Mercurial > repos > biomonika > linkyx

annotate scripts/get_sequences_based_on_ids.pl @ 13:ef5c8ed727b0

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toolshed12
author biomonika <biomonika@psu.edu>
date Wed, 10 Sep 2014 10:49:56 -0400
parents 1955f03f092e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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biomonika <biomonika@psu.edu>
parents:
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1 use Bio::DB::Fasta;
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biomonika <biomonika@psu.edu>
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2
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biomonika <biomonika@psu.edu>
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3 my $fastaFile = shift;
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biomonika <biomonika@psu.edu>
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4 my $queryFile = shift;
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biomonika <biomonika@psu.edu>
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5
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biomonika <biomonika@psu.edu>
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6 my $db = Bio::DB::Fasta->new( $fastaFile );
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biomonika <biomonika@psu.edu>
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7 open (IN, $queryFile);
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biomonika <biomonika@psu.edu>
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8 while (<IN>){
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biomonika <biomonika@psu.edu>
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9 chomp;
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biomonika <biomonika@psu.edu>
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10 $seq = $_;
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biomonika <biomonika@psu.edu>
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11 my $sequence = $db->seq($seq);
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biomonika <biomonika@psu.edu>
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12 if (!defined( $sequence )) {
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biomonika <biomonika@psu.edu>
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13 die "Sequence $seq not found. \n"
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biomonika <biomonika@psu.edu>
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14 }
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biomonika <biomonika@psu.edu>
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15 print ">$seq\n", "$sequence\n";
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biomonika <biomonika@psu.edu>
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16 }