From 508e3a6973a59061775be6563bb75f5de6c3cb71 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 18 May 2010 14:46:41 +0000
Subject: [PATCH] extract seq now also extract SCORES if present

git-svn-id: http://biopieces.googlecode.com/svn/trunk@958 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/extract_seq | 29 ++++++++++++++++++++---------
 1 file changed, 20 insertions(+), 9 deletions(-)

diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq
index d5760d5..40260cc 100755
--- a/bp_bin/extract_seq
+++ b/bp_bin/extract_seq
@@ -69,23 +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" };
-- 
2.39.5