From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 20 Aug 2009 12:57:01 +0000 (+0000)
Subject: finished rescan_seq
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=12462f9b3f5475dae288a9936b5a3bae7f969d68;p=biopieces.git

finished rescan_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@642 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/rescan_seq b/bp_bin/rescan_seq
index 0e431ee..826a1f2 100755
--- a/bp_bin/rescan_seq
+++ b/bp_bin/rescan_seq
@@ -41,9 +41,10 @@ my ( $options, $in, $out, $record, $re_data, $re, $matches, $match, %re_hash, $r
 
 $options = Maasha::Biopieces::parse_options(
     [
-        { long => 'res_enz',    short => 'r', type => 'list',  mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
-        { long => 'res_enz_in', short => 'R', type => 'file!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
-        { long => 'no_matches', short => 'M', type => 'flag',  mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'res_enz',      short => 'r', type => 'list',  mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'res_enz_in',   short => 'R', type => 'file!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'res_enz_only', short => 'o', type => 'flag',  mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'no_matches',   short => 'M', type => 'flag',  mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
     ]   
 );
 
@@ -70,6 +71,7 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
             $matches = Maasha::RestrictEnz::re_scan( $record->{ 'SEQ' }, $re );
 
+            %{ $new_record }              = %{ $record } if not $options->{ 'res_enz_only' };
             $new_record->{ 'RE' }         = $re->{ 'name' };
             $new_record->{ 'RE_COUNT' }   = scalar @{ $matches };
             $new_record->{ 'RE_MATCHES' } = join( ";", @{ $matches } ) if not $options->{ 'no_matches' };
diff --git a/code_perl/Maasha/RestrictEnz.pm b/code_perl/Maasha/RestrictEnz.pm
index 1974439..836835b 100644
--- a/code_perl/Maasha/RestrictEnz.pm
+++ b/code_perl/Maasha/RestrictEnz.pm
@@ -129,7 +129,7 @@ void scan( char *seq, char *pat, int seq_len, int pat_len )
     Inline_Stack_Vars;
     Inline_Stack_Reset;
 
-    for ( i = 0; i < seq_len - pat_len; i++ )
+    for ( i = 0; i < seq_len - pat_len + 1; i++ )
     {
         if ( match( &seq[ i ], pat, pat_len ) ) {
           Inline_Stack_Push( sv_2mortal( newSViv( i ) ) );