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smith-chem-wisc / Spritz

Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data
https://smith-chem-wisc.github.io/Spritz/
MIT License
7 stars 11 forks source link

latest spritz gui and snakemake #160

Closed bintiibrahim closed 4 years ago

bintiibrahim commented 4 years ago

you can probably ignore the GtfSharp and TransferUniProtModification conflicts with mine, i didn't change any of those. :)

bintiibrahim commented 4 years ago

@acesnik this PR actually contains the latest snakemake code AND the GUI edits. i think i'll close this PR https://github.com/acesnik/SpritzSnake/pull/17 because it doesn't match with the edits in this PR.

acesnik commented 4 years ago

Hmm, sounds good. The conflicts here are confusing in GitHub, too. I would like the two repositories to match up before we make more changes. Maybe I'll just add the current snakemake code without deleting anything, and then we can layer in these changes.

acesnik commented 4 years ago

download_protein_xml.py needs to accomodate multiple species. Right now, the UniProt proteome is still hardcoded.

acesnik commented 4 years ago

Do we need to consider using different SnpEff codon tables for different organisms?

bintiibrahim commented 4 years ago

download_protein_xml.py needs to accomodate multiple species. Right now, the UniProt proteome is still hardcoded.

I've actually made this accomodation. In the rule download_protein_xml you'll see that I'm calling get_proteome.py and download_xml.py

acesnik commented 4 years ago

Tried to address all the conflicts here https://github.com/smith-chem-wisc/Spritz/pull/162. Going to close this one.