added usearch_seq biopiece

git-svn-id: http://biopieces.googlecode.com/svn/trunk@998 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/usearch_seq b/bp_bin/usearch_seq
new file mode 100755 (executable)
index 0000000..e563893
--- /dev/null
+++ b/bp_bin/usearch_seq
@@ -0,0 +1,225 @@
+#!/usr/bin/env perl
+
+# Copyright (C) 2007-2010 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# USEARCH sequences in the stream against a specified database or genome.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Data::Dumper;
+use Maasha::Biopieces;
+use Maasha::Common;
+use Maasha::Seq;
+use Maasha::Fasta;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $TYPE_HASH, $options, $in, $out, $tmp_dir, $tmp_in, $tmp_out, $q_type, $record, $entry, $fh_in, $fh_out );
+
+$TYPE_HASH = {
+    'L' => 'LibSeed',
+    'S' => 'NewSeed',
+    'H' => 'Hit',
+    'R' => 'Reject',
+    'D' => 'LibCluster',
+    'C' => 'NewCluster',
+    'N' => 'NoHit'
+};
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'database', short => 'd', type => 'file',   mandatory => 'no', default => undef,  allowed => undef, disallowed => undef },
+        { long => 'genome',   short => 'g', type => 'genome', mandatory => 'no', default => undef,  allowed => undef, disallowed => undef },
+        { long => 'id',       short => 'i', type => 'float',  mandatory => 'no', default => '0.90', allowed => undef, disallowed => undef },
+    ]   
+);
+
+Maasha::Common::error( qq(both --database and --genome specified) ) if     $options->{ "genome" } and     $options->{ "database" };
+Maasha::Common::error( qq(no --database or --genome specified) )    if not $options->{ "genome" } and not $options->{ "database" };
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$options->{ "database" } = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna" if $options->{ 'genome' };
+
+$tmp_dir = Maasha::Biopieces::get_tmpdir();
+$tmp_in  = "$tmp_dir/usearch_query.seq";
+$tmp_out = "$tmp_dir/usearch.uc";
+
+$fh_out = Maasha::Filesys::file_write_open( $tmp_in );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
+    {
+        $q_type = Maasha::Seq::seq_guess_type( $record->{ 'SEQ' } ) if not $q_type;
+
+        Maasha::Fasta::put_entry( $entry, $fh_out );
+    }
+
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+close $fh_out;
+
+
+if ( $options->{ 'verbose' } )
+{
+    Maasha::Common::run(
+        "uclust",
+        join( " ",
+            "--input $tmp_in",
+            "--lib $options->{ 'database' }",
+            "--libonly",
+            "--uc $tmp_out",
+            "--id $options->{ 'id' }",
+            "--rev",
+        ),
+        1
+    );
+}
+else
+{
+    Maasha::Common::run(
+        "uclust",
+        join( " ",
+            "--input $tmp_in",
+            "--lib $options->{ 'database' }",
+            "--libonly",
+            "--uc $tmp_out",
+            "--id $options->{ 'id' }",
+            "--rev",
+            "> /dev/null 2>&1"
+        ),
+        1
+    );
+}
+
+unlink $tmp_in;
+
+$fh_in = Maasha::Filesys::file_read_open( $tmp_out );
+
+while ( $entry = get_tab_entry( $fh_in ) )
+{
+    $record = uclust_tab2biopiece( $entry );
+
+    Maasha::Biopieces::put_record( $record, $out ) if $record->{ 'TYPE' } eq 'Hit';
+}
+
+close $fh_out;
+
+unlink $tmp_out;
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+sub get_tab_entry
+{
+    # Martin A. Hansen, May 2009.
+
+    # Get the next tabular entry from a filehandle to a USEARCH file.
+
+    my ( $fh,   # filehandle
+       ) = @_;
+
+    # Returns a list
+
+    my ( $line, @fields );
+
+    while ( $line = <$fh> )
+    {
+        next if $line =~ /^#/;
+    
+        @fields = split /\s+/, $line;
+
+        return wantarray ? @fields : \@fields;
+    }
+
+    return undef;
+}
+
+
+sub uclust_tab2biopiece
+{
+    # Martin A. Hansen, May 2009.
+
+    # Get the next USEARCH tabular entry and convert it to
+    # a biopiece record that is returned.
+
+    my ( $entry,    # USEARCH tabular entry
+       ) = @_;
+
+    # Returns a hashref.
+
+    my ( %record );
+
+    $record{ "REC_TYPE" }  = "USEARCH";
+    $record{ "TYPE" }      = $TYPE_HASH->{ $entry->[ 0 ] };
+    $record{ "CLUSTER" }   = $entry->[ 1 ];
+    $record{ "ALIGN_LEN" } = $entry->[ 2 ];
+    $record{ "ID" }        = $entry->[ 3 ];
+    $record{ "STRAND" }    = $entry->[ 4 ];
+    $record{ "Q_BEG" }     = $entry->[ 5 ];
+    $record{ "S_BEG" }     = $entry->[ 6 ];
+    $record{ "CIGAR" }     = $entry->[ 7 ];
+    $record{ "Q_ID" }      = $entry->[ 8 ];
+    $record{ "S_ID" }      = $entry->[ 9 ];
+
+    if ( $record{ 'TYPE' } eq 'Hit' )
+    {
+        $record{ "Q_END" } = $record{ "Q_BEG" } + $record{ "ALIGN_LEN" } - 1;
+        $record{ "S_END" } = $record{ "S_BEG" } + $record{ "ALIGN_LEN" } - 1;
+    }
+
+    return wantarray ? %record : \%record;
+}
+
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__