Mercurial > repos > biomonika > linkyx

diff scripts/get_sequence_based_on_id.pl @ 9:695d28139f3e

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
toolshed8
author biomonika <biomonika@psu.edu>
date Tue, 09 Sep 2014 14:31:02 -0400
parents 1955f03f092e
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/get_sequence_based_on_id.pl	Tue Sep 09 14:31:02 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";
\ No newline at end of file