gpertea / gffread

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

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Failure to convert gene and child CDSes to exons with parent mRNAs which are children of gene

hermidalc opened this issue · comments

https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/221/805/GCA_002221805.1_ViralProj14310/GCA_002221805.1_ViralProj14310_genomic.gff.gz

The following gene features fail to get converted to two mRNAs with child exons. I know this looks like a weird edge case, but it's an NCBI genome GFF, and maybe worth handling properly by gffread

AP005154.1	DDBJ	gene	42789	43484	.	-	.	ID=gene-cI;Name=cI;gbkey=Gene;gene=cI;gene_biotype=protein_coding
AP005154.1	DDBJ	CDS	42789	43484	.	-	0	ID=cds-BAC78103.1;Parent=gene-cI;Dbxref=NCBI_GP:BAC78103.1;Name=BAC78103.1;Note=ORF c64%3B~similar to phage lambda CI;gbkey=CDS;gene=cI;product=CI protein;protein_id=BAC78103.1;transl_table=11
AP005154.1	DDBJ	CDS	43109	43354	.	-	0	ID=cds-BAC78104.1;Parent=gene-cI;Dbxref=NCBI_GP:BAC78104.1;Name=BAC78104.1;Note=ORF c65;gbkey=CDS;gene=cI;product=hypothetical protein;protein_id=BAC78104.1;transl_table=11