From bcc615d3a5fa95dd8f5bf86a5e4aabf022879ac8 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Thu, 17 Jun 2010 12:22:58 +0000 Subject: [PATCH] added list switch to *_vals biopieces git-svn-id: http://biopieces.googlecode.com/svn/trunk@990 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/max_vals | 16 +++++++++++++--- bp_bin/mean_vals | 3 +-- bp_bin/median_vals | 14 +++++++++++--- bp_bin/min_vals | 15 ++++++++++++--- 4 files changed, 37 insertions(+), 11 deletions(-) diff --git a/bp_bin/max_vals b/bp_bin/max_vals index 4cb794b..d25bee4 100755 --- a/bp_bin/max_vals +++ b/bp_bin/max_vals @@ -29,6 +29,7 @@ use warnings; use strict; use Maasha::Biopieces; +use Maasha::Calc; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @@ -38,12 +39,16 @@ my ( $options, $in, $out, $record, $key, $fh, %max_hash, $max_record ); $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 => 'keys', short => 'k', type => 'list', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, + { 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 => 'keys', short => 'k', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'list', short => 'l', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, ] ); +Maasha::Common::error( qq(both --keys and --list specified) ) if $options->{ "keys" } and $options->{ "list" }; +Maasha::Common::error( qq(no --keys or --list specified) ) if not $options->{ "keys" } and not $options->{ "list" }; + $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); @@ -61,6 +66,11 @@ while ( $record = Maasha::Biopieces::get_record( $in ) ) } } + if ( $options->{ 'list' } and $record->{ $options->{ 'list' } } ) { + $record->{ $options->{ 'list' } . "_MAX" } = sprintf( "%.2f", Maasha::Calc::list_max( [ split ";", $record->{ $options->{ 'list' } } ] ) ); + } + + Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" }; } diff --git a/bp_bin/mean_vals b/bp_bin/mean_vals index 44ce791..583ec4e 100755 --- a/bp_bin/mean_vals +++ b/bp_bin/mean_vals @@ -63,8 +63,7 @@ while ( $record = Maasha::Biopieces::get_record( $in ) ) } } - if ( $options->{ 'list' } and $record->{ $options->{ 'list' } } ) - { + if ( $options->{ 'list' } and $record->{ $options->{ 'list' } } ) { $record->{ $options->{ 'list' } . "_MEAN" } = sprintf( "%.2f", Maasha::Calc::mean( [ split ";", $record->{ $options->{ 'list' } } ] ) ); } diff --git a/bp_bin/median_vals b/bp_bin/median_vals index 91cdd36..36bfff5 100755 --- a/bp_bin/median_vals +++ b/bp_bin/median_vals @@ -39,12 +39,16 @@ my ( $options, $in, $out, $record, $key, %median_hash, $median, $fh ); $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 => 'keys', short => 'k', type => 'list', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, + { 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 => 'keys', short => 'k', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'list', short => 'l', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, ] ); +Maasha::Common::error( qq(both --keys and --list specified) ) if $options->{ "keys" } and $options->{ "list" }; +Maasha::Common::error( qq(no --keys or --list specified) ) if not $options->{ "keys" } and not $options->{ "list" }; + $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); @@ -54,6 +58,10 @@ while ( $record = Maasha::Biopieces::get_record( $in ) ) push @{ $median_hash{ $key } }, $record->{ $key } if defined $record->{ $key }; } + if ( $options->{ 'list' } and $record->{ $options->{ 'list' } } ) { + $record->{ $options->{ 'list' } . "_MEDIAN" } = sprintf( "%.2f", Maasha::Calc::median( [ split ";", $record->{ $options->{ 'list' } } ] ) ); + } + Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" }; } diff --git a/bp_bin/min_vals b/bp_bin/min_vals index bff25a7..1f73ed0 100755 --- a/bp_bin/min_vals +++ b/bp_bin/min_vals @@ -29,6 +29,7 @@ use warnings; use strict; use Maasha::Biopieces; +use Maasha::Calc; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @@ -38,12 +39,16 @@ my ( $options, $in, $out, $record, $key, $fh, %min_hash, $min_record ); $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 => 'keys', short => 'k', type => 'list', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, + { 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 => 'keys', short => 'k', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'list', short => 'l', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, ] ); +Maasha::Common::error( qq(both --keys and --list specified) ) if $options->{ "keys" } and $options->{ "list" }; +Maasha::Common::error( qq(no --keys or --list specified) ) if not $options->{ "keys" } and not $options->{ "list" }; + $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); @@ -61,6 +66,10 @@ while ( $record = Maasha::Biopieces::get_record( $in ) ) } } + if ( $options->{ 'list' } and $record->{ $options->{ 'list' } } ) { + $record->{ $options->{ 'list' } . "_MIN" } = sprintf( "%.2f", Maasha::Calc::list_min( [ split ";", $record->{ $options->{ 'list' } } ] ) ); + } + Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" }; } -- 2.39.5