gene 738532 739137 . - . gene_id "ENSG00000269831.1"; transcript_id "ENSG00000269831.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL669831.1"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL669831.1"; level 3; +1 ENSEMBL transcript 738532 739137 . - . gene_id "ENSG00000269831.1"; transcript_id "ENST00000599533.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL669831.1"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL669831.1-201"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL exon 739121 739137 . - . gene_id "ENSG00000269831.1"; transcript_id "ENST00000599533.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL669831.1"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL669831.1-201"; exon_number 1; exon_id "ENSE00003063549.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL CDS 739121 739137 . - 0 gene_id "ENSG00000269831.1"; transcript_id "ENST00000599533.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL669831.1"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL669831.1-201"; exon_number 1; exon_id "ENSE00003063549.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL exon 738788 738812 . - . gene_id "ENSG00000269831.1"; transcript_id "ENST00000599533.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL669831.1"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL669831.1-201"; exon_number 2; exon_id "ENSE00003084653.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL CDS 738788 738812 . - 1 gene_id "ENSG00000269831.1"; transcript_id "ENST00000599533.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL669831.1"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL669831.1-201"; exon_number 2; exon_id "ENSE00003084653.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL exon 738532 738618 . - . gene_id "ENSG00000269831.1"; transcript_id "ENST00000599533.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL669831.1"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL669831.1-201"; exon_number 3; exon_id "ENSE00003138540.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL CDS 738532 738618 . - 0 gene_id "ENSG00000269831.1"; transcript_id "ENST00000599533.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL669831.1"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL669831.1-201"; exon_number 3; exon_id "ENSE00003138540.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL gene 818043 819983 . + . gene_id "ENSG00000269308.1"; transcript_id "ENSG00000269308.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL645608.2"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL645608.2"; level 3; +1 ENSEMBL transcript 818043 819983 . + . gene_id "ENSG00000269308.1"; transcript_id "ENST00000594233.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL645608.2"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL645608.2-201"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL exon 818043 818058 . + . gene_id "ENSG00000269308.1"; transcript_id "ENST00000594233.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL645608.2"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL645608.2-201"; exon_number 1; exon_id "ENSE00003079649.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL CDS 818043 818058 . + 0 gene_id "ENSG00000269308.1"; transcript_id "ENST00000594233.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL645608.2"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL645608.2-201"; exon_number 1; exon_id "ENSE00003079649.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL exon 819496 819513 . + . gene_id "ENSG00000269308.1"; transcript_id "ENST00000594233.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL645608.2"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL645608.2-201"; exon_number 2; exon_id "ENSE00003048391.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL CDS 819496 819513 . + 2 gene_id "ENSG00000269308.1"; transcript_id "ENST00000594233.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL645608.2"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL645608.2-201"; exon_number 2; exon_id "ENSE00003048391.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL exon 819961 819983 . + . gene_id "ENSG00000269308.1"; transcript_id "ENST00000594233.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL645608.2"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL645608.2-201"; exon_number 3; exon_id "ENSE00003055565.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL CDS 819961 819980 . + 2 gene_id "ENSG00000269308.1"; transcript_id "ENST00000594233.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL645608.2"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL645608.2-201"; exon_number 3; exon_id "ENSE00003055565.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL stop_codon 819981 819983 . + 0 gene_id "ENSG00000269308.1"; transcript_id "ENST00000594233.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL645608.2"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL645608.2-201"; exon_number 3; exon_id "ENSE00003055565.1"; level 3; tag "basic"; tag "appris_principal"; +1 ENSEMBL UTR 819981 819983 . + . gene_id "ENSG00000269308.1"; transcript_id "ENST00000594233.1"; gene_type "protein_coding"; gene_status "NOVEL"; gene_name "AL645608.2"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "AL645608.2-201"; level 3; tag "basic"; tag "appris_principal";