From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 11 Dec 2009 19:07:17 +0000 (+0000)
Subject: fixed bug in translate_seq
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=731f02ba5d556aaa8e44a85e7cec1be549f4216f;p=biopieces.git

fixed bug in translate_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@802 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/align_seq b/bp_bin/align_seq
index af114e1..632d732 100755
--- a/bp_bin/align_seq
+++ b/bp_bin/align_seq
@@ -49,7 +49,7 @@ $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
 
 while ( $record = Maasha::Biopieces::get_record( $in ) ) 
 {
-    if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
+    if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {  # TODO use biopieces2fasta() instead
         push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
     } elsif ( $record->{ "Q_ID" } and $record->{ "SEQ" } ) {
         push @entries, [ $record->{ "Q_ID" }, $record->{ "SEQ" } ];
diff --git a/bp_bin/translate_seq b/bp_bin/translate_seq
index ba6b07f..d62188a 100755
--- a/bp_bin/translate_seq
+++ b/bp_bin/translate_seq
@@ -50,7 +50,7 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 {
     if ( $record->{ "SEQ" } )
     {
-        if ( Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) eq "dna" )
+        if ( Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) =~ /DNA/i )
         {
             foreach $frame ( @{ $options->{ "frames" } } )
             {