gffutils
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daler
GFF and GTF file manipulation and interconversion
Hello Thank you very much for developing such useful tools. it is very fast. I need your help in getting introns. the following code gave 0 size intron somehow, the...
PR #152 resolved an [issue](https://github.com/daler/gffutils/pull/152#issuecomment-569561421) that came up while trying to handle calling merge_all() repeatedly. I attempted to create a criteria that would exclude children of a record created by...
Canonical transcripts was not functional with newer (>3.5) pythons and newer versions of the class feature (it assumes raw string representation of sequences, which is no longer the case) I've...
Fixes for contig/chromosome switching and overlapping features.
How to write out to file is not currently obvious (xref #37, #88). Having a class or function to handle this will help with discoverability and will be an obvious...
This is vital for full biopython record support. Even if it is just a matter of returning the file handle pointing after `##FASTA` for gffutils.Feature.sequence() to pick up. #99
This is not an issue, more a question. It takes some serious SQL-wrangling to get parent-child or grandparent-child information about gene-transcript-exon relationships. Have you thought about using a graph database...
A feature that I'd find very useful is parsing of gffutils GFF records into a (lightweight) Gene-like object. Something like: ``` # recs is a set of GFF records gene_obj...
add a mechanism for cleaning a database of features that have an annotated parent, but that parent does not exist.