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Complete genomes can be 'complete' or 'chromosome'

See original GitHub issue

We have a problem with bacterial genomes that sometimes the assembly_summary.txt file says complete and sometimes it says chromosome for finished bacterial genomes.

This is partially to do with the fact that bacteria usually only have 1 chromosome, but partially because they have plasmids too. It’s confusing.

If I want both, can I do -l complete -l chromosome to get both? Or so I run 2 commands with same -o folder?

Issue Analytics

  • State:closed
  • Created 7 years ago
  • Comments:7 (5 by maintainers)

github_iconTop GitHub Comments

tseemanncommented, Sep 11, 2016

I am thinking if --assembly-level or --format contain a “comma” , character then you could convert into a regexp and match using regexps in your filtering logic.

For example --format genbank,fasta,wgs would become ^(genbank|fasta|wgs)$

And --format protein-cds would just be ^(protein-cds)$ etc

I’ve used this method in my tools before and it works well. You could also use a hash/dict lookup by creating a want_format[ xxx ] = True/False system instead of regexp. This method also has the advantage that if you preset all the valid options to False then you can validate input easily.

kblincommented, Sep 10, 2016

I will add this to the documentation. I’m just beginning to think that the features are outgrowing the README file and I need to start doing this properly.

Read more comments on GitHub >

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