gffutils

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Command-line interface for gffutils

7

What sort of functionality should be exposed to the CLI? For example a universal GTFGFFrefFlat conversion script would be useful.

daler

See http://www.biostars.org/p/64363/#64463

daler

Hi there, A breaking change in `argh` seems to have impacted `gffutils-cli` : https://argh.readthedocs.io/en/latest/changes.html#version-0-30-0-2023-10-21 ``` mamba create -y -p gffutils_cli_env2 'argh>=0.30.0' 'gffutils' conda run -p ./gffutils_cli_env2 gffutils-cli children symlinks/{gff_name}.db {transcript_id}...

photocyte

create_db() does not parse directives from GFF files starting in v0.11.0

3

I am trying to read in a GFF that doesn't adhere to spec so I can use `gffutils` to fix it and then write out a corrected file. I've gotten...

dtdoering

Field separators in quoted attributes cause error

4

Testing [this](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/009/045/GCF_000009045.1_ASM904v1/GCF_000009045.1_ASM904v1_genomic.gtf.gz) GTF file with gffutils and an AttributeStringError exception was raised on line 349, parser.py. After some exploration I noticed that lines containing attributes with ";" (field separator) in...

zwpwjwtz

I would like to work on this task

aqeelat

replace base split by regex split to fix ; inside quotes

2

This PR fixes https://github.com/daler/gffutils/issues/212 where semicolons inside quoted string values were causing issues. I was not able to replicate the `AttributeStringError` mentioned in the issue since the usage was not...

DevangThakkar

merge_strategy='create_unique' not always creating unique id's

2

The software [liftoff](https://github.com/agshumate/Liftoff) compares two assemblies of very closely related genomes, one of which has gene annotations, and the other does not. It then tries to find which regions in...

novigit

Map transcript coordinates to genome coordinates

3

I have the coordinates of domains mapped to transcripts so that the coordinates are relative to transcripts. Now I would like to transfer these transcript-coordinates to genome-coordinates. I wonder if...

dariober

I'm applying `db.parents(id)` to features that have up to 3 parents, e.g. the nesting is `id -> protein_match -> mRNA -> gene`. It appears that the 3rd level, gene, is...

dariober