X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fread_2bit;h=7eebe05309df6b0d26004332d38e270b23f94cee;hb=5de6112b70b59420b245ce636a8b2e3c90acbe00;hp=c8c800fbc01100b8cd9e82c26358933e470ca42e;hpb=f246d97ce9ddc906801ed22b4e79567dc8914c45;p=biopieces.git

diff --git a/bp_bin/read_2bit b/bp_bin/read_2bit
index c8c800f..7eebe05 100755
--- a/bp_bin/read_2bit
+++ b/bp_bin/read_2bit
@@ -1,6 +1,108 @@
 #!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Read nucleotide sequences in 2bit format from one or more files.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
 use warnings;
 use strict;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::TwoBit;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $file, $data_in, $mask, $toc, $line, $num );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'num',     short => 'n', type => 'uint',   mandatory => 'no', default => undef, allowed => undef, disallowed => '0'   },
+        { long => 'no_mask', short => 'N', type => 'flag',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) {
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+$mask = 1 if not $options->{ "no_mask" };
+
+$num = 1;
+
+foreach $file ( @{ $options->{ "data_in" } } )
+{
+    $data_in = Maasha::Filesys::file_read_open( $file );
+
+    $toc = Maasha::TwoBit::twobit_get_TOC( $data_in );
+
+    foreach $line ( @{ $toc } )
+    {
+        $record->{ "SEQ_NAME" } = $line->[ 0 ];
+        $record->{ "SEQ" }      = Maasha::TwoBit::twobit_get_seq( $data_in, $line->[ 1 ], undef, undef, $mask );
+        $record->{ "SEQ_LEN" }  = length $record->{ "SEQ" };
+
+        Maasha::Biopieces::put_record( $record, $out );
+
+        goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+        $num++;
+    }
+
+    close $data_in;
+}
+
+NUM:
+
+close $data_in if $data_in;
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use Maasha::Biotools;
+__END__