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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,167 @@ | ||
| package MIP::Cli::Mip::Qccollect; | ||
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||
| use 5.026; | ||
| use Carp; | ||
| use Cwd; | ||
| use File::Spec::Functions qw{ catfile }; | ||
| use open qw{ :encoding(UTF-8) :std }; | ||
| use strict; | ||
| use utf8; | ||
| use warnings; | ||
| use warnings qw{ FATAL utf8 }; | ||
|
|
||
| ## CPANM | ||
| use autodie qw{ :all }; | ||
| use Moose::Util::TypeConstraints; | ||
| use MooseX::App::Command; | ||
| use MooseX::Types::Moose qw{ ArrayRef Bool HashRef Int Str }; | ||
|
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| ## MIPs lib/ | ||
| use MIP::Constants qw{ $NEWLINE }; | ||
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| our $VERSION = 1.00; | ||
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| command_short_description(q{MIP qccollect command}); | ||
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| command_long_description(q{Entry point for collecting MIP QC metrics}); | ||
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| command_usage( | ||
| q{qccollect <options> -si [sample_info.yaml] -r [regexp.yaml] -o [outfile]}); | ||
|
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| ## Define, check and get Cli supplied parameters | ||
| _build_usage(); | ||
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| sub run { | ||
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| ## Input from Cli | ||
| my ($arg_href) = @_; | ||
|
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| ## Remove Moose::App extra variable | ||
| delete $arg_href->{extra_argv}; | ||
|
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| # Flatten argument(s) | ||
| my $evaluate_plink_gender = $arg_href->{evaluate_plink_gender}; | ||
| my $print_regexp = $arg_href->{print_regexp}; | ||
| my $regexp_file = $arg_href->{regexp_file}; | ||
| my $sample_info_file = $arg_href->{sample_info_file}; | ||
| my $skip_evaluation = $arg_href->{skip_evaluation}; | ||
| my $log_file = $arg_href->{log_file}; | ||
| my $print_regexp_outfile = $arg_href->{print_regexp_outfile}; | ||
| my $outfile = $arg_href->{outfile}; | ||
|
|
||
| use MIP::Log::MIP_log4perl qw{ initiate_logger }; | ||
| use MIP::Main::Qccollect qw{ mip_qccollect }; | ||
| use MIP::Qcc_regexp qw{ regexp_to_yaml }; | ||
|
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| ## Creates log object | ||
| my $log = initiate_logger( | ||
| { | ||
| file_path => $log_file, | ||
| log_name => uc q{mip_qccollect}, | ||
| } | ||
| ); | ||
|
|
||
| ## Write default regexp to YAML if demanded | ||
| regexp_to_yaml( | ||
| { | ||
| log => $log, | ||
| print_regexp_outfile => $print_regexp_outfile, | ||
| } | ||
| ); | ||
|
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| mip_qccollect( | ||
| { | ||
| evaluate_plink_gender => $evaluate_plink_gender, | ||
| regexp_file => $regexp_file, | ||
| sample_info_file => $sample_info_file, | ||
| skip_evaluation => $skip_evaluation, | ||
| log => $log, | ||
| outfile => $outfile, | ||
| } | ||
| ); | ||
| return; | ||
| } | ||
|
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||
| sub _build_usage { | ||
|
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| ## Function : Get and/or set input parameters | ||
| ## Returns : | ||
| ## Arguments: | ||
|
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| my ($arg_href) = @_; | ||
|
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| option( | ||
| q{evaluate_plink_gender} => ( | ||
| cmd_aliases => [qw{ epg }], | ||
| documentation => q{Evaluate plink gender}, | ||
| is => q{rw}, | ||
| isa => Bool, | ||
| ) | ||
| ); | ||
|
|
||
| option( | ||
| q{log_file} => ( | ||
| cmd_aliases => [qw{ l }], | ||
| default => catfile( cwd(), q{qccollect.log} ), | ||
| documentation => q{Log file}, | ||
| is => q{rw}, | ||
| isa => Str, | ||
| ) | ||
| ); | ||
|
|
||
| option( | ||
| q{outfile} => ( | ||
| cmd_aliases => [qw{ o }], | ||
| cmd_tags => [q{YAML}], | ||
| default => q{qcmetrics.yaml}, | ||
| documentation => q{Data file output}, | ||
| is => q{rw}, | ||
| isa => Str, | ||
| ) | ||
| ); | ||
|
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||
| option( | ||
| q{print_regexp_outfile} => ( | ||
| cmd_aliases => [qw{ prego }], | ||
| cmd_flag => q{regexp_outfile}, | ||
| cmd_tags => [q{YAML}], | ||
| documentation => q{Regexp YAML outfile}, | ||
| is => q{rw}, | ||
| isa => Str, | ||
| ) | ||
| ); | ||
|
|
||
| option( | ||
| q{regexp_file} => ( | ||
| cmd_aliases => [qw{ rxf }], | ||
| cmd_tags => [q{YAML}], | ||
| documentation => q{Regular expression file path}, | ||
| is => q{rw}, | ||
| isa => Str, | ||
| required => 1, | ||
| ) | ||
| ); | ||
|
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| option( | ||
| q{sample_info_file} => ( | ||
| cmd_aliases => [qw{ sif }], | ||
| cmd_tags => [q{YAML}], | ||
| documentation => q{File for sample info used in the analysis}, | ||
| is => q{rw}, | ||
| isa => Str, | ||
| required => 1, | ||
| ) | ||
| ); | ||
|
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| option( | ||
| q{skip_evaluation} => ( | ||
| cmd_aliases => [qw{ ske }], | ||
| documentation => q{Skip evaluation step}, | ||
| is => q{rw}, | ||
| isa => Bool, | ||
| ) | ||
| ); | ||
| return; | ||
| } | ||
|
|
||
| 1; |
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