X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fvmatch_seq;h=c02b98d1f8d895fa0791c8f057e7ffc02081a9cf;hb=af282a65d141826c15944437b07a0353dd14e79c;hp=f98275cff4e50b928795f6c0276d51b43c01ef82;hpb=f7e5c1b54c562cc1b25fe419cacd4da9ac01f129;p=biopieces.git

diff --git a/bp_bin/vmatch_seq b/bp_bin/vmatch_seq
deleted file mode 120000
index f98275c..0000000
--- a/bp_bin/vmatch_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/vmatch_seq
\ No newline at end of file
diff --git a/bp_bin/vmatch_seq b/bp_bin/vmatch_seq
new file mode 100755
index 0000000..c02b98d
--- /dev/null
+++ b/bp_bin/vmatch_seq
@@ -0,0 +1,294 @@
+#!/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__