migrated write_align

git-svn-id: http://biopieces.googlecode.com/svn/trunk@394 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/write_align b/bp_bin/write_align
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..dcbe3452a4c413d289721b70244911659726e0a4 100755 (executable)
--- a/bp_bin/write_align
+++ b/bp_bin/write_align
@@ -1,6 +1,96 @@
-#!/usr/bin/env perl
+#!/usr/bin/env perl -w
+
+# 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 ( $run_time_beg, $run_time_end, $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;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    $run_time_beg = Maasha::Biopieces::run_time();
+
+    Maasha::Biopieces::log_biopiece();
+}
+
+END
+{
+    Maasha::Biopieces::close_stream( $in );
+    Maasha::Biopieces::close_stream( $out );
+
+    $run_time_end = Maasha::Biopieces::run_time();
+
+    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use Maasha::BioRun;
+__END__

diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm
index c54c9ef8c664ce134c6354b5d3a459c3805e0353..e5845d33b0c26bd4efa52cd4d31bdd5180c06a06 100644 (file)
--- a/code_perl/Maasha/BioRun.pm
+++ b/code_perl/Maasha/BioRun.pm
@@ -156,7 +156,6 @@ sub run_script
     elsif ( $script eq "soap_seq" )                 { script_soap_seq(                  $in, $out, $options ) }
     elsif ( $script eq "match_seq" )                { script_match_seq(                 $in, $out, $options ) }
     elsif ( $script eq "create_vmatch_index" )      { script_create_vmatch_index(       $in, $out, $options ) }
-    elsif ( $script eq "write_align" )              { script_write_align(               $in, $out, $options ) }
     elsif ( $script eq "write_bed" )                { script_write_bed(                 $in, $out, $options ) }
     elsif ( $script eq "write_psl" )                { script_write_psl(                 $in, $out, $options ) }
     elsif ( $script eq "write_fixedstep" )          { script_write_fixedstep(           $in, $out, $options ) }
@@ -490,16 +489,6 @@ sub get_options
             no_stream|x
         );
     }
-    elsif ( $script eq "write_align" )
-    {
-        @options = qw(
-            wrap|w=s
-            no_stream|x
-            no_ruler|R
-            no_consensus|C
-            data_out|o=s
-        );
-    }
     elsif ( $script eq "write_bed" )
     {
         @options = qw(
@@ -3011,42 +3000,6 @@ sub script_create_vmatch_index
 }
 
 
-sub script_write_align
-{
-    # Martin A. Hansen, August 2007.
-
-    # Write pretty alignments aligned sequences in stream.
-
-    my ( $in,        # handle to in stream
-         $out,       # handle to out stream
-         $options,   # options hash
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( $fh, $record, @entries );
-
-    $fh = 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 ], $fh, $options->{ "wrap" } );
-    } elsif ( scalar ( @entries ) > 2 ) {
-        Maasha::Align::align_print_multi( \@entries, $fh, $options->{ "wrap" }, $options->{ "no_ruler" }, $options->{ "no_consensus" } );
-    }
-
-    close $fh if $fh;
-}
-
-
 sub script_write_bed
 {
     # Martin A. Hansen, August 2007.