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RacconC / gtftools

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if no gene_name in gtf #4

Closed ScienceAdvances closed 1 year ago

ScienceAdvances commented 1 year ago

if no gene_name in gtf

In recent release of Homo_sapiens.GRCh38.109.gtf, there is no "gene_name" in some lines. If I use "gtftools --gene gene Homo_sapiens.GRCh38.109.gtf" , it will throw an error.

File "/APP/mambaforge/envs/p2/lib/python2.7/site-packages/gtftools/gtftools.py", line 267, in get_gene_bed
    symbol = line.split('gene_name')[1].split('"')[1].upper()
IndexError: list index out of range)
For example:
1 havana gene 5301928 5307394 . - . gene_id "ENSG00000284616"; gene_version "1"; gene_source "havana"; gene_biotype "lncRNA";
1 havana transcript 5301928 5307394 . - . gene_id "ENSG00000284616"; gene_version "1"; transcript_id "ENST00000641871"; transcript_version "1"; gene_source "havana"; gene_biotype "lncRNA"; transcript_source "havana"; transcript_biotype "lncRNA"; tag "basic"; tag "Ensembl_canonical";
1 havana exon 5306942 5307394 . - . gene_id "ENSG00000284616"; gene_version "1"; transcript_id "ENST00000641871"; transcript_version "1"; exon_number "1"; gene_source "havana"; gene_biotype "lncRNA"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00003812690"; exon_version "1"; tag "basic"; tag "Ensembl_canonical";