adding N to the "gap characters"

[dunleavy005]

In https://github.com/fhcrc/seqmagick/blob/master/seqmagick/transform.py#L24, the list of allowable gap characters are defined. However, I'd like to be able to trim off alignment columns with all N's and unfortunately cannot use seqmagick mogrify --squeeze FASTA_FILE to do that. Can "N" be added to GAP_CHARS?

[matsen]

Let's discuss how to do this. @metasoarous -- any ideas? N isn't a gap. What if we added a flag to modify GAP_CHARS?

[metasoarous]

This seems like something that would only ever apply during squeeze, so having a separate but compatible option like --squeeze-ambiguous might be the best route here. Thoughts?

[matsen]

Sounds like a lovely solution. 🖖