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gamcil / clinker

Gene cluster comparison figure generator
MIT License
507 stars 66 forks source link

docs on gff+fasta #86

Open nick-youngblut opened 2 years ago

nick-youngblut commented 2 years ago

I read the README, and it appeared that genbank files were the only supported format for input, but I see in the issues (e.g., https://github.com/gamcil/clinker/issues/10) that fasta + gff is supported. It would help to add info to the README about the fasta + gff feature

arghya1611 commented 1 year ago

I second Nick here. The tool looks promising but the Readme is quite poor/outdated. The help message has also not been updated. The issue of parsing fails when no CDS is reported for a particular contig also still remains as mentioned in issue #10 (ValueError: Found no CDS features in NODE_29_length_767_cov_1.376562 [rhodo-clean.gff])

I would really like the tool, but some support here is appreciated

gamcil commented 1 year ago

Sorry about the delay. Have added a note to the readme about GFF support, also added a fix as of 0.0.25 so it shouldn't crash when no CDS features are found parsing GFF records (#10). Have also updated the help in the README, a note about tool scope and some description of the gene function group functionality. Any other suggestions for improvements to the README @arghya1611 ?