Mercurial > repos > biomonika > linkyx

annotate scripts/reformat_trinity_header.sh @ 0:1955f03f092e

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author biomonika <biomonika@psu.edu>
date Tue, 02 Sep 2014 14:16:04 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1955f03f092e initial commit
biomonika <biomonika@psu.edu>
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1 #!/bin/bash
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
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biomonika <biomonika@psu.edu>
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3 results=$1 #reformatted fasta sequence written here
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
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4 trinity_fasta=${2}
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biomonika <biomonika@psu.edu>
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5
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
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6 perl -pe 's/(>[\S]+).+/$1/' $trinity_fasta >$results
1955f03f092e initial commit
biomonika <biomonika@psu.edu>
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7 samtools faidx $results
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biomonika <biomonika@psu.edu>
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8
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biomonika <biomonika@psu.edu>
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