3 # Copyright (C) 2007-2009 Martin A. Hansen.
5 # This program is free software; you can redistribute it and/or
6 # modify it under the terms of the GNU General Public License
7 # as published by the Free Software Foundation; either version 2
8 # of the License, or (at your option) any later version.
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
15 # You should have received a copy of the GNU General Public License
16 # along with this program; if not, write to the Free Software
17 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
19 # http://www.gnu.org/copyleft/gpl.html
22 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
24 # Create a Vmatch index from sequences in stream for use with [vmatch_seq].
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 use Maasha::Biopieces;
37 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
40 my ( $default, $formats, $options, $in, $out, $record, $file_tmp, $fh_tmp, $type, $entry );
42 $options = Maasha::Biopieces::parse_options(
44 { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
45 { long => 'index_name', short => 'i', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
46 { long => 'prefix_length', short => 'p', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 },
50 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
51 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
53 $file_tmp = $options->{ 'index_name' };
54 $fh_tmp = Maasha::Filesys::file_write_open( $file_tmp );
56 while ( $record = Maasha::Biopieces::get_record( $in ) )
58 if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
60 Maasha::Fasta::put_entry( $entry, $fh_tmp );
62 $type = Maasha::Seq::seq_guess_type( $record->{ 'SEQ' } ) if not defined $type;
65 Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
70 if ( $type eq "protein" ) {
71 Maasha::Common::run( "mkvtree", "-db $file_tmp -protein -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" );
73 Maasha::Common::run( "mkvtree", "-db $file_tmp -dna -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" );
79 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
84 $run_time_beg = Maasha::Biopieces::run_time();
86 Maasha::Biopieces::log_biopiece();
91 Maasha::Biopieces::close_stream( $in );
92 Maasha::Biopieces::close_stream( $out );
94 $run_time_end = Maasha::Biopieces::run_time();
96 Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
100 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<