Mercurial > repos > mmseq > mmseq
view mmseq/mmseq.sh @ 9:e3b8eefe6586
Incorporate samtools invocation
author | mwoodbri |
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date | Thu, 27 Oct 2011 19:00:59 -0400 |
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#!/bin/sh PREFIX=temp FA=$(grep -P "index\t$2\t" $3/sam_fa_indices.loc | cut -f3) samtools view -bt $FA.fai -o $PREFIX.bam $1 2> /dev/null samtools sort -n $PREFIX.bam $PREFIX.namesorted 2> /dev/null bam2hits $FA $PREFIX.namesorted.bam > $PREFIX.hits 2> /dev/null mmseq $PREFIX.hits $PREFIX > /dev/null mv $PREFIX.mmseq $4 mv $PREFIX.identical.mmseq $5 mv $PREFIX.gene.mmseq $6