refactoring of assemble_pairs

[biopieces.git] / bp_bin / write_align

diff --git a/bp_bin/write_align b/bp_bin/write_align
index c8c800fbc01100b8cd9e82c26358933e470ca42e..f0a0598d68aeff4d5e92e11bd2fb539749401cc0 100755 (executable)
--- a/bp_bin/write_align
+++ b/bp_bin/write_align
@@ -1,6 +1,94 @@
 #!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Write aligned sequences from the stream as a pretty alignment.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
 use warnings;
 use strict;
+use Maasha::Biopieces;
+use Maasha::Align;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $data_out, @entries );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'no_stream',    short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'data_out',     short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'wrap',         short => 'w', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => '0'   },
+        { long => 'no_ruler',     short => 'R', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'no_consensus', short => 'C', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$data_out = Maasha::Biopieces::write_stream( $options->{ "data_out" } ) ;
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
+        push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
+    }
+
+    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+if ( scalar( @entries ) == 2 ) {
+    Maasha::Align::align_print_pairwise( $entries[ 0 ], $entries[ 1 ], $data_out, $options->{ "wrap" } );
+} elsif ( scalar ( @entries ) > 2 ) {
+    Maasha::Align::align_print_multi( \@entries, $data_out, $options->{ "wrap" }, $options->{ "no_ruler" }, $options->{ "no_consensus" } );
+}
+
+close $data_out;
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use Maasha::Biotools;
+__END__