Mercurial > repos > biomonika > linkyx

diff scripts/get_sequence_based_on_id.pl @ 0:05c27700e5ca

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initial commit
author biomonika <biomonika@psu.edu>
date Thu, 04 Sep 2014 18:24:19 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/get_sequence_based_on_id.pl	Thu Sep 04 18:24:19 2014 -0400
@@ -0,0 +1,14 @@
+use Bio::DB::Fasta;
+
+my $fastaFile = shift;
+my $queryFile = shift;
+
+my $db = Bio::DB::Fasta->new( $fastaFile );
+    $seq = $queryFile;
+    chomp($queryFile);
+
+    my $sequence = $db->seq($seq);
+    if  (!defined( $sequence )) {
+            die "Sequence $seq not found. \n" 
+    }   
+    print ">$seq\n", "$sequence\n";
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