-#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Sort records in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, @keys, $key, @sort_cmd, $sort_str, $sort_sub, @records, $record, $i );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'keys', short => 'k', type => 'list', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ { long => 'reverse', short => 'r', 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" } );
+
+foreach $key ( @{ $options->{ "keys" } } )
+{
+ if ( $key =~ s/n$// ) {
+ push @sort_cmd, qq(\$a->{ "$key" } <=> \$b->{ "$key" });
+ } else {
+ push @sort_cmd, qq(\$a->{ "$key" } cmp \$b->{ "$key" });
+ }
+}
+
+$sort_str = join " or ", @sort_cmd;
+$sort_sub = eval "sub { $sort_str }"; # NB security issue!
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) {
+ push @records, $record;
+}
+
+@records = sort $sort_sub @records;
+
+if ( $options->{ "reverse" } )
+{
+ for ( $i = scalar @records - 1; $i >= 0; $i-- ) {
+ Maasha::Biopieces::put_record( $records[ $i ], $out );
+ }
+}
+else
+{
+ for ( $i = 0; $i < scalar @records; $i++ ) {
+ Maasha::Biopieces::put_record( $records[ $i ], $out );
+ }
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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 "rename_keys" ) { script_rename_keys( $in, $out, $options ) }
elsif ( $script eq "uniq_vals" ) { script_uniq_vals( $in, $out, $options ) }
- elsif ( $script eq "sort_records" ) { script_sort_records( $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 ) }
invert|i
);
}
- elsif ( $script eq "sort_records" )
- {
- @options = qw(
- reverse|r
- keys|k=s
- );
- }
elsif ( $script eq "plot_histogram" )
{
@options = qw(
Maasha::Common::error( qq(both --in_file and --genome specified) ) if $script eq "soap_seq" and $options{ "genome" } and $options{ "in_file" };
Maasha::Common::error( qq(no --genome specified) ) if $script =~ /get_genome_align|get_genome_phastcons|plot_phastcons_profiles|plot_karyogram/ and not $options{ "genome" };
Maasha::Common::error( qq(no --key specified) ) if $script =~ /plot_lendist|plot_histogram/ and not $options{ "key" };
- Maasha::Common::error( qq(no --keys speficied) ) if $script =~ /sort_records/ and not $options{ "keys" };
if ( $script eq "upload_to_ucsc" )
{
}
-sub script_sort_records
-{
- # Martin A. Hansen, August 2007.
-
- # Sort to sort records according to keys.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( @keys, $key, @sort_cmd, $sort_str, $sort_sub, @records, $record, $i );
-
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( $key =~ s/n$// ) {
- push @sort_cmd, qq(\$a->{ "$key" } <=> \$b->{ "$key" });
- } else {
- push @sort_cmd, qq(\$a->{ "$key" } cmp \$b->{ "$key" });
- }
- }
-
- $sort_str = join " or ", @sort_cmd;
- $sort_sub = eval "sub { $sort_str }"; # NB security issue!
-
- while ( $record = Maasha::Biopieces::get_record( $in ) ) {
- push @records, $record;
- }
-
- @records = sort $sort_sub @records;
-
- if ( $options->{ "reverse" } )
- {
- for ( $i = scalar @records - 1; $i >= 0; $i-- ) {
- Maasha::Biopieces::put_record( $records[ $i ], $out );
- }
- }
- else
- {
- for ( $i = 0; $i < scalar @records; $i++ ) {
- Maasha::Biopieces::put_record( $records[ $i ], $out );
- }
- }
-}
-
-
sub script_plot_histogram
{
# Martin A. Hansen, September 2007.
projects / biopieces.git / commitdiff