added assemble_contigs

git-svn-id: http://biopieces.googlecode.com/svn/trunk@682 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/assemble_contigs b/bp_bin/assemble_contigs
new file mode 100755 (executable)
index 0000000..3e73a76
--- /dev/null
+++ b/bp_bin/assemble_contigs
@@ -0,0 +1,148 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Calculate coverage of reads mapped to a backbone sequence.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+
+use Data::Dumper;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::UCSC::Wiggle;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $contig_hash, $i, $s_id, $strand, $new_record, $contig, $beg, $end, @array, $min, $max, $mean );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'bridge', short => 'b', 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 ) ) 
+{
+    if ( $record->{ 'S_ID' } and $record->{ 'STRAND' } )
+    {
+        if ( $record->{ 'Q_ID' } and $record->{ 'S_BEG' } and $record->{ 'S_END' } )
+        {
+            for ( $i = $record->{ 'S_BEG' }; $i <= $record->{ 'S_END' }; $i++ ) {
+                $contig_hash->{ $record->{ 'S_ID' } }->{ $record->{ 'STRAND' } }->[ $i ]++;
+            }
+        }
+
+        if ( $record->{ 'Q_ID1' } and $record->{ 'S_BEG1' } and $record->{ 'S_END1' } and 
+             $record->{ 'Q_ID2' } and $record->{ 'S_BEG2' } and $record->{ 'S_END2' }
+        )
+        {
+            if ( $options->{ 'bridge' } )
+            {
+                ( $record->{ 'S_BEG1' }, $record->{ 'S_END2' } ) = ( $record->{ 'S_BEG2' }, $record->{ 'S_END1' } ) if ( $record->{ 'S_BEG1' } > $record->{ 'S_END2' } );
+
+                for ( $i = $record->{ 'S_BEG1' }; $i <= $record->{ 'S_END2' }; $i++ ) {
+                    $contig_hash->{ $record->{ 'S_ID' } }->{ $record->{ 'STRAND' } }->[ $i ]++;
+                }
+            }
+            else
+            {
+                for ( $i = $record->{ 'S_BEG1' }; $i <= $record->{ 'S_END1' }; $i++ ) {
+                    $contig_hash->{ $record->{ 'S_ID' } }->{ $record->{ 'STRAND' } }->[ $i ]++;
+                }
+
+                for ( $i = $record->{ 'S_BEG2' }; $i <= $record->{ 'S_END2' }; $i++ ) {
+                    $contig_hash->{ $record->{ 'S_ID' } }->{ $record->{ 'STRAND' } }->[ $i ]++;
+                }
+            }
+        }
+    }
+
+    # Maasha::Biopieces::put_record( $record, $out );
+}
+
+$contig = 0;
+
+foreach $s_id ( keys %{ $contig_hash } )
+{
+    foreach $strand ( keys %{ $contig_hash->{ $s_id } } )
+    {
+        $beg = 0;
+        $end = 0;
+
+        while ( ( $beg, $end ) = Maasha::UCSC::Wiggle::fixedstep_scan( $contig_hash->{ $s_id }->{ $strand }, $beg ) )
+        {
+            @array = @{ $contig_hash->{ $s_id }->{ $strand } }[ $beg .. $end - 1 ];
+
+            ( $min, $max ) = Maasha::Calc::minmax( \@array );
+            $mean          = Maasha::Calc::mean( \@array );
+
+            $new_record->{ 'S_ID' }        = $s_id;
+            $new_record->{ 'STRAND' }      = $strand;
+            $new_record->{ 'CONTIG_ID' }   = $contig;
+            $new_record->{ 'CONTIG_BEG' }  = $beg;
+            $new_record->{ 'CONTIG_END' }  = $end;
+            $new_record->{ 'CONTIG_LEN' }  = $end - $beg + 1;
+            $new_record->{ 'CONTIG_MIN' }  = $min;
+            $new_record->{ 'CONTIG_MAX' }  = $max;
+            $new_record->{ 'CONTIG_MEAN' } = sprintf "%.2f", $mean;
+            $new_record->{ 'CONTIG' }      = join ( ";", @array );
+
+            $beg = $end + 1;
+            $contig++;
+
+            Maasha::Biopieces::put_record( $new_record, $out );
+        }
+    }
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__

diff --git a/code_perl/Maasha/Matrix.pm b/code_perl/Maasha/Matrix.pm
index 4a29c4d96797bb2b7cc25753a34f78addc6c64d4..ed90a25ab943d7171e00aef0bbd1c3337be1ac17 100644 (file)
--- a/code_perl/Maasha/Matrix.pm
+++ b/code_perl/Maasha/Matrix.pm
@@ -906,11 +906,11 @@ sub list_check_sort
 }
 
 
-sub list_shrink
+sub list_deflate
 {
     # Martin A. Hansen, September 2009.
 
-    # Shrinks a list of values to a specified size 
+    # Defaltes a list of values to a specified size 
     # and at the same time average the values.
 
     my ( $list,
@@ -919,19 +919,28 @@ sub list_shrink
 
     # Returns nothing.
 
-    my ( $old_size, $bucket_size, $i, @new_list );
+    my ( $old_size, $bucket_size, $bucket_rest, $i, @new_list );
 
     $old_size = scalar @{ $list };
 
-    Maasha::Common::error( qq(can't shrink to a bigger list: $old_size < $new_size ) ) if $old_size < $new_size;
+    Maasha::Common::error( qq(Can't shrink to a bigger list: $old_size < $new_size ) ) if $old_size < $new_size;
 
-    $bucket_size = int( $old_size / $new_size );
+    $bucket_size  = int( $old_size / $new_size );
+    $bucket_rest  = $old_size - ( $new_size * $bucket_size );
 
-    for ( $i = 0; $i < $old_size - $bucket_size + 1; $i += $bucket_size ) {
-        push @new_list, Maasha::Calc::mean( [ splice @{ $list }, $i, $bucket_size ] );
+    print STDERR "old_size: $old_size    new_size: $new_size   bucket_size: $bucket_size   bucket_rest: $bucket_rest\n";
+
+    $i = 0;
+
+    while ( $i < $new_size )
+    {
+        # push @new_list, [ @{ $list }[ $i * $bucket_size .. $i * $bucket_size + $bucket_size - 1 ] ];
+        push @new_list, Maasha::Calc::mean( [ @{ $list }[ $i * $bucket_size .. $i * $bucket_size + $bucket_size - 1 ] ] );
+
+        $i ++;
     }
 
-    $list = \@new_list;
+    @{ $list } = @new_list;
 }