-#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Plot chromosome distribution histogram.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Plot;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $default, $terminals, $record, %data_hash, @data_list, $elem, $sort_key, $count, $result, $fh );
+
+$default = "Chromosome Distribution";
+$terminals = "dumb,x11,aqua,post,svg";
+
+$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 => 'terminal', short => 't', type => 'string', mandatory => 'no', default => 'dumb', allowed => $terminals, disallowed => undef },
+ { long => 'title', short => 'T', type => 'string', mandatory => 'no', default => $default, allowed => undef, disallowed => undef },
+ { long => 'xlabel', short => 'X', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'ylabel', short => 'Y', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ ]
+);
+
+$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->{ "CHR" } ) { # generic
+ $data_hash{ $record->{ "CHR" } }++;
+ } elsif ( $record->{ "REC_TYPE" } eq "PATSCAN" and $record->{ "S_ID" } =~ /^chr/i ) { # patscan
+ $data_hash{ $record->{ "S_ID" } }++;
+ } elsif ( $record->{ "REC_TYPE" } eq "PSL" and $record->{ "S_ID" } =~ /^chr/i ) { # BLAT / PSL
+ $data_hash{ $record->{ "S_ID" } }++;
+ } elsif ( $record->{ "REC_TYPE" } eq "BLAST" and $record->{ "S_ID" } =~ /^chr/i ) { # BLAST
+ $data_hash{ $record->{ "S_ID" } }++;
+ }
+
+ Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+foreach $elem ( keys %data_hash )
+{
+ $sort_key = $elem;
+
+ $sort_key =~ s/chr//i;
+
+ $sort_key =~ s/^X(.*)/99$1/;
+ $sort_key =~ s/^Y(.*)/99$1/;
+ $sort_key =~ s/^Z(.*)/999$1/;
+ $sort_key =~ s/^M(.*)/9999$1/;
+ $sort_key =~ s/^U(.*)/99999$1/;
+
+ $count = $sort_key =~ tr/_//;
+
+ $sort_key =~ s/_.*/"999999" x $count/ex;
+
+ push @data_list, [ $elem, $data_hash{ $elem }, $sort_key ];
+}
+
+@data_list = sort { $a->[ 2 ] <=> $b->[ 2 ] } @data_list;
+
+$result = Maasha::Plot::histogram_chrdist( \@data_list, $options );
+
+$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
+
+print $fh "$_\n" foreach @{ $result };
+
+close $fh;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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;
elsif ( $script eq "remove_ucsc_tracks" ) { script_remove_ucsc_tracks( $in, $out, $options ) }
elsif ( $script eq "plot_histogram" ) { script_plot_histogram( $in, $out, $options ) }
elsif ( $script eq "plot_lendist" ) { script_plot_lendist( $in, $out, $options ) }
- elsif ( $script eq "plot_chrdist" ) { script_plot_chrdist( $in, $out, $options ) }
elsif ( $script eq "plot_karyogram" ) { script_plot_karyogram( $in, $out, $options ) }
elsif ( $script eq "plot_matches" ) { script_plot_matches( $in, $out, $options ) }
elsif ( $script eq "plot_seqlogo" ) { script_plot_seqlogo( $in, $out, $options ) }
key|k=s
);
}
- elsif ( $script eq "plot_chrdist" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- terminal|t=s
- title|T=s
- xlabel|X=s
- ylabel|Y=s
- );
- }
elsif ( $script eq "plot_karyogram" )
{
@options = qw(
$first = 1;
- $fh = write_stream( $options->{ "data_out" }, $options->{ "compress" } );
+ $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" }, $options->{ "compress" } );
while ( $record = Maasha::Biopieces::get_record( $in ) )
{
my ( $fh, $record, $entry );
- $fh = write_stream( $options->{ "data_out" }, $options->{ "compress" } );
+ $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" }, $options->{ "compress" } );
while ( $record = Maasha::Biopieces::get_record( $in ) )
{
$tmp_file = "$BP_TMP/write_2bit.fna";
$fh_tmp = Maasha::Common::write_open( $tmp_file );
- $fh_out = write_stream( $options->{ "data_out" } );
+ $fh_out = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
while ( $record = Maasha::Biopieces::get_record( $in ) )
{
my ( $record, $fh, $entry );
- $fh = write_stream( $options->{ "data_out" }, $options->{ "compress" } );
+ $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" }, $options->{ "compress" } );
while ( $record = Maasha::Biopieces::get_record( $in ) )
{
my ( $record, $fh );
- $fh = write_stream( $options->{ "data_out" } );
+ $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
while ( $record = Maasha::Biopieces::get_record( $in ) )
{
$logo = Maasha::Plot::seq_logo( \@entries );
- $fh = write_stream( $options->{ "data_out" } );
+ $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
print $fh $logo;
$plot = Maasha::Plot::lineplot_simple( $AoA, $options, $BP_TMP );
- $fh = write_stream( $options->{ "data_out" } );
+ $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
print $fh "$_\n" foreach @{ $plot };
$result = Maasha::Plot::histogram_simple( \@data_list, $options );
- $fh = write_stream( $options->{ "data_out" } );
+ $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
print $fh "$_\n" foreach @{ $result };
$result = Maasha::Plot::histogram_lendist( \@data_list, $options );
- $fh = write_stream( $options->{ "data_out" } );
-
- print $fh "$_\n" foreach @{ $result };
-
- close $fh;
-}
-
-
-sub script_plot_chrdist
-{
- # Martin A. Hansen, August 2007.
-
- # Plot chromosome distribution using GNU plot.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, %data_hash, @data_list, $elem, $sort_key, $count, $result, $fh );
-
- $options->{ "title" } ||= "Chromosome Distribution";
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- if ( $record->{ "CHR" } ) { # generic
- $data_hash{ $record->{ "CHR" } }++;
- } elsif ( $record->{ "REC_TYPE" } eq "PATSCAN" and $record->{ "S_ID" } =~ /^chr/i ) { # patscan
- $data_hash{ $record->{ "S_ID" } }++;
- } elsif ( $record->{ "REC_TYPE" } eq "PSL" and $record->{ "S_ID" } =~ /^chr/i ) { # BLAT / PSL
- $data_hash{ $record->{ "S_ID" } }++;
- } elsif ( $record->{ "REC_TYPE" } eq "BLAST" and $record->{ "S_ID" } =~ /^chr/i ) { # BLAST
- $data_hash{ $record->{ "S_ID" } }++;
- }
-
- Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- foreach $elem ( keys %data_hash )
- {
- $sort_key = $elem;
-
- $sort_key =~ s/chr//i;
-
- $sort_key =~ s/^X(.*)/99$1/;
- $sort_key =~ s/^Y(.*)/99$1/;
- $sort_key =~ s/^Z(.*)/999$1/;
- $sort_key =~ s/^M(.*)/9999$1/;
- $sort_key =~ s/^U(.*)/99999$1/;
-
- $count = $sort_key =~ tr/_//;
-
- $sort_key =~ s/_.*/"999999" x $count/ex;
-
- push @data_list, [ $elem, $data_hash{ $elem }, $sort_key ];
- }
-
- @data_list = sort { $a->[ 2 ] <=> $b->[ 2 ] } @data_list;
-
- $result = Maasha::Plot::histogram_chrdist( \@data_list, $options );
-
- $fh = write_stream( $options->{ "data_out" } );
+ $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
print $fh "$_\n" foreach @{ $result };
$result = Maasha::Plot::karyogram( \%data_hash, \%options );
- $fh = write_stream( $options->{ "data_out" } );
+ $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
print $fh $result;
$result = Maasha::Plot::dotplot_matches( \@data, $options, $BP_TMP );
- $fh = write_stream( $options->{ "data_out" } );
+ $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
print $fh "$_\n" foreach @{ $result };
use Data::Dumper;
use SVG;
use IPC::Open2;
-use Time::HiRes qw( gettimeofday );
use Maasha::Common;
-use Maasha::Calc;
+use Maasha::Filesys;
+use Maasha::Seq;
use vars qw ( @ISA @EXPORT );
use constant {
$tmp_file = "$tmp_dir/lineplot_simple.tab";
- $fh_out = Maasha::Common::write_open( $tmp_file );
+ $fh_out = Maasha::Filesys::file_write_open( $tmp_file );
map { print $fh_out join( "\t", @{ $_ } ), "\n" } @{ $data };
$forward_file = "$tmp_dir/match_f.tab";
$backward_file = "$tmp_dir/match_r.tab";
- $fh_forward = Maasha::Common::write_open( $forward_file );
- $fh_backward = Maasha::Common::write_open( $backward_file );
+ $fh_forward = Maasha::Filesys::file_write_open( $forward_file );
+ $fh_backward = Maasha::Filesys::file_write_open( $backward_file );
$q_max = 0;
$s_max = 0;
# stalk => "gray66",
);
- $fh = Maasha::Common::read_open( $file );
+ $fh = Maasha::Filesys::file_read_open( $file );
while ( $line = <$fh> )
{
projects / biopieces.git / commitdiff