rewrite begin

[biopieces.git] / bp_bin / write_tab

diff --git a/bp_bin/write_tab b/bp_bin/write_tab
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..bc6fbd9e04e21fd8f103f507b28523eb633267f3 100755 (executable)
--- a/bp_bin/write_tab
+++ b/bp_bin/write_tab
@@ -1,6 +1,151 @@
-#!/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 tabular output from the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use warnings;
 use strict;
+use Maasha::Fasta;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_out, @vals, $ok, $key, @keys, $A, $B, %no_keys, $sort_keys, $check_sort );
+
+$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 => 'comment',   short => 'c', type => 'flag',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'delimit',   short => 'd', type => 'string', mandatory => 'no', default => "\t",  allowed => undef, disallowed => undef },
+        { long => 'keys',      short => 'k', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'no_keys',   short => 'K', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'compress',  short => 'Z', 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" }, $options->{ "compress" } );
+
+map { $no_keys{ $_ } = 1 } @{ $options->{ "no_keys" } };
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    undef @vals;
+    $ok = 1;
+    
+    if ( $options->{ "keys" } )
+    {
+        map { $ok = 0 if not exists $record->{ $_ } } @{ $options->{ "keys" } };
+
+        if ( $ok )
+        {
+            foreach $key ( @{ $options->{ "keys" }  } )
+            {
+                if ( exists $record->{ $key } )
+                {
+                    push @keys, $key if $options->{ "comment" };
+                    push @vals, $record->{ $key };
+                }
+            }
+         }
+    }
+    else
+    {
+        if ( not $check_sort )
+        {
+            $sort_keys = 1;
+
+            map { $sort_keys = 0 if $_ !~ /^V(\d+)$/ } keys %{ $record };
+
+            $check_sort = 1;
+        }
+
+        if ( $sort_keys )
+        {
+            foreach $key ( sort { $A = $a; $B = $b; $A =~ s/^V(\d+)$/$1/; $B =~ s/^V(\d+)$/$1/; $A <=> $B } keys %{ $record } )
+            {
+                next if exists $no_keys{ $key };
+
+                push @keys, $key if $options->{ "comment" };
+                push @vals, $record->{ $key };
+            }
+        }
+        else
+        {
+            foreach $key ( keys %{ $record } )
+            {
+                next if exists $no_keys{ $key };
+
+                push @keys, $key if $options->{ "comment" };
+                push @vals, $record->{ $key };
+            }
+        
+        }
+    }
+
+    if ( @keys and $options->{ "comment" } )
+    {
+        print $data_out "#", join( $options->{ "delimit" }, @keys ), "\n";
+
+        delete $options->{ "comment" };
+    }
+
+    print $data_out join( $options->{ "delimit" }, @vals ), "\n" if @vals;
+
+    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+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__