X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fextract_seq;h=40260cc9e490b3629fb131f8435b8f6c3c81144c;hb=6b4c2afa4b4b581a9c36083a1d059e846ee4b560;hp=158804270a88ef4920acb7f41b34b63c9764bc23;hpb=66938be910a5642b50ddf28991649858b5c36580;p=biopieces.git

diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq
index 1588042..40260cc 100755
--- a/bp_bin/extract_seq
+++ b/bp_bin/extract_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;
 
@@ -68,23 +69,34 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     {
         if ( defined $beg and defined $end )
         {
-            if ( $end - $beg + 1 > length $record->{ "SEQ" } ) {
-                $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
-            } else {
-                $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg, $end - $beg + 1;
+            if ( $end - $beg + 1 > length $record->{ "SEQ" } )
+            {
+                $record->{ "SEQ" }    = substr $record->{ "SEQ" }, $beg;
+                $record->{ "SCORES" } = substr $record->{ "SEQ" }, $beg if $record->{ "SCORES" };
+            }
+            else
+            {
+                $record->{ "SEQ" }    = substr $record->{ "SEQ" }, $beg, $end - $beg + 1;
+                $record->{ "SCORES" } = substr $record->{ "SCORES" }, $beg, $end - $beg + 1 if $record->{ "SCORES" };
             }
         }
         elsif ( defined $beg and defined $len )
         {
-            if ( $len > length $record->{ "SEQ" } ) {
-                $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
-            } else {
-                $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg, $len;
+            if ( $len > length $record->{ "SEQ" } )
+            {
+                $record->{ "SEQ" }    = substr $record->{ "SEQ" }, $beg;
+                $record->{ "SCORES" } = substr $record->{ "SCORES" }, $beg if $record->{ "SCORES" };
+            }
+            else
+            {
+                $record->{ "SEQ" }    = substr $record->{ "SEQ" }, $beg, $len;
+                $record->{ "SCORES" } = substr $record->{ "SCORES" }, $beg, $len if $record->{ "SCORES" };
             }
         }
         elsif ( defined $beg )
         {
-            $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
+            $record->{ "SEQ" }    = substr $record->{ "SEQ" }, $beg;
+            $record->{ "SCORES" } = substr $record->{ "SCORES" }, $beg if $record->{ "SCORES" };
         }
 
         $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };