Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

convert_metagenemark_gff_to_gff3.py produces invalid GFF3 #33

Closed
jonathancrabtree opened this issue Mar 23, 2015 · 1 comment
Closed

Comments

@jonathancrabtree
Copy link
Contributor

convert_metagenemark_gff_to_gff3.py echoes comment lines from MetaGeneMark unchanged. This is a problem when the comment is "##FASTA" (i.e., as part of a predicted polypeptide) GFF3 parsers are required to interpret such a line as the beginning of the GFF3 FASTA sequence section. One possible solution would be to tack on an extra "#" before echoing the comments. The situation is exacerbated by the fact that the current Biocode GFF3 parser will accept any line starting with "##FASTA" (e.g., "##FASTATKAANICDYENLAFMG") as the FASTA section delimiter (issue #32).

@jorvis jorvis closed this as completed in 38e612d Mar 23, 2015
@jorvis
Copy link
Owner

jorvis commented Mar 23, 2015

I think your proposal was a reasonable one. I committed 38e612d for this. Here, I didn't see the harm in prefixing anything starting with ##FASTA so that other parsers don't have the same issue.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants