Mercurial > repos > biomonika > linkyx

annotate scripts/get_sequences_based_on_ids.pl @ 32:cf7cd22fc5d3 default tip

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author biomonika
date Tue, 10 Feb 2015 12:09:34 -0500
parents 1955f03f092e
children
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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 }