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Translate gene #205

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Translate gene #205

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jpjarnoux
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@jpjarnoux jpjarnoux commented Mar 28, 2024 •
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Two things have been done here:

  1. Added the ability to write the translated sequence of all genes using MMSeqs2 with the --proteins option, which works like the other options in the ppanggolin fasta command.
  2. In MSA, if the gene sequence length is not divisible by 3, PPanGGOLiN prints a warning message. To be more flexible, the last one or two nucleotides are deleted if the sequence size is not modulo 3. A debug message will issued the partial genes.

@axbazin axbazin self-requested a review April 9, 2024 07:16
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MMseqs2 create db must be forced in mode 1. So in translate_genes we must force the mode.

axbazin
axbazin reviewed Jun 4, 2024
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@JeanMainguy JeanMainguy self-requested a review June 5, 2024 14:23
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JeanMainguy requested changes Jun 6, 2024
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.github/workflows/main.yml
@@ -100,6 +100,7 @@ jobs:
ppanggolin fasta -p stepbystep/pangenome.h5 --output stepbystep -f --prot_families module_0
ppanggolin fasta -p stepbystep/pangenome.h5 --output stepbystep -f --prot_families core
ppanggolin fasta -p stepbystep/pangenome.h5 --output stepbystep -f --gene_families module_0 --genes module_0
ppanggolin fasta -p stepbystep/pangenome.h5 --output stepbystep -f --proteins cloud --threads 1 --keep_tmp
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You way want to use the NUM_CPU variable here

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@JeanMainguy JeanMainguy JeanMainguy requested changes

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@jpjarnoux @JeanMainguy @axbazin