major code upgrade 1

[biopieces.git] / code_perl / Maasha / Fasta.pm

diff --git a/code_perl/Maasha/Fasta.pm b/code_perl/Maasha/Fasta.pm
index cf399cf16ba07854f230ca67f0a8e285d53dcd79..c4920a805c8805d50390c2804b22e528c11069df 100644 (file)
--- a/code_perl/Maasha/Fasta.pm
+++ b/code_perl/Maasha/Fasta.pm
@@ -488,4 +488,30 @@ sub index_retrieve
 }
 
 
+sub biopiece2fasta
+{
+    # 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;
+    }
+}
+
+
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