From 816283f2865cd4249b16f2aeb833b9ebadd0205c Mon Sep 17 00:00:00 2001 From: martinahansen Date: Sun, 24 May 2009 19:23:10 +0000 Subject: [PATCH] migrated random_records git-svn-id: http://biopieces.googlecode.com/svn/trunk@398 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/random_records | 128 ++++++++++++++++++++++++++++++++++++- code_perl/Maasha/BioRun.pm | 77 ---------------------- 2 files changed, 125 insertions(+), 80 deletions(-) diff --git a/bp_bin/random_records b/bp_bin/random_records index fdf5bd2..f45f942 100755 --- a/bp_bin/random_records +++ b/bp_bin/random_records @@ -1,6 +1,128 @@ -#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Select a number of random records from the stream. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Biopieces; +use Maasha::Filesys; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $tmp_dir, $tmp_file, $fh_out, $fh_in, $count, $i, %rand_hash, $rand, $max ); + +$options = Maasha::Biopieces::parse_options( + [ + { long => 'num', short => 'n', type => 'uint', mandatory => 'no', default => 10, allowed => undef, disallowed => 0 }, + ] +); + +$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/random_records.tmp"; + +$fh_out = Maasha::Filesys::file_write_open( $tmp_file ); + +$count = 0; + +while ( $record = Maasha::Biopieces::get_record( $in ) ) +{ + Maasha::Biopieces::put_record( $record, $fh_out ); + + $count++; +} + +close $fh_out; + +$max = 0; +$i = 0; + +Maasha::Common::error( qq(Requested random records > records in stream) ) if $options->{ "num" } > $count; + +while ( $i < $options->{ "num" } ) +{ + $rand = int( rand( $count ) ); + + if ( not exists $rand_hash{ $rand } ) + { + $rand_hash{ $rand } = 1; + + $max = $rand if $rand > $max; + + $i++; + } +} + +$fh_in = Maasha::Filesys::file_read_open( $tmp_file ); + +$count = 0; + +while ( $record = Maasha::Biopieces::get_record( $fh_in ) ) +{ + Maasha::Biopieces::put_record( $record, $out ) if exists $rand_hash{ $count }; + + last if $count == $max; + + $count++; +} + +close $fh_in; + +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 ); +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +__END__ -use Maasha::BioRun; diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm index 53c09c7..4863090 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -172,7 +172,6 @@ sub run_script elsif ( $script eq "compute" ) { script_compute( $in, $out, $options ) } elsif ( $script eq "flip_tab" ) { script_flip_tab( $in, $out, $options ) } elsif ( $script eq "count_records" ) { script_count_records( $in, $out, $options ) } - elsif ( $script eq "random_records" ) { script_random_records( $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 ) } @@ -642,12 +641,6 @@ sub get_options data_out|o=s ); } - elsif ( $script eq "random_records" ) - { - @options = qw( - num|n=s - ); - } elsif ( $script eq "sort_records" ) { @options = qw( @@ -3870,76 +3863,6 @@ sub script_count_records } -sub script_random_records -{ - # Martin A. Hansen, August 2007. - - # Pick a number or random records from stream. - - my ( $in, # handle to in stream - $out, # handle to out stream - $options, # options hash - ) = @_; - - # Returns nothing. - - my ( $record, $tmp_file, $fh_out, $fh_in, $count, $i, %rand_hash, $rand, $max ); - - $options->{ "num" } ||= 10; - - $tmp_file = "$BP_TMP/random_records.tmp"; - - $fh_out = Maasha::Common::write_open( $tmp_file ); - - $count = 0; - - while ( $record = Maasha::Biopieces::get_record( $in ) ) - { - Maasha::Biopieces::put_record( $record, $fh_out ); - - $count++; - } - - close $fh_out; - - $max = 0; - $i = 0; - - Maasha::Common::error( qq(Requested random records > records in stream) ) if $options->{ "num" } > $count; - - while ( $i < $options->{ "num" } ) - { - $rand = int( rand( $count ) ); - - if ( not exists $rand_hash{ $rand } ) - { - $rand_hash{ $rand } = 1; - - $max = $rand if $rand > $max; - - $i++; - } - } - - $fh_in = Maasha::Common::read_open( $tmp_file ); - - $count = 0; - - while ( $record = Maasha::Biopieces::get_record( $fh_in ) ) - { - Maasha::Biopieces::put_record( $record, $out ) if exists $rand_hash{ $count }; - - last if $count == $max; - - $count++; - } - - close $fh_in; - - unlink $tmp_file; -} - - sub script_sort_records { # Martin A. Hansen, August 2007. -- 2.39.5