migrated tile_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@441 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/tile_seq b/bp_bin/tile_seq
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..500f70530b04be7d6a8298ee21726443ad76bc70 100755 (executable)
--- a/bp_bin/tile_seq
+++ b/bp_bin/tile_seq
@@ -1,6 +1,108 @@
-#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Using the first sequence in the stream as reference, tile all subsequent sequences based on pairwise alignments.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use warnings;
 use strict;
+use Maasha::Biopieces;
+use Maasha::Align;
+
+use constant {
+    SEQ_NAME => 0,
+    SEQ      => 1,
+};
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $first, $ref_entry, @entries );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'identity',       short => 'i', type => 'uint', mandatory => 'no', default => 70,    allowed => undef, disallowed => 0 },
+        { long => 'supress_indels', short => 's', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$first = 1;
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+    {
+        if ( $first )
+        {
+            $ref_entry = [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
+
+            $first = 0;
+        }
+        else
+        {
+            push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
+        }
+    }
+    else
+    {
+        Maasha::Biopieces::put_record( $record, $out );
+    }
+}
+
+@entries = Maasha::Align::align_tile( $ref_entry, \@entries, $options );
+
+map { Maasha::Biopieces::put_record( { SEQ_NAME => $_->[ SEQ_NAME ], SEQ => $_->[ SEQ ] }, $out ) } @entries;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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 );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
 
-use Maasha::BioRun;

diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm
index aa82088fabd69a5d42a7e97a4732fa730b06fc87..e8a5d5aab0b8fdde78ac1c22964fc8b54fa54213 100644 (file)
--- a/code_perl/Maasha/BioRun.pm
+++ b/code_perl/Maasha/BioRun.pm
@@ -135,7 +135,6 @@ sub run_script
     elsif ( $script eq "remove_indels" )            { script_remove_indels(             $in, $out, $options ) }
     elsif ( $script eq "get_genome_align" )         { script_get_genome_align(          $in, $out, $options ) }
     elsif ( $script eq "get_genome_phastcons" )     { script_get_genome_phastcons(      $in, $out, $options ) }
-    elsif ( $script eq "tile_seq" )                 { script_tile_seq(                  $in, $out, $options ) }
     elsif ( $script eq "soap_seq" )                 { script_soap_seq(                  $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 ) }
@@ -322,13 +321,6 @@ sub get_options
             flank|f=s
         );
     }
-    elsif ( $script eq "tile_seq" )
-    {
-        @options = qw(
-            identity|i=s
-            supress_indels|s
-        );
-    }
     elsif ( $script eq "soap_seq" )
     {
         @options = qw(
@@ -582,7 +574,7 @@ sub get_options
 
     # print STDERR Dumper( \%options );
 
-    $real = "beg|end|word_size|wrap|tile_size|len|prefix_length|mismatches|offset|num|skip|cpus|window_size|step_size";
+    $real = "beg|end|word_size|wrap|len|prefix_length|mismatches|offset|num|skip|cpus|window_size|step_size";
 
     foreach $opt ( keys %options )
     {
@@ -1672,51 +1664,6 @@ sub script_get_genome_phastcons
 }
 
 
-sub script_tile_seq
-{
-    # Martin A. Hansen, February 2008.
-
-    # Using the first sequence in stream as reference, tile
-    # all subsequent sequences based on pairwise alignments.
-
-    my ( $in,        # handle to in stream
-         $out,       # handle to out stream
-         $options,   # options hash
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( $record, $first, $ref_entry, @entries );
-
-    $first = 1;
-
-    while ( $record = Maasha::Biopieces::get_record( $in ) ) 
-    {
-        if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
-        {
-            if ( $first )
-            {
-                $ref_entry = [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
-
-                $first = 0;
-            }
-            else
-            {
-                push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
-            }
-        }
-        else
-        {
-            Maasha::Biopieces::put_record( $record, $out );
-        }
-    }
-
-    @entries = Maasha::Align::align_tile( $ref_entry, \@entries, $options );
-
-    map { Maasha::Biopieces::put_record( { SEQ_NAME => $_->[ SEQ_NAME ], SEQ => $_->[ SEQ ] }, $out ) } @entries;
-}
-
-
 sub script_soap_seq
 {
     # Martin A. Hansen, July 2008.