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iqbal-lab-org / make_prg

Code to create a PRG from a Multiple Sequence Alignment file
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make_prg update PR series: 5. CLI changes #37

Closed leoisl closed 1 year ago

leoisl commented 2 years ago
  1. Adds --suffix parameter to make_prg from_msa. This is in general useful, but it is actually required to use make_prg in a snakemake pipeline. The main issue I faced is that a snakemake pipeline is creating a dir of MSAs to be fed into make_prg from_msa, but currently just using the --input parameter and giving a dir as input tries to build a PRG from every file in the dir, including the .snakemake_timestamp file. This allows us to further filter out which files we want to build a PRG from;
  2. Adds --long-deletion-threshold parameter to make_prg update. Current make_prg update implementation has issues dealing with long deletions, this parameter controls the size of the deletion we consider and ignore.
mbhall88 commented 2 years ago

@leoisl just wondering if you have an ETA on this (and therefore v0.3)? I am working on drprg again which relies on make_prg, so it would be nice to use the latest conda version rather than the binary from your fork.

leoisl commented 1 year ago

I logged the last remaining comment as an issue and I am moving to submit more PRs so we can finally merge and release this