added record2fasta to allow for aliasing of SEQ_NAME to Q_ID or S_ID

git-svn-id: http://biopieces.googlecode.com/svn/trunk@187 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm
index d375e2d60a568fc0368ac98a42e28c226bd6a115..554ac36b6e757afddc5d70333770d6d61331792c 100644 (file)
--- a/code_perl/Maasha/Biopieces.pm
+++ b/code_perl/Maasha/Biopieces.pm
@@ -2037,7 +2037,7 @@ sub script_format_genome
 
     # Returns nothing.
 
-    my ( $dir, $genome, $fasta_dir, $phastcons_dir, $vals, $fh_out, $record, $format, $index );
+    my ( $dir, $genome, $fasta_dir, $phastcons_dir, $vals, $fh_out, $record, $format, $index, $entry );
 
     $dir    = $options->{ 'dir' } || $ENV{ 'BP_DATA' };
     $genome = $options->{ 'genome' };
@@ -2072,9 +2072,9 @@ sub script_format_genome
 
     while ( $record = get_record( $in ) ) 
     {
-        if ( $fh_out and $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+        if ( $fh_out and $entry = record2fasta( $record ) )
         {
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_out, $options->{ "wrap" } );
+            Maasha::Fasta::put_entry( $entry, $fh_out, $options->{ "wrap" } );
         }
         elsif ( $fh_out and $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "STEP" } and $record->{ "VALS" } )
         {
@@ -3296,8 +3296,6 @@ sub script_patscan_seq
 
             $i++;
         }
-
-#        put_record( $record, $out );
     }
 
     close $fh_out;
@@ -3367,7 +3365,7 @@ sub script_create_blast_db
 
     # Returns nothing.
 
-    my ( $fh, $seq_type, $path, $record );
+    my ( $fh, $seq_type, $path, $record, $entry );
 
     $path = $options->{ "database" };
 
@@ -3377,11 +3375,11 @@ sub script_create_blast_db
     {
         put_record( $record, $out ) if not $options->{ "no_stream" };
 
-        if ( $record->{ "SEQ" } and $record->{ "SEQ_NAME" } )
+        if ( $entry = record2fasta( $record ) )
         {
-            $seq_type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $seq_type;
+            $seq_type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not $seq_type;
 
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh );
+            Maasha::Fasta::put_entry( $entry, $fh );
         }
     }
 
@@ -3410,7 +3408,7 @@ sub script_blast_seq
 
     # Returns nothing.
 
-    my ( $genome, $q_type, $s_type, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $line, @fields );
+    my ( $genome, $q_type, $s_type, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $line, @fields, $entry );
 
     $options->{ "e_val" }  = 10 if not defined $options->{ "e_val" };
     $options->{ "filter" } = "F";
@@ -3426,11 +3424,11 @@ sub script_blast_seq
 
     while ( $record = get_record( $in ) ) 
     {
-        if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+        if ( $entry = record2fasta( $record ) )
         {
-            $q_type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $q_type;
+            $q_type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not $q_type;
 
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_out );
+            Maasha::Fasta::put_entry( $entry, $fh_out );
         }
 
         put_record( $record, $out );
@@ -3520,7 +3518,7 @@ sub script_blat_seq
 
     # Returns nothing.
 
-    my ( $blat_args, $genome_file, $query_file, $fh_in, $fh_out, $type, $record, $result_file, $entries );
+    my ( $blat_args, $genome_file, $query_file, $fh_in, $fh_out, $type, $record, $result_file, $entries, $entry );
 
     $genome_file = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna";
 
@@ -3543,10 +3541,10 @@ sub script_blat_seq
 
     while ( $record = get_record( $in ) ) 
     {
-        if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+        if ( $entry = record2fasta( $record ) )
         {
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_out, 80 );
-            $type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
+            $type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not $type;
+            Maasha::Fasta::put_entry( $entry, $fh_out, 80 );
         }
 
         put_record( $record, $out );
@@ -3584,7 +3582,7 @@ sub script_soap_seq
 
     # Returns nothing.
 
-    my ( $genome, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $line, @fields );
+    my ( $genome, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $line, @fields, $entry );
 
     $options->{ "mismatches" } ||= 2;
     $options->{ "gap_size" }   ||= 0;
@@ -3599,8 +3597,8 @@ sub script_soap_seq
 
     while ( $record = get_record( $in ) ) 
     {
-        if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_out );
+        if ( $entry = record2fasta( $record ) ) {
+            Maasha::Fasta::put_entry( $entry, $fh_out );
         }
 
         put_record( $record, $out );
@@ -3694,7 +3692,7 @@ sub script_create_vmatch_index
 
     # Returns nothing.
 
-    my ( $record, $file_tmp, $fh_tmp, $type );
+    my ( $record, $file_tmp, $fh_tmp, $type, $entry );
 
     if ( $options->{ "index_name" } )
     {
@@ -3704,11 +3702,11 @@ sub script_create_vmatch_index
 
     while ( $record = get_record( $in ) ) 
     {
-        if ( $options->{ "index_name" } and $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+        if ( $options->{ "index_name" } and $entry = record2fasta( $record ) )
         {
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_tmp );
+            Maasha::Fasta::put_entry( $entry, $fh_tmp );
 
-            $type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
+            $type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not defined $type;
         }
 
         put_record( $record, $out ) if not $options->{ "no_stream" };
@@ -3795,14 +3793,14 @@ sub script_write_fasta
 
     # Returns nothing.
 
-    my ( $record, $fh );
+    my ( $record, $fh, $entry );
 
     $fh = write_stream( $options->{ "data_out" }, $options->{ "compress" } );
 
     while ( $record = get_record( $in ) ) 
     {
-        if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh, $options->{ "wrap" } );
+        if ( $entry = record2fasta( $record ) ) {
+            Maasha::Fasta::put_entry( $entry, $fh, $options->{ "wrap" } );
         }
 
         put_record( $record, $out ) if not $options->{ "no_stream" };
@@ -4142,7 +4140,7 @@ sub script_write_2bit
 
     # Returns nothing.
 
-    my ( $record, $mask, $tmp_file, $fh_tmp, $fh_in, $fh_out );
+    my ( $record, $mask, $tmp_file, $fh_tmp, $fh_in, $fh_out, $entry );
 
     $mask = 1 if not $options->{ "no_mask" };
 
@@ -4153,8 +4151,8 @@ sub script_write_2bit
 
     while ( $record = get_record( $in ) ) 
     {
-        if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_tmp );
+        if ( $entry = record2fasta( $record ) ) {
+            Maasha::Fasta::put_entry( $entry, $fh_tmp );
         }
 
         put_record( $record, $out ) if not $options->{ "no_stream" };
@@ -4186,17 +4184,17 @@ sub script_write_solid
 
     # Returns nothing.
 
-    my ( $record, $fh, $seq_cs );
+    my ( $record, $fh, $entry );
 
     $fh = write_stream( $options->{ "data_out" }, $options->{ "compress" } );
 
     while ( $record = get_record( $in ) ) 
     {
-        if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+        if ( $entry = record2fasta( $record ) )
         {
-            $seq_cs = Maasha::Solid::seq2color_space( uc $record->{ "SEQ" } );
+            $entry->[ SEQ ] = Maasha::Solid::seq2color_space( uc $entry->[ SEQ ] );
 
-            Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $seq_cs ], $fh, $options->{ "wrap" } );
+            Maasha::Fasta::put_entry( $entry, $fh, $options->{ "wrap" } );
         }
 
         put_record( $record, $out ) if not $options->{ "no_stream" };
@@ -5855,6 +5853,32 @@ sub script_upload_to_ucsc
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+sub record2fasta
+{
+    # Martin A. Hansen, July 2008.
+
+    # Given a biopiece record converts it to a FASTA record.
+    # If no generic SEQ or SEQ_NAME is found, the Q_* and S_* are
+    # tried in that order.
+
+    my ( $record,    # record
+       ) = @_;
+
+    # Returns a tuple.
+
+    my ( $seq_name, $seq );
+
+    $seq_name = $record->{ "SEQ_NAME" } || $record->{ "Q_ID" }  || $record->{ "S_ID" };
+    $seq      = $record->{ "SEQ" }      || $record->{ "Q_SEQ" } || $record->{ "S_SEQ" };
+
+    if ( defined $seq_name and defined $seq ) {
+        return wantarray ? ( $seq_name, $seq ) : [ $seq_name, $seq ];
+    } else {
+        return;
+    }
+}
+
+
 sub read_stream
 {
     # Martin A. Hansen, July 2007.