fixed bug in uclust_seq

[biopieces.git] / bp_bin / patscan_seq

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
index 611481c8123258ae574855c599dcaacf89fa943e..ca4fc983f47629bb78e960ea21f15f335bb68f5f 100755 (executable)
--- a/bp_bin/patscan_seq
+++ b/bp_bin/patscan_seq
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
 # Copyright (C) 2007-2009 Martin A. Hansen.
 
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Common;
@@ -81,7 +82,7 @@ else
 
     while ( $record = Maasha::Biopieces::get_record( $in ) ) 
     {
-        if ( $entry = Maasha::Biopieces::biopiece2fasta( $record ) )
+        if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
         {
             $type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
         
@@ -97,7 +98,7 @@ else
 
     close $fh_out;
 
-    $arg .= " -p" if $type eq "protein";
+    $arg .= " -p" if $type eq "PROTEIN";
 }
 
 foreach $pattern ( @{ $patterns } )