--- /dev/null
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Vmatch sequences in the stream against a specified database.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Data::Dumper;
+use Maasha::Biopieces;
+use Maasha::Common;
+use Maasha::Filesys;
+use Maasha::Seq;
+use Maasha::Fasta;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, @index_files, $tmp_dir, $query_file, $fh_out, $fh_in, $record, $entry,
+ $vmatch_args, $result_file, $count_hash );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'genome', short => 'g', type => 'genome', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'index_name', short => 'i', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'count', short => 'c', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'max_hits', short => 'm', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 },
+ { long => 'hamming_dist', short => 'h', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 },
+ { long => 'edit_dist', short => 'e', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 },
+ ]
+);
+
+$options->{ 'count' } = 1 if $options->{ 'max_hits' };
+
+Maasha::Common::error( qq(both --index_hame and --genome specified) ) if $options->{ "genome" } and $options->{ "index_name" };
+Maasha::Common::error( qq(no --index_name or --genome specified) ) if not $options->{ "genome" } and not $options->{ "index_name" };
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+@index_files = get_index_files( $options );
+
+$tmp_dir = Maasha::Biopieces::get_tmpdir();
+
+$query_file = "$tmp_dir/query.seq";
+$result_file = "$tmp_dir/vmatch.out";
+
+$fh_out = Maasha::Filesys::file_write_open( $query_file );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
+ {
+ next if length $record->{ 'SEQ' } < 12; # assuming that the index is created for 12 as minimum length
+
+ Maasha::Fasta::put_entry( $entry, $fh_out, 100 );
+ }
+
+ Maasha::Biopieces::put_record( $record, $out ); # must this be here?
+}
+
+close $fh_out;
+
+$vmatch_args = vmatch_args( $options, $query_file );
+
+map { Maasha::Common::run( "vmatch", "$vmatch_args $_ >> $result_file" ) } @index_files;
+
+unlink $query_file;
+
+$fh_in = Maasha::Filesys::file_read_open( $result_file );
+
+if ( $options->{ "count" } )
+{
+ $count_hash = vmatch_count_hits( $result_file ) if ( $options->{ "count" } );
+
+ if ( $options->{ "max_hits" } )
+ {
+ while ( $record = vmatch_get_entry( $fh_in ) )
+ {
+ $record->{ 'SCORE' } = $count_hash->{ $record->{ 'Q_ID' } };
+
+ next if $record->{ 'SCORE' } > $options->{ 'max_hits' };
+
+ Maasha::Biopieces::put_record( $record, $out );
+ }
+
+ }
+ else
+ {
+ while ( $record = vmatch_get_entry( $fh_in ) )
+ {
+ $record->{ 'SCORE' } = $count_hash->{ $record->{ 'Q_ID' } };
+
+ Maasha::Biopieces::put_record( $record, $out );
+ }
+ }
+}
+else
+{
+ while ( $record = vmatch_get_entry( $fh_in ) ) {
+ Maasha::Biopieces::put_record( $record, $out );
+ }
+}
+
+close $fh_in;
+
+unlink $result_file;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+sub get_index_files
+{
+ # Martin A. Hansen, May 2009.
+
+ # Get the index_files from the index_name or genome options.
+
+ my ( $options, # hashref
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @index_files, %hash );
+
+ if ( $options->{ "index_name" } )
+ {
+ @index_files = $options->{ "index_name" };
+ }
+ else
+ {
+ @index_files = Maasha::Filesys::ls_files( "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/vmatch" );
+
+ map { $_ =~ /^(.+)\.[a-z1]{3,4}$/; $hash{ $1 } = 1 } @index_files;
+
+ @index_files = sort keys %hash;
+ }
+
+ return wantarray ? @index_files : \@index_files;
+}
+
+
+sub vmatch_args
+{
+ # Martin A. Hansen, May 2009.
+
+ # Given an option hashref and query file, compiles the arguments for running
+ # Vmatch on the commandline.
+
+ my ( $options, # hashref
+ $query_file, # path to query file
+ ) = @_;
+
+ # Returns a string.
+
+ my ( $vmatch_args );
+
+ $vmatch_args = "-complete -d -p -showdesc 100 -q $query_file";
+
+ $vmatch_args .= " -h " . $options->{ "hamming_dist" } if $options->{ "hamming_dist" };
+ $vmatch_args .= " -e " . $options->{ "edit_dist" } if $options->{ "edit_dist" };
+
+ return $vmatch_args;
+}
+
+
+sub vmatch_count_hits
+{
+ # Martin A. Hansen, April 2008.
+
+ # Given a Vmatch result files, count duplications based
+ # on q_id. The counts are returned in a hash.
+
+ my ( $file, # vmatch result file
+ ) = @_;
+
+ # Returns a list.
+
+ my ( $fh_in, $line, @fields, %count_hash );
+
+ $fh_in = Maasha::Filesys::file_read_open( $file );
+
+ while ( $line = <$fh_in> )
+ {
+ chomp $line;
+
+ next if $line =~ /^#/;
+
+ @fields = split " ", $line;
+
+ $count_hash{ $fields[ 5 ] }++;
+ }
+
+ close $fh_in;
+
+ return wantarray ? %count_hash : \%count_hash;
+}
+
+
+sub vmatch_get_entry
+{
+ # Martin A. Hansen, January 2008.
+
+ # Parses vmatch output records.
+
+ my ( $fh, # file handle to vmatch result file.
+ ) = @_;
+
+ # Returns a hash.
+
+ my ( $line, @fields, %record );
+
+ while ( $line = <$fh> )
+ {
+ chomp $line;
+
+ next if $line =~ /^#/;
+ $line =~ s/^\s+//;
+
+ @fields = split " ", $line;
+
+ $record{ "REC_TYPE" } = "VMATCH";
+
+ $record{ "S_LEN" } = $fields[ 0 ];
+ $record{ "S_ID" } = $fields[ 1 ];
+ $record{ "S_BEG" } = $fields[ 2 ];
+
+ if ( $fields[ 3 ] eq "D" ) {
+ $record{ "STRAND" } = "+";
+ } else {
+ $record{ "STRAND" } = "-";
+ }
+
+ $record{ "Q_LEN" } = $fields[ 4 ];
+ $record{ "Q_ID" } = $fields[ 5 ];
+ $record{ "Q_BEG" } = $fields[ 6 ];
+ $record{ "MATCH_DIST" } = $fields[ 7 ];
+ $record{ "E_VAL" } = $fields[ 8 ];
+ $record{ "SCORE" } = $fields[ 9 ];
+ $record{ "IDENT" } = $fields[ 10 ];
+
+ $record{ "Q_END" } = $record{ "Q_BEG" } + $record{ "Q_LEN" } - 1;
+ $record{ "S_END" } = $record{ "S_BEG" } + $record{ "S_LEN" } - 1;
+
+ return wantarray ? %record : \%record;
+ }
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+ Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
projects / biopieces.git / blobdiff