gene_rast_thing

./genes.py genes.tsv index_files/*

Setup

1. Install Python 3.x version of miniconda

2. Install dependencies

   conda install bio
   

Shit manual pipeline

1. Do gene thing

   ./gene.py genes.tsv  RAST/*
   

2. Align

   ./align.sh output
   

3. Rename output files so they sort gooder

   ls -1 output_aln/* | while read f; do nn=$(echo $f | sed 's|output_aln/fig_321327_43_peg_\([0-9]\+\).aln.fasta|\1.aln.fasta|'); mv $f output_aln/$nn; done
   

4. Make bigass fasta concatted file

   ./sequence_files_concat.py --identifier-pattern "(fig\|\d+\.\d+\.peg)" output_aln/* > out.fasta
   

5. Trim out all '-' columns

   ./trim_alignment.py out.fasta > out.trim.fasta