refactoring of assemble_pairs

[biopieces.git] / bp_bin / extract_seq

diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq
index c900bc77eef4d92afdf2492f15ccfec7d9fe57b6..40260cc9e490b3629fb131f8435b8f6c3c81144c 100755 (executable)
--- 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" };
@@ -93,26 +105,22 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -120,4 +128,3 @@ END
 
 
 __END__
-