From cc1ef35be6744b2517927ea61f9fb21360b5f576 Mon Sep 17 00:00:00 2001 From: jclaud01 <jean-baptiste.claude@ens-lyon.fr> Date: Mon, 12 Jun 2017 17:56:24 +0200 Subject: [PATCH] Add Parent and gene attribute for rsem-gff3-to-gtf compabilities --- annot/tiny_v2.gff | 4 ++- annot/tiny_v2.gtf | 68 +++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 71 insertions(+), 1 deletion(-) create mode 100644 annot/tiny_v2.gtf diff --git a/annot/tiny_v2.gff b/annot/tiny_v2.gff index 011aafc..0c5f393 100644 --- a/annot/tiny_v2.gff +++ b/annot/tiny_v2.gff @@ -105,5 +105,7 @@ NC_000001 GenBank exon 108617 108668 0 + 1 gene_id=exon000025;ID=exon000025;Dbxr NC_000001 GenBank CDS 96636 96791 0 + 1 gene_id=HHLA3.p03;ID=HHLA3.p03;Parent=HHLA3.t03;Dbxref=GI:81295798,CCDS:CCDS649.1,GeneID:11147,HGNC:HGNC:4906,MIM:604372;Name=HHLA3;Note=isoform 3 is encoded by transcript variant 3%3B Derived by automated computational analysis using gene prediction method: BestRefSeq.;codon_start=1;product=HERV-H LTR-associating protein 3 isoform 3;protein_id=NP_001031723.1;translation=length.76; NC_000001 GenBank CDS 108128 108202 0 + 1 gene_id=HHLA3.p03;ID=HHLA3.p03;Parent=HHLA3.t03;Dbxref=GI:81295798,CCDS:CCDS649.1,GeneID:11147,HGNC:HGNC:4906,MIM:604372;Name=HHLA3;Note=isoform 3 is encoded by transcript variant 3%3B Derived by automated computational analysis using gene prediction method: BestRefSeq.;codon_start=1;product=HERV-H LTR-associating protein 3 isoform 3;protein_id=NP_001031723.1;translation=length.76; NC_000001a GenBank chromosome 1 3001 0 + 1 gene_id=NC_000001a.chr;ID=NC_000001a.chr;Alias=1;Dbxref=BioProject:PRJNA168,taxon:9606;Name=NC_000001;Note=Homo sapiens chromosome 1%2C GRCh37.p13 Primary Assembly.,REFSEQ INFORMATION: The reference sequence is identical to CM000663.1. [WARNING] On Feb 3,2014 this sequence was replaced by NC_000001.11. On Jun 10,2009 this sequence version replaced NC_000001.9. Assembly Name: GRCh37.p13 Primary Assembly The DNA sequence is composed of genomic sequence,primarily finished clones that were sequenced as part of the Human Genome Project. PCR products and WGS shotgun sequence have been added where necessary to fill gaps or correct errors. All such additions are manually curated by GRC staff. For more information see: http://genomereference.org. ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Status :: Full annotation Annotation Version :: Homo sapiens Annotation Release 105 Annotation Pipeline :: NCBI eukaryotic genome annotation pipeline Annotation Software Version :: 5.1 Annotation Method :: Best-placed RefSeq,Gnomon Features Annotated :: Gene,mRNA,CDS,ncRNA ##Genome-Annotation-Data-END## ;chromosome=1;comment1=REFSEQ INFORMATION: The reference sequence is identical to CM000663.1. [WARNING] On Feb 3%2C 2014 this sequence was replaced by NC_000001.11. On Jun 10%2C 2009 this sequence version replaced NC_000001.9. Assembly Name: GRCh37.p13 Primary Assembly The DNA sequence is composed of genomic sequence%2C primarily finished clones that were sequenced as part of the Human Genome Project. PCR products and WGS shotgun sequence have been added where necessary to fill gaps or correct errors. All such additions are manually curated by GRC staff. For more information see: http://genomereference.org. ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Status :: Full annotation Annotation Version :: Homo sapiens Annotation Release 105 Annotation Pipeline :: NCBI eukaryotic genome annotation pipeline Annotation Software Version :: 5.1 Annotation Method :: Best-placed RefSeq%3B Gnomon Features Annotated :: Gene%3B mRNA%3B CDS%3B ncRNA ##Genome-Annotation-Data-END## ;date=13-AUG-2013;mol_type=genomic DNA;organism=Homo sapiens; -NC_000001a GenBank pseudogene 1418 2229 0 - 1 gene_id=PFN1P1;ID=PFN1P1;Dbxref=GeneID:730138,HGNC:HGNC:42989;Name=PFN1P1;Note=profilin 1 pseudogene 1%3B Derived by automated computational analysis using gene prediction method: Curated Genomic.;pseudo=_no_value; +NC_000001a GenBank CDS 1418 2229 0 - 1 gene_id=PFN1P1;Parent=PFN1P1;ID=PFN1P1;Dbxref=GeneID:730138,HGNC:HGNC:42989;Name=PFN1P1;Note=profilin 1 pseudogene 1%3B Derived by automated computational analysis using gene prediction method: Curated Genomic.;pseudo=_no_value; +NC_000001a GenBank gene 1418 2229 0 - 1 gene_id=PFN1P1;ID=PFN1P1;Dbxref=GeneID:730138,HGNC:HGNC:42989;Name=PFN1P1;Note=profilin 1 pseudogene 1%3B Derived by automated computational analysis using gene prediction method: Curated Genomic.;pseudo=_no_value; +NC_000001a GenBank pseudogene 1418 2229 0 - 1 gene_id=PFN1P1;Parent=PFN1P1;ID=PFN1P1;Dbxref=GeneID:730138,HGNC:HGNC:42989;Name=PFN1P1;Note=profilin 1 pseudogene 1%3B Derived by automated computational analysis using gene prediction method: Curated Genomic.;pseudo=_no_value; NC_000001a GenBank exon 1418 2229 0 - 1 gene_id=exon000026;Parent=PFN1P1;ID=exon000026;Dbxref=GeneID:730138,HGNC:HGNC:42989;Name=PFN1P1;Note=profilin 1 pseudogene 1%3B Derived by automated computational analysis using gene prediction method: Curated Genomic.;pseudo=_no_value; diff --git a/annot/tiny_v2.gtf b/annot/tiny_v2.gtf new file mode 100644 index 0000000..bb48f7a --- /dev/null +++ b/annot/tiny_v2.gtf @@ -0,0 +1,68 @@ +NC_000001 GenBank exon 686 4531 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t01"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 12540 12640 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t01"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 16404 16502 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t01"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 18449 18528 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t01"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 34072 34233 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t01"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 37814 37945 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t01"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 42448 42592 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t01"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 47908 47974 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t01"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 55429 55474 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t01"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 57165 57250 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t01"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 66537 66641 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t01"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 77742 77783 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t01"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 95663 96418 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t01"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 2272 4531 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t02"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 12540 12640 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t02"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 16404 16502 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t02"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 18449 18528 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t02"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 34072 34233 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t02"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 37814 37945 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t02"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 42448 42592 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t02"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 55429 55448 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t02"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 2276 4531 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t03"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 18449 18528 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t03"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 34072 34233 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t03"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 37814 37945 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t03"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 42448 42592 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t03"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 47908 47974 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t03"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 55429 55474 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t03"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 57165 57250 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t03"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 66537 66641 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t03"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 77742 77783 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t03"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 95663 96472 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t03"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 2276 4531 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t04"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 12540 12640 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t04"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 18449 18528 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t04"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 34072 34233 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t04"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 37814 37945 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t04"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 42448 42592 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t04"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 47908 47974 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t04"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 55429 55474 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t04"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 57165 57250 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t04"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 66537 66641 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t04"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 77742 77783 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t04"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 95663 96472 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t04"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 2276 4531 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t05"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 16404 16502 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t05"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 18449 18528 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t05"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 34072 34233 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t05"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 35188 35304 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t05"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 37814 37945 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t05"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 42448 42592 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t05"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 47908 47974 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t05"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 55429 55474 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t05"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 57165 57250 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t05"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 66537 66641 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t05"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 77742 77783 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t05"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 95663 96472 . - . gene_id "ANKRD13C"; transcript_id "ANKRD13C.t05"; gene_name "ANKRD13C"; transcript_name "ANKRD13C"; +NC_000001 GenBank exon 96494 96892 . + . gene_id "HHLA3"; transcript_id "HHLA3.t01"; gene_name "HHLA3"; transcript_name "HHLA3"; +NC_000001 GenBank exon 108128 108221 . + . gene_id "HHLA3"; transcript_id "HHLA3.t01"; gene_name "HHLA3"; transcript_name "HHLA3"; +NC_000001 GenBank exon 109301 109707 . + . gene_id "HHLA3"; transcript_id "HHLA3.t01"; gene_name "HHLA3"; transcript_name "HHLA3"; +NC_000001 GenBank exon 96494 96795 . + . gene_id "HHLA3"; transcript_id "HHLA3.t02"; gene_name "HHLA3"; transcript_name "HHLA3"; +NC_000001 GenBank exon 108128 108221 . + . gene_id "HHLA3"; transcript_id "HHLA3.t02"; gene_name "HHLA3"; transcript_name "HHLA3"; +NC_000001 GenBank exon 108617 108668 . + . gene_id "HHLA3"; transcript_id "HHLA3.t02"; gene_name "HHLA3"; transcript_name "HHLA3"; +NC_000001 GenBank exon 109301 109707 . + . gene_id "HHLA3"; transcript_id "HHLA3.t02"; gene_name "HHLA3"; transcript_name "HHLA3"; +NC_000001 GenBank exon 96494 96791 . + . gene_id "HHLA3"; transcript_id "HHLA3.t03"; gene_name "HHLA3"; transcript_name "HHLA3"; +NC_000001 GenBank exon 108128 108221 . + . gene_id "HHLA3"; transcript_id "HHLA3.t03"; gene_name "HHLA3"; transcript_name "HHLA3"; +NC_000001 GenBank exon 109301 109707 . + . gene_id "HHLA3"; transcript_id "HHLA3.t03"; gene_name "HHLA3"; transcript_name "HHLA3"; +NC_000001a GenBank exon 1418 2229 . - . gene_id "PFN1P1"; transcript_id "PFN1P1"; gene_name "PFN1P1"; transcript_name "PFN1P1"; -- GitLab