From fb0d4231f99ab2f078cfaf8c58dc49272e502658 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 7 Nov 2008 10:42:23 +0000
Subject: [PATCH] finished assemble_tag_contigs

git-svn-id: http://biopieces.googlecode.com/svn/trunk@297 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/assemble_tag_contigs   |   6 ++
 code_perl/Maasha/Biopieces.pm | 149 ++++++++++++++++++++++++++++++++++
 2 files changed, 155 insertions(+)
 create mode 100755 bp_bin/assemble_tag_contigs

diff --git a/bp_bin/assemble_tag_contigs b/bp_bin/assemble_tag_contigs
new file mode 100755
index 0000000..4cd1d44
--- /dev/null
+++ b/bp_bin/assemble_tag_contigs
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biopieces;
diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm
index 51821ac..c5c3c9d 100644
--- a/code_perl/Maasha/Biopieces.pm
+++ b/code_perl/Maasha/Biopieces.pm
@@ -185,6 +185,7 @@ sub run_script
     elsif ( $script eq "read_solexa" )              { script_read_solexa(               $in, $out, $options ) }
     elsif ( $script eq "read_solid" )               { script_read_solid(                $in, $out, $options ) }
     elsif ( $script eq "read_mysql" )               { script_read_mysql(                $in, $out, $options ) }
+    elsif ( $script eq "assemble_tag_contigs" )     { script_assemble_tag_contigs(      $in, $out, $options ) }
     elsif ( $script eq "format_genome" )            { script_format_genome(             $in, $out, $options ) }
     elsif ( $script eq "length_seq" )               { script_length_seq(                $in, $out, $options ) }
     elsif ( $script eq "uppercase_seq" )            { script_uppercase_seq(             $in, $out, $options ) }
@@ -2076,6 +2077,154 @@ sub script_read_mysql
 }
 
 
+sub script_assemble_tag_contigs
+{
+    # Martin A. Hansen, November 2008.
+
+    # Assemble tags from the stream into
+    # tag contigs.
+
+    my ( $in,        # handle to in stream
+         $out,       # handle to out stream
+         $options,   # options hash
+       ) = @_;
+
+    # Returns nothing.
+
+    my ( $record, $new_record, %fh_hash, $fh_out, $chr, $array, $pos, $beg, $end, $score, $file, $id );
+
+    while ( $record = get_record( $in ) ) 
+    {
+        $record->{ "CHR" }     = $record->{ "S_ID" }  if not defined $record->{ "CHR" };
+        $record->{ "CHR_BEG" } = $record->{ "S_BEG" } if not defined $record->{ "CHR_BEG" };
+        $record->{ "CHR_END" } = $record->{ "S_END" } if not defined $record->{ "CHR_END" };
+
+        if ( $record->{ "CHR" } and defined $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
+        {
+            $fh_hash{ $record->{ "CHR" } } = Maasha::Common::write_open( "$BP_TMP/$record->{ 'CHR' }" ) if not exists $fh_hash{ $record->{ "CHR" } };
+
+            $fh_out = $fh_hash{ $record->{ "CHR" } };
+        
+            Maasha::UCSC::bed_put_entry( $record, $fh_out, 5 );
+        }
+    }
+
+    map { close $_ } keys %fh_hash;
+
+    foreach $chr ( sort keys %fh_hash )
+    {
+        $array = tag_contigs_assemble( "$BP_TMP/$chr" );
+
+        $pos = 0;
+        $id  = 0;
+
+        while ( ( $beg, $end, $score ) = tag_contigs_scan( $array, $pos ) and $beg )
+        {
+            $new_record = {
+                CHR     => $chr,
+                CHR_BEG => $beg,
+                CHR_END => $end - 1,
+                Q_ID    => sprintf( "TC%06d", $id ),
+                SCORE   => $score,
+                STRAND  => $record->{ 'STRAND' } || '+',
+            };
+
+            put_record( $new_record, $out );
+
+            $pos = $end;
+            $id++;
+        }
+
+        unlink "$BP_TMP/$chr";
+    }
+}
+
+
+sub tag_contigs_assemble
+{
+    # Martin A. Hansen, November 2008.
+
+    # Given a BED file with entries from only one
+    # chromosome assembles tag contigs from these
+    # ignoring strand information. Only tags with
+    # a score higher than the clone count over
+    # genomic loci (the SCORE field) is included
+    # in the tag contigs.
+
+    #       -----------              tags
+    #          -------------
+    #               ----------
+    #                     ----------
+    #       ========================  tag contig
+
+
+    my ( $path,   # full path to BED file
+       ) = @_;
+
+    # Returns an arrayref.
+
+    my ( $fh, $entry, $clones, $score, @array );
+
+    $fh = Maasha::Common::read_open( $path );
+
+    while ( $entry = Maasha::UCSC::bed_get_entry( $fh ) )
+    {
+        if ( $entry->{ 'Q_ID' } =~ /(\d+)$/ )
+        {
+            $clones = $1;
+
+            $score = int( $clones / $entry->{ 'SCORE' } );
+        
+            map { $array[ $_ ] += $score } $entry->{ 'CHR_BEG' } .. $entry->{ 'CHR_END' } if $score >= 1;
+        }
+    }
+
+    close $fh;
+
+    return wantarray ? @array : \@array;
+}
+
+
+sub tag_contigs_scan
+{
+    # Martin A. Hansen, November 2008.
+    
+    # Scans an array with tag contigs and locates
+    # the next contig from a given position. The
+    # score of the tag contig is determined as the
+    # maximum value of the tag contig. If a tag contig
+    # is found a triple is returned with beg, end and score
+    # otherwise an empty triple is returned.
+
+    my ( $array,   # array to scan
+         $beg,     # position to start scanning from
+       ) = @_;
+
+    # Returns an arrayref.
+
+    my ( $end, $score );
+
+    $score = 0;
+
+    while ( $beg < scalar @{ $array } and not $array->[ $beg ] ) { $beg++ }
+
+    $end = $beg;
+
+    while ( $array->[ $end ] )
+    {
+        $score = Maasha::Calc::max( $score, $array->[ $end ] );
+    
+        $end++
+    }
+
+    if ( $score > 0 ) {
+        return wantarray ? ( $beg, $end, $score ) : [ $beg, $end, $score ];
+    } else {
+        return wantarray ? () : [];
+    }
+}
+
+
 sub script_format_genome
 {
     # Martin A. Hansen, Juli 2008.
-- 
2.39.5