--- /dev/null
+#!/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__