+use Maasha::Biopieces;
+use Maasha::Plot;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $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 => $default, allowed => undef, disallowed => undef },
+ { long => 'xlabel', short => 'X', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'ylabel', short => 'Y', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'logscale_y', short => 'L', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ ]
+);
+
+$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->{ "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;
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+ Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+