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package BioX::Wrapper; |
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use File::Find::Rule; |
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use File::Basename; |
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use File::Path qw(make_path remove_tree); |
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use File::Find::Rule; |
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use Cwd; |
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use DateTime; |
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use Moose; |
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420549
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use Moose::Util::TypeConstraints; |
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with 'MooseX::Getopt'; |
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with 'MooseX::Getopt::Usage'; |
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with 'MooseX::Getopt::Usage::Role::Man'; |
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with 'MooseX::SimpleConfig'; |
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# For pretty man pages! |
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$ENV{TERM}='xterm-256color'; |
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our $VERSION = '1.5'; |
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=head1 BioX::Wrapper |
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Base class for BioX::Wrapper |
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=head2 Wrapper Options |
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=cut |
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30
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=head3 example.yml |
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--- |
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indir: "/path/to/files" |
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outdir: "path/to/testdir" |
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=cut |
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38
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has '+configfile' => ( |
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required => 0, |
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documentation => q{ |
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If you get tired of putting all your options on the command line create a config file instead. |
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--- |
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indir: "/path/to/files" |
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outdir: "path/to/testdir" |
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} |
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); |
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=head3 comment_char |
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50
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For a bash script a comment is "#", but is other characters for other languages |
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=cut |
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has 'comment_char' => ( |
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is => 'rw', |
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isa => 'Str', |
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default => '#', |
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); |
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60
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=head2 print_opts |
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62
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Print out the command line options |
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=cut |
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66
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sub print_opts { |
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0
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0
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my($self) = @_; |
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69
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0
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my $now = DateTime->now(); |
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0
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print "$self->{comment_char}\n"; |
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0
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print "$self->{comment_char} Generated at: $now\n"; |
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0
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print "$self->{comment_char} This file was generated with the following options\n"; |
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0
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for(my $x=0; $x<=$#ARGV; $x++){ |
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0
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0
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next unless $ARGV[$x]; |
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0
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print "$self->{comment_char}\t$ARGV[$x]\t"; |
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0
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0
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if($ARGV[$x+1]){ |
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0
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print $ARGV[$x+1]; |
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} |
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0
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print "\n"; |
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0
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$x++; |
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} |
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85
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0
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print "$self->{comment_char}\n\n"; |
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} |
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88
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=head3 indir |
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90
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A path to your vcf files can be given, and using File::Find::Rule it will recursively search for vcf or vcf.gz |
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92
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=cut |
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94
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has 'indir' => ( |
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is => 'rw', |
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isa => 'Str|Undef', |
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required => 0, |
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); |
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100
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=head3 outdir |
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102
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Path to write out annotation files. It creates the structure |
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outdir |
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--annovar_interim |
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--annovar_final |
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--vcf-annotate_interim #If you choose to reannotate VCF file |
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--vcf-annotate_final #If you choose to reannotate VCF file |
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110
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A lot of interim files are created by annovar, and the only one that really matters unless you debugging a new database is the multianno file found in annovar_final |
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112
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If not given the outdirectory is assumed to be the current working directory. |
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114
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=cut |
115
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116
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has 'outdir' => ( |
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is => 'rw', |
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isa => 'Str', |
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required => 1, |
120
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default => sub { return getcwd() }, |
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); |
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123
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1; |
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__END__ |
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126
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=encoding utf-8 |
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128
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=head1 NAME |
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130
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BioX::Wrapper - Base class for BioX::Wrappers |
131
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132
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=head1 SYNOPSIS |
133
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134
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use BioX::Wrapper; |
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136
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=head1 DESCRIPTION |
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138
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BioX::Wrapper is |
139
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140
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=head1 Acknowledgements |
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142
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This module was originally developed at and for Weill Cornell Medical |
143
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College in Qatar within ITS Advanced Computing Team. With approval from |
144
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WCMC-Q, this information was generalized and put on github, for which |
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the authors would like to express their gratitude. |
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147
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=head1 AUTHOR |
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149
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Jillian Rowe E<lt>jillian.e.rowe@gmail.comE<gt> |
150
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151
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=head1 COPYRIGHT |
152
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153
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Copyright 2015 - Weill Cornell Medical College in Qatar |
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155
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=head1 LICENSE |
156
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157
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This library is free software; you can redistribute it and/or modify |
158
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it under the same terms as Perl itself. |
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160
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=head1 SEE ALSO |
161
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162
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=cut |