added -c switch to write_bed

git-svn-id: http://biopieces.googlecode.com/svn/trunk@310 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm
index a09f78eaeca2cfd49b2f83a9f1ceb5ced5df9649..d5a33fed710ae821170a2366d7c62cabca462166 100644 (file)
--- a/code_perl/Maasha/Biopieces.pm
+++ b/code_perl/Maasha/Biopieces.pm
@@ -674,6 +674,7 @@ sub get_options
     elsif ( $script eq "write_bed" )
     {
         @options = qw(
+            cols|c=s
             no_stream|x
             data_out|o=s
             compress|Z
@@ -4445,7 +4446,9 @@ sub script_write_bed
 
     # Returns nothing.
 
-    my ( $fh, $record, $new_record );
+    my ( $cols, $fh, $record, $new_record );
+
+    $cols = $options->{ 'cols' }->[ 0 ];
 
     $fh = write_stream( $options->{ "data_out" }, $options->{ "compress" } );
 
@@ -4453,7 +4456,9 @@ sub script_write_bed
     {
         if ( $record->{ "REC_TYPE" } eq "BED" )                                             # ---- Hits from BED ----
         {
-            Maasha::UCSC::bed_put_entry( $record, $fh, $record->{ "BED_COLS" } );
+            $cols ||= $record->{ "BED_COLS" };
+
+            Maasha::UCSC::bed_put_entry( $record, $fh, $cols );
         }
         elsif ( $record->{ "REC_TYPE" } eq "PSL" and $record->{ "S_ID" } =~ /^chr/i )       # ---- Hits from BLAT (PSL) ----
         {
@@ -4464,11 +4469,15 @@ sub script_write_bed
             $new_record->{ "SCORE" }   = $record->{ "SCORE" } || 999;
             $new_record->{ "STRAND" }  = $record->{ "STRAND" };
 
-            Maasha::UCSC::bed_put_entry( $new_record, $fh, 6 );
+            $cols ||= 6;
+
+            Maasha::UCSC::bed_put_entry( $new_record, $fh, $cols );
         }
         elsif ( $record->{ "REC_TYPE" } eq "PATSCAN" and $record->{ "CHR" } )               # ---- Hits from patscan_seq ----
         {
-            Maasha::UCSC::bed_put_entry( $record, $fh, 6 );
+            $cols ||= 6;
+
+            Maasha::UCSC::bed_put_entry( $record, $fh, $cols );
         }
         elsif ( $record->{ "REC_TYPE" } eq "BLAST" and $record->{ "S_ID" } =~ /^chr/i )     # ---- Hits from BLAST ----
         {
@@ -4479,7 +4488,9 @@ sub script_write_bed
             $new_record->{ "SCORE" }   = $record->{ "SCORE" } || 999; # or use E_VAL somehow
             $new_record->{ "STRAND" }  = $record->{ "STRAND" };
 
-            Maasha::UCSC::bed_put_entry( $new_record, $fh, 6 );
+            $cols ||= 6;
+
+            Maasha::UCSC::bed_put_entry( $new_record, $fh, $cols );
         }
         elsif ( $record->{ "REC_TYPE" } eq "VMATCH" and $record->{ "S_ID" } =~ /^chr/i )    # ---- Hits from Vmatch ----
         {
@@ -4490,9 +4501,11 @@ sub script_write_bed
             $new_record->{ "SCORE" }   = $record->{ "SCORE" } || 999; # or use E_VAL somehow
             $new_record->{ "STRAND" }  = $record->{ "STRAND" };
 
-            Maasha::UCSC::bed_put_entry( $new_record, $fh, 6 );
+            $cols ||= 6;
+
+            Maasha::UCSC::bed_put_entry( $new_record, $fh, $cols );
         }
-        elsif ( $record->{ "REC_TYPE" } eq "SOAP" and $record->{ "S_ID" } =~ /^chr/i )    # ---- Hits from Vmatch ----
+        elsif ( $record->{ "REC_TYPE" } eq "SOAP" and $record->{ "S_ID" } =~ /^chr/i )    # ---- Hits from Soap ----
         {
             $new_record->{ "CHR" }     = $record->{ "S_ID" };
             $new_record->{ "CHR_BEG" } = $record->{ "S_BEG" };
@@ -4501,11 +4514,13 @@ sub script_write_bed
             $new_record->{ "SCORE" }   = $record->{ "SCORE" } || 999;
             $new_record->{ "STRAND" }  = $record->{ "STRAND" };
 
-            Maasha::UCSC::bed_put_entry( $new_record, $fh, 6 );
+            $cols ||= 6;
+
+            Maasha::UCSC::bed_put_entry( $new_record, $fh, $cols );
         }
         elsif ( $record->{ "CHR" } and defined $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )  # ---- Generic data from tables ----
         {
-            Maasha::UCSC::bed_put_entry( $record, $fh );
+            Maasha::UCSC::bed_put_entry( $record, $fh, $cols );
         }
 
         put_record( $record, $out ) if not $options->{ "no_stream" };