refactoring of assemble_pairs

[biopieces.git] / bp_bin / rescan_seq

diff --git a/bp_bin/rescan_seq b/bp_bin/rescan_seq
index 22e0596480f8b654ab3b8e5f3edf41c057224227..826a1f233da5d0a4c2ee1249e25da3643a90dd36 100755 (executable)
--- a/bp_bin/rescan_seq
+++ b/bp_bin/rescan_seq
@@ -37,13 +37,14 @@ use Maasha::Patscan;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $options, $in, $out, $record, $re_data, $re, $matches, $match, %re_hash, $res_enz );
+my ( $options, $in, $out, $record, $re_data, $re, $matches, $match, %re_hash, $res_enz, $new_record );
 
 $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 },
     ]   
 );
 
@@ -70,15 +71,16 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 
             $matches = Maasha::RestrictEnz::re_scan( $record->{ 'SEQ' }, $re );
 
-            if ( scalar @{ $matches } > 0 )
-            {
-                $record->{ $re->{ 'name' } . "_COUNT" }   = scalar @{ $matches };
-                $record->{ $re->{ 'name' } . "_MATCHES" } = join( ";", @{ $matches } ) if not $options->{ 'no_matches' };
-            }
+            %{ $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' };
+
+            Maasha::Biopieces::put_record( $new_record, $out );
         }
     }
 
-    Maasha::Biopieces::put_record( $record, $out );
+    # Maasha::Biopieces::put_record( $record, $out );
 }
 
 Maasha::Biopieces::close_stream( $in );