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 FASTA sequence index from sequences in stream for use with [get_seq].
26 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
32 use Maasha::Biopieces;
37 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
40 my ( $default, $formats, $options, $in, $out, $record, $tmp_dir, $file_out, $fh_out, $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 => 'directory', short => 'd', type => 'dir', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
46 { long => 'index_name', short => 'i', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
50 Maasha::Filesys::dir_create_if_not_exists( $options->{ 'directory' } );
52 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
53 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
55 $file_out = "$options->{ 'directory' }/$options->{ 'index_name' }.seq";
56 $fh_out = Maasha::Filesys::file_write_open( $file_out );
58 while ( $record = Maasha::Biopieces::get_record( $in ) )
60 if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) {
61 Maasha::Fasta::put_entry( $entry, $fh_out );
64 Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
69 Maasha::Fasta::fasta_index( $file_out, $options->{ 'directory' }, $options->{ 'index_name' } . ".index" );
71 Maasha::Biopieces::close_stream( $in );
72 Maasha::Biopieces::close_stream( $out );
75 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
80 Maasha::Biopieces::status_set();
86 Maasha::Biopieces::status_log();
90 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<