From 88bf14365d03f675a6606829562af59540ef3b4a Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 1 Mar 2010 11:30:33 +0000
Subject: [PATCH] added wiggle to BGB

git-svn-id: http://biopieces.googlecode.com/svn/trunk@879 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_perl/Maasha/BGB/Wiggle.pm | 173 +++++++++++++++++++++++++++++++++
 1 file changed, 173 insertions(+)
 create mode 100644 code_perl/Maasha/BGB/Wiggle.pm

diff --git a/code_perl/Maasha/BGB/Wiggle.pm b/code_perl/Maasha/BGB/Wiggle.pm
new file mode 100644
index 0000000..9bf8afa
--- /dev/null
+++ b/code_perl/Maasha/BGB/Wiggle.pm
@@ -0,0 +1,173 @@
+package Maasha::BGB::Wiggle;
+
+# Copyright (C) 2010 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+# Routines for creating Biopieces Browser wiggle tracks.
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Data::Dumper;
+use Maasha::Common;
+use Maasha::Calc;
+use Maasha::Filesys;
+use Maasha::KISS;
+use Maasha::Matrix;
+
+use vars qw( @ISA @EXPORT );
+
+@ISA = qw( Exporter );
+
+use constant {
+    S_ID             => 0,
+    S_BEG            => 1,
+    S_END            => 2,
+    Q_ID             => 3,
+    SCORE            => 4,
+    STRAND           => 5,
+    HITS             => 6,
+    ALIGN            => 7,
+    BLOCK_COUNT      => 8,
+    BLOCK_BEGS       => 9,
+    BLOCK_LENS       => 10,
+    BLOCK_TYPE       => 11,
+};
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+sub wiggle_encode
+{
+    # Martin A. Hansen, February 2010.
+   
+    # Read a KISS file and encode a Wiggle list.
+
+    my ( $file,   # KISS file
+       ) = @_;
+
+    # Returns a list.
+    
+    my ( $fh, $entry, $vals, $i );
+
+    $fh = Maasha::Filesys::file_read_open( $file );
+
+    while ( $entry = Maasha::KISS::kiss_entry_get( $fh ) ) {
+        map { $vals->[ $_ ]++ } ( $entry->[ S_BEG ] .. $entry->[ S_END ] );
+    }
+
+    close $fh;
+
+    for ( $i = 0; $i < scalar @{ $vals }; $i++ ) {
+        $vals->[ $i ] = 0 if not defined $vals->[ $i ];
+    }
+
+    return wantarray ? @{ $vals } : $vals;
+}
+
+
+sub wiggle_normalize
+{
+    my ( $vals,   # Wiggle values
+         $size,   # Deflated list size
+       ) = @_;
+
+    # Returns a list
+
+    if ( scalar @{ $vals } < $size ) {
+        Maasha::Matrix::list_inflate( $vals, $size );
+    } elsif ( scalar @{ $vals } > $size ) {
+        Maasha::Matrix::list_deflate( $vals, $size );
+    }
+
+    return wantarray ? @{ $vals } : $vals;
+}
+
+
+sub wiggle_store
+{
+    # Martin A. Hansen, February 2010.
+
+    # Store a list of wiggle values as a byte array to a 
+    # specified file.
+    
+    my ( $file,   # path to file
+         $vals,   # Wiggle values
+       ) = @_;
+
+    # Returns nothing.
+
+    my ( $bin, $fh );
+
+    $bin = pack( "S*", @{ $vals } );
+
+    $fh = Maasha::Filesys::file_write_open( $file );
+
+    print $fh $bin;
+
+    close $fh;
+}
+
+
+sub wiggle_retrieve
+{
+    # Martin A. Hansen, February 2010.
+
+    # Restore an interval of Wiggle values from
+    # a specified Wiggle file and return these
+    # as a list.
+
+    my ( $file,   # path to wiggle file
+         $beg,    # begin position
+         $end,    # end position
+       ) = @_;
+
+    # Returns a list.
+
+    my ( $fh, $bin, @vals );
+
+    Maasha::Common::error( qq(begin < 0: $beg) ) if $beg < 0;
+    Maasha::Common::error( qq(begin > end: $beg > $end) ) if $beg > $end;
+
+    $fh = Maasha::Filesys::file_read_open( $file );
+
+    sysseek( $fh, $beg * 2, 0 );
+    sysread( $fh, $bin, ( $end - $beg + 1 ) * 2 );
+
+    close $fh;
+
+    @vals = unpack( "S*", $bin );
+
+    return wantarray ? @vals : \@vals;
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+1;
+
+
+__END__
-- 
2.39.5