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 # Write nucleotide sequences in 2bit format.
26 # WARNING WARNING There is a bug that prevents 2bit output to be read by Jim Kents tools. WARNING WARNING
27 # Possibly the padding is wrong.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
35 use Maasha::Biopieces;
40 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
43 my ( $options, $in, $out, $record, $mask, $tmp_dir, $tmp_file, $fh_tmp, $fh_in, $fh_out, $entry );
45 $options = Maasha::Biopieces::parse_options(
47 { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
48 { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
49 { long => 'no_mask', short => 'N', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
53 $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
54 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
56 $mask = 1 if not $options->{ "no_mask" };
58 $tmp_dir = Maasha::Biopieces::get_tmpdir();
60 $tmp_file = "$tmp_dir/write_2bit.fna";
62 $fh_tmp = Maasha::Filesys::file_write_open( $tmp_file );
64 $fh_out = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
66 while ( $record = Maasha::Biopieces::get_record( $in ) )
68 if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) {
69 Maasha::Fasta::put_entry( $entry, $fh_tmp );
72 Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
77 $fh_in = Maasha::Filesys::file_read_open( $tmp_file );
79 Maasha::TwoBit::fasta2twobit( $fh_in, $fh_out, $mask );
86 Maasha::Biopieces::close_stream( $in );
87 Maasha::Biopieces::close_stream( $out );
90 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
95 Maasha::Biopieces::status_set();
101 Maasha::Biopieces::status_log();
105 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<