#!/usr/bin/env perl # PODNAME: resample-ali.pl # ABSTRACT: Resample ALI files using (variable length) bootstrap or jackknife use Modern::Perl '2011'; use autodie; use File::Basename; use Getopt::Euclid qw(:vars); use Path::Class qw(dir file); use POSIX; use Smart::Comments; use Bio::MUST::Core; use Bio::MUST::Core::Utils qw(change_suffix append_suffix); use aliased 'Bio::MUST::Core::Ali'; use aliased 'Bio::MUST::Core::SeqMask::Weights'; # setup resampling method my $method = $ARGV_resampling . '_masks'; # setup replicate numbering format my $field = ceil( log($ARGV_replicates) / log(10) ); for my $infile (@ARGV_infiles) { ### Processing: $infile my $ali = Ali->load($infile); # create output directory named after input file and resampling mode my $outdir = append_suffix( change_suffix($infile, q{}), "-$ARGV_resampling" ); for my $width (@ARGV_width) { # create output subdirectory named after width my $subdir = dir( $outdir, 'width-' . $width )->relative; ### REPDIR: $subdir->stringify $subdir->mkpath(); # generate resampling masks for Ali my @masks = Weights->$method( $ali, { 'rep' => $ARGV_replicates, 'width' => $width } ); # apply masks to generate pseudo-replicates for my $rep (0..$ARGV_replicates-1) { my $new_ali = $masks[$rep]->filtered_ali($ali); my $filename = sprintf 'replicate-%0*d.ali', $field, $rep; ### REP file: $filename my $outfile = file($subdir, $filename); $new_ali->store($outfile); } } } __END__ =pod =head1 NAME resample-ali.pl - Resample ALI files using (variable length) bootstrap or jackknife =head1 VERSION version 0.250380 =head1 USAGE resample-ali.pl <infiles> [optional arguments] =head1 REQUIRED ARGUMENTS =over =item <infiles> Path to input ALI files [repeatable argument]. =for Euclid: infiles.type: readable repeatable =back =head1 OPTIONAL ARGUMENTS =over =item --resampling=<mode> Mode of resampling to perform on the ALI [default: bootstrap]. The following modes are available: bootstrap and jackknife. =for Euclid: mode.type: string, mode eq 'bootstrap' || mode eq 'jackknife' mode.type.error: <mode> must be one of bootstrap or jackknife (not mode) mode.default: 'bootstrap' =item --rep[licates]=<n> Number of pseudo-replicates [default: 100]. =for Euclid: n.type: int >= 0 n.default: 100 =item --width=<n>... Number of positions to be included in each pseudo-replicate [default: 1]. When specified as a fraction between 0 and 1 (included), it is interpreted as relative to the width of the ALI. Thus 10000 would mean 10,000 sites whereas 0.5 would mean half the width of the ALI. Hence, the default is to generate pseudo-replicates of the same width as the ALI. Multiple values can be provided if they are whitespace-separated. =for Euclid: n.type: number n.default: [ 1 ] =item --version =item --usage =item --help =item --man Print the usual program information =back =head1 AUTHOR Denis BAURAIN <denis.baurain@uliege.be> =head1 COPYRIGHT AND LICENSE This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN. This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself. =cut