Created
April 6, 2018 00:45
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run-hmmer.sh
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#!/bin/sh | |
# run hmmer using hmm files | |
#INDIR=$1 #directory to search for .fastq.gz files | |
INDIR=~/work/NPRB | |
cd ~/work/hmm | |
for hmmfile in *.hmm; do | |
hmm=`basename $hmmfile .hmm`; | |
echo $hmm | |
ls -l $INDIR | |
for seqfile in $INDIR/*fastq.gz; do | |
basefile=`basename $seqfile .fastq.gz`; | |
basedir=`dirname $seqfile` | |
echo $basefile; | |
# ~/apps/bbmap/reformat.sh in=$seqfile out1=$basedir/$basefile.R1.fasta.gz out2=$basedir/$basefile.R2.fasta.gz fastawrap=0 | |
if [ ! -e $basedir/$basefile.R1.faa.gz ]; then | |
~/apps/orfm/orfm $basedir/$basefile.R1.fasta.gz | gzip -c > $basedir/$basefile.R1.faa.gz | |
~/apps/orfm/orfm $basedir/$basefile.R2.fasta.gz | gzip -c > $basedir/$basefile.R2.faa.gz | |
fi; | |
~/apps/hmmer/binaries/hmmsearch -o txt/$hmm.$basefile.R1.txt --pfamtblout pfam/$hmm.$basefile.R1.pfam --max -A aln/$hmm.$basefile.R1.aln --tblout tsv/$hmm.$basefile.R1.tsv --notextw --cpu 3 -Z 1000000 -E 0.1 $hmmfile $basedir/$basefile.R1.faa.gz & | |
~/apps/hmmer/binaries/hmmsearch -o txt/$hmm.$basefile.R2.txt --pfamtblout pfam/$hmm.$basefile.R2.pfam --max -A aln/$hmm.$basefile.R2.aln --tblout tsv/$hmm.$basefile.R2.tsv --notextw --cpu 4 -Z 1000000 -E 0.1 $hmmfile $basedir/$basefile.R2.faa.gz & | |
wait | |
done; | |
done; |
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