refactoring of assemble_pairs

[biopieces.git] / bp_bin / fold_seq

diff --git a/bp_bin/fold_seq b/bp_bin/fold_seq
index c8eba697e3023ca76811611407d4bbb96af6e6f8..4543920c2f749484ac3dddcd7311a677075780d4 100755 (executable)
--- a/bp_bin/fold_seq
+++ b/bp_bin/fold_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;
 
@@ -44,11 +45,9 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 {
     if ( $record->{ "SEQ" } )
     {
-        if ( not $type ) {
-            $type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } );
-        }
+        $type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
         
-        if ( $type ne "protein" )
+        if ( $type ne "PROTEIN" )
         {
             ( $struct, $index ) = Maasha::Seq::fold_struct_rnafold( $record->{ "SEQ" } );
             $record->{ "SEC_STRUCT" }  = $struct;