Mercurial > repos > biomonika > linkyx

annotate scripts/get_sequence_based_on_id.pl @ 30:57b2221536fc

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remove custom samtools package to its own package on TTS
author biomonika
date Tue, 10 Feb 2015 11:33:33 -0500
parents 1955f03f092e
children
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biomonika <biomonika@psu.edu>
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1 use Bio::DB::Fasta;
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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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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 $seq = $queryFile;
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biomonika <biomonika@psu.edu>
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8 chomp($queryFile);
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9
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biomonika <biomonika@psu.edu>
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10 my $sequence = $db->seq($seq);
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biomonika <biomonika@psu.edu>
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11 if (!defined( $sequence )) {
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biomonika <biomonika@psu.edu>
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12 die "Sequence $seq not found. \n"
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biomonika <biomonika@psu.edu>
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13 }
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biomonika <biomonika@psu.edu>
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14 print ">$seq\n", "$sequence\n";