-#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Performs computations on records in stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Common;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $eval_key, @keys, $eval_val );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'eval', short => 'e', type => 'string', mandatory => 'yes', 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 ( $options->{ "eval" } =~ /^(\S+)\s*=\s*(.+)$/ )
+ {
+ $eval_key = $1;
+ $eval_val = $2;
+
+ if ( not @keys )
+ {
+ @keys = split /\s+|\+|-|\*|\/|\*\*/, $eval_val;
+
+ @keys = grep { exists $record->{ $_ } } @keys;
+ }
+
+ map { $eval_val =~ s/\Q$_\E/$record->{ $_ }/g } @keys;
+
+ $record->{ $eval_key } = eval "$eval_val";
+ Maasha::Common::error( qq(eval "$eval_key = $eval_val" failed -> $@) ) if $@;
+ }
+ else
+ {
+ Maasha::Common::error( qq(Bad compute expression: "$options->{ 'eval' }"\n) );
+ }
+
+ Maasha::Biopieces::put_record( $record, $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 );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use Maasha::BioRun;
+__END__
-#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Count the number of times values of given keys exists in stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Filesys;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $num, $record, %count_hash, @records, $tmp_dir, $tmp_file, $fh_out, $fh_in, $cache );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'keys', short => 'k', type => 'list', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$tmp_dir = Maasha::Biopieces::get_tmpdir();
+
+$tmp_file = "$tmp_dir/count_cache.tmp";
+
+$fh_out = Maasha::Filesys::file_write_open( $tmp_file );
+
+$cache = 0;
+$num = 0;
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ map { $count_hash{ $_ }{ $record->{ $_ } }++ if exists $record->{ $_ } } @{ $options->{ "keys" } };
+
+ push @records, $record;
+
+ if ( scalar @records > 5_000_000 ) # too many records to hold in memory - use disk cache
+ {
+ map { Maasha::Biopieces::put_record( $_, $fh_out ) } @records;
+
+ undef @records;
+
+ $cache = 1;
+ }
+
+ print STDERR "verbose: records read $num\n" if ( $options->{ 'verbose' } and ( $num % 1_000_000 ) == 0 );
+
+ $num++;
+}
+
+close $fh_out;
+
+if ( $cache )
+{
+ $num = 0;
+
+ $fh_in = Maasha::Common::read_open( $tmp_file );
+
+ while ( $record = Maasha::Biopieces::get_record( $fh_in ) )
+ {
+ map { $record->{ $_ . "_COUNT" } = $count_hash{ $_ }{ $record->{ $_ } } if exists $record->{ $_ } } @{ $options->{ "keys" } };
+
+ Maasha::Biopieces::put_record( $record, $out );
+
+ print STDERR "verbose: cache read $num\n" if ( $options->{ 'verbose' } and ( $num % 1_000_000 ) == 0 );
+
+ $num++;
+ }
+
+ close $fh_in;
+}
+
+foreach $record ( @records )
+{
+ map { $record->{ $_ . "_COUNT" } = $count_hash{ $_ }{ $record->{ $_ } } if exists $record->{ $_ } } @{ $options->{ "keys" } };
+
+ Maasha::Biopieces::put_record( $record, $out );
+}
+
+unlink $tmp_file;
+
+Maasha::Filesys::dir_remove( $tmp_dir );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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 );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use Maasha::BioRun;
+__END__
elsif ( $script eq "uniq_vals" ) { script_uniq_vals( $in, $out, $options ) }
elsif ( $script eq "merge_vals" ) { script_merge_vals( $in, $out, $options ) }
elsif ( $script eq "merge_records" ) { script_merge_records( $in, $out, $options ) }
- elsif ( $script eq "compute" ) { script_compute( $in, $out, $options ) }
elsif ( $script eq "flip_tab" ) { script_flip_tab( $in, $out, $options ) }
elsif ( $script eq "sort_records" ) { script_sort_records( $in, $out, $options ) }
- elsif ( $script eq "count_vals" ) { script_count_vals( $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 ) }
merge|m=s
);
}
- elsif ( $script eq "compute" )
- {
- @options = qw(
- eval|e=s
- );
- }
elsif ( $script eq "sort_records" )
{
@options = qw(
keys|k=s
);
}
- elsif ( $script eq "count_vals" )
- {
- @options = qw(
- 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|count_vals|sum_vals|mean_vals|median_vals|length_vals/ and not $options{ "keys" };
+ Maasha::Common::error( qq(no --keys speficied) ) if $script =~ /sort_records|sum_vals|mean_vals|median_vals|length_vals/ and not $options{ "keys" };
if ( $script eq "upload_to_ucsc" )
{
}
-sub script_compute
-{
- # Martin A. Hansen, August 2007.
-
- # Evaluate extression for records in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $eval_key, @keys, $eval_val );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- if ( $options->{ "eval" } )
- {
- if ( $options->{ "eval" } =~ /^(\S+)\s*=\s*(.+)$/ )
- {
- $eval_key = $1;
- $eval_val = $2;
-
- if ( not @keys )
- {
- @keys = split /\s+|\+|-|\*|\/|\*\*/, $eval_val;
-
- @keys = grep { exists $record->{ $_ } } @keys;
- }
-
- map { $eval_val =~ s/\Q$_\E/$record->{ $_ }/g } @keys;
-
- $record->{ $eval_key } = eval "$eval_val";
- Maasha::Common::error( qq(eval "$eval_key = $eval_val" failed -> $@) ) if $@;
- }
- else
- {
- Maasha::Common::error( qq(Bad compute expression: "$options->{ 'eval' }"\n) );
- }
- }
-
- Maasha::Biopieces::put_record( $record, $out );
- }
-}
-
-
sub script_flip_tab
{
# Martin A. Hansen, June 2008.
}
-sub script_count_vals
-{
- # Martin A. Hansen, August 2007.
-
- # Count records in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $num, $record, %count_hash, @records, $tmp_file, $fh_out, $fh_in, $cache );
-
- $tmp_file = "$BP_TMP/count_cache.tmp";
-
- $fh_out = Maasha::Common::write_open( $tmp_file );
-
- $cache = 0;
- $num = 0;
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- map { $count_hash{ $_ }{ $record->{ $_ } }++ if exists $record->{ $_ } } @{ $options->{ "keys" } };
-
- push @records, $record;
-
- if ( scalar @records > 5_000_000 ) # too many records to hold in memory - use disk cache
- {
- map { Maasha::Biopieces::put_record( $_, $fh_out ) } @records;
-
- undef @records;
-
- $cache = 1;
- }
-
- print STDERR "verbose: records read $num\n" if ( $options->{ 'verbose' } and ( $num % 1_000_000 ) == 0 );
-
- $num++;
- }
-
- close $fh_out;
-
- if ( $cache )
- {
- $num = 0;
-
- $fh_in = Maasha::Common::read_open( $tmp_file );
-
- while ( $record = Maasha::Biopieces::get_record( $fh_in ) )
- {
- map { $record->{ $_ . "_COUNT" } = $count_hash{ $_ }{ $record->{ $_ } } if exists $record->{ $_ } } @{ $options->{ "keys" } };
-
- Maasha::Biopieces::put_record( $record, $out );
-
- print STDERR "verbose: cache read $num\n" if ( $options->{ 'verbose' } and ( $num % 1_000_000 ) == 0 );
-
- $num++;
- }
-
- close $fh_in;
- }
-
- foreach $record ( @records )
- {
- map { $record->{ $_ . "_COUNT" } = $count_hash{ $_ }{ $record->{ $_ } } if exists $record->{ $_ } } @{ $options->{ "keys" } };
-
- Maasha::Biopieces::put_record( $record, $out );
- }
-
- unlink $tmp_file;
-}
-
-
sub script_plot_histogram
{
# Martin A. Hansen, September 2007.
projects / biopieces.git / commitdiff