Mercurial > repos > mmseq > mmseq
comparison 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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8:2dffdc276fd8 | 9:e3b8eefe6586 |
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1 #!/bin/sh | |
2 PREFIX=temp | |
3 FA=$(grep -P "index\t$2\t" $3/sam_fa_indices.loc | cut -f3) | |
4 samtools view -bt $FA.fai -o $PREFIX.bam $1 2> /dev/null | |
5 samtools sort -n $PREFIX.bam $PREFIX.namesorted 2> /dev/null | |
6 bam2hits $FA $PREFIX.namesorted.bam > $PREFIX.hits 2> /dev/null | |
7 mmseq $PREFIX.hits $PREFIX > /dev/null | |
8 mv $PREFIX.mmseq $4 | |
9 mv $PREFIX.identical.mmseq $5 | |
10 mv $PREFIX.gene.mmseq $6 |