added find_genes

git-svn-id: http://biopieces.googlecode.com/svn/trunk@817 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/find_genes b/bp_bin/find_genes
new file mode 100755 (executable)
index 0000000..f80fa88
--- /dev/null
+++ b/bp_bin/find_genes
@@ -0,0 +1,143 @@
+#!/usr/bin/env perl
+
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Find genes in sequences in stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Data::Dumper;
+use Maasha::Common;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $tmp_dir, $tmp_file, $fh_out, $fh_in, $entry, $chunk, @lines, $line, $s_id, $type, $s_beg, $s_end, $strand, @fields );
+
+$options = Maasha::Biopieces::parse_options();
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$tmp_dir  = Maasha::Biopieces::get_tmpdir();
+$tmp_file = "$tmp_dir/tmp.seq";
+$fh_out   = Maasha::Filesys::file_write_open( $tmp_file );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+    if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) {
+        Maasha::Fasta::put_entry( $entry, $fh_out );
+    }
+
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+Maasha::Common::run( "draft_prodigal.pl", "< $tmp_file > $tmp_file.out 2> /dev/null" );
+
+$fh_in = Maasha::Filesys::file_read_open( "$tmp_file.out" );
+
+$/ = "//\n";
+
+while ( $chunk = <$fh_in> )
+{
+    chomp $chunk;
+
+    @lines = split /\n/, $chunk;
+
+    $line = shift @lines;
+
+    if ( $line =~ /.*>(.+)/ )
+    {
+        $s_id = $1;
+
+        foreach $line ( @lines )
+        {
+            @fields = split " ", $line;
+
+            $type   = $fields[ 0 ];
+
+            if ( $fields[ 1 ] =~ /complement/ ) {
+                $strand = "-"; 
+            } else {
+                $strand = "+"; 
+            }
+
+            if ( $fields[ 1 ] =~ /(\d+)\.\.>?(\d+)/ )
+            {
+                $s_beg = $1;
+                $s_end = $2;
+            }
+            else
+            {
+                Maasha::Common::error( qq(BAD locator: $line) );
+            }
+
+            $record = {
+                S_ID   => $s_id,
+                S_BEG  => $s_beg - 1,
+                S_END  => $s_end - 1,
+                Q_ID   => $type,
+                STRAND => $strand,
+            };
+
+            Maasha::Biopieces::put_record( $record, $out );
+        }
+    }
+    else
+    {
+        Maasha::Commom::error( qq(BAD definition: $line) );
+    }
+}
+
+close $fh_in;
+
+$/ = "\n";
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__