File Coverage

lib/App/Sandy/Types.pm

Criterion	Covered	Total	%
statement	3	3	100.0
branch			n/a
condition			n/a
subroutine	1	1	100.0
pod			n/a
total	4	4	100.0

package App::Sandy::Types;
# ABSTRACT: Moose type constraints for App::Sandy project

use Moose::Util::TypeConstraints;

our $VERSION = '0.25'; # VERSION

subtype 'My:IntGt0'
	=> as      'Int'
	=> where   { $_ > 0 }
	=> message { "Value must be an integer greater than zero, not '$_'" };

subtype 'My:IntGe0'
	=> as      'Int'
	=> where   { $_ >= 0 }
	=> message { "Value must be an integer greater or equal to zero, not '$_'" };

subtype 'My:NumGt0'
	=> as      'Num'
	=> where   { $_ > 0 }
	=> message { "Value must be a number greater than zero, not '$_'" };

subtype 'My:NumGe0'
	=> as      'Num'
	=> where   { $_ >= 0 }
	=> message { "Value must be a number greater or equal to zero, not '$_'" };

subtype 'My:NumHS'
	=> as      'Num'
	=> where   { $_ >= 0 && $_ <= 1 }
	=> message { "Value must be a number between zero and one, not '$_'" };

subtype 'My:File'
	=> as      'Str'
	=> where   { -f $_ }
	=> message { "'$_' must be a file" };

subtype 'My:Fasta'
	=> as      'My:File'
	=> where   { $_ =~ /.+\.(fasta|fa|fna|ffn)(\.gz)*$/ }
	=> message { "'$_' must be a fasta file: Check the extension (.fasta, .fa, .fna, .ffn - compressed, or not, by gzip, as in .fasta.gz etc)" };

subtype 'My:Weight'
	=> as      'HashRef'
	=> where   { exists $_->{down} && exists $_->{up} }
	=> message { "'$_' is not a Weight object" };

subtype 'My:Weights'
	=> as      'ArrayRef[My:Weight]'
	=> message { "'$_' is not a Weight object array" };

subtype 'My:QualityP'
	=> as      'Str';

coerce 'My:QualityP'
	=> from    'Str'
	=> via     { lc $_ };

subtype 'My:QualityH'
	=> as      'HashRef'
	=> where   { exists $_->{matrix} && exists $_->{deepth} && exists $_->{partil} }
	=> message { "'$_' is not a valid quality hash" };

subtype 'My:IdFa'
	=> as      'HashRef'
	=> where   { exists $_->{seq} && exists $_->{size} }
	=> message { "'$_' is not a valid fasta id" };

subtype 'My:IdxFasta'
	=> as      'HashRef[My:IdFa]'
	=> message { "'$_' is not a valid indexed fasta" };

subtype 'My:StrandBias'
	=> as      'Str'
	=> where   { $_ eq 'plus' || $_ eq 'minus' || $_ eq 'random' }
	=> message { "'$_' is not a valid strand-bias: 'plus', 'minus' or 'random'" };

subtype 'My:SeqIdWeight'
	=> as      'Str'
	=> where   { $_ eq 'length' || $_ eq 'same' || $_ eq 'count' }
	=> message { "'$_' is not a valid seqid-weight: 'length', 'same' or 'count'" };

subtype 'My:SeqType'
	=> as      'Str'
	=> where   { $_ eq 'single-end' || $_ eq 'paired-end' }
	=> message { "'$_' is not a valid sequencing-type: 'single-end' or 'paired-end'" };

subtype 'My:CountLoopBy'
	=> as      'Str'
	=> where   { $_ eq 'coverage' || $_ eq 'number-of-reads' }
	=> message { "'$_' is not a valid count_loops_by: 'coverage' or 'number-of-reads'" };

subtype 'My:Piece'
	=> as      'HashRef'
	=> where   { exists $_->{ref} && exists $_->{start} && exists $_->{len} && exists $_->{pos} && exists $_->{offset} }
	=> message { "Invalid piece inserted to piece_table" };

subtype 'My:PieceTable'
	=> as      'HashRef'
	=> where   { exists $_->{size} && exists $_->{table} && ref $_->{table} eq 'App::Sandy::PieceTable' }
	=> message { "Invalid piece table entry" };

subtype 'My:Format'
	=> as      'Str'
	=> where   { $_ eq 'fastq' || $_ eq 'fastq.gz' || $_ eq 'bam' || $_ eq 'sam' }
	=> message { "Invalid output format: '$_': 'fastq', 'fastq.gz', 'bam', 'sam'" };

subtype 'My:Level'
	=> as      'Int'
	=> where   { /^[1-9]$/ }
	=> message { "Invalid compression level: '$_': 1-9"};


subtype 'My:TupleElem'
	=> as      'ArrayRef[Int]'
	=> where   { @$_ == 2 }
	=> message { "Invalid tuple element" };

subtype 'My:Tuple'
	=> as      'ArrayRef[My:TupleElem]'
	=> message { "Invalid tuple" };

subtype 'My:FastaBlackList'
	=> as      'HashRef[My:Tuple]'
	=> message { "Fasta blacklist is chr => Tuple" };

1; ## --- end class App::Sandy::Types

__END__

=pod

=encoding UTF-8

=head1 NAME

App::Sandy::Types - Moose type constraints for App::Sandy project

=head1 VERSION

version 0.25

=head1 AUTHORS

=over 4

=item *

Thiago L. A. Miller <[e-mail]>

=item *

J. Leonel Buzzo <[e-mail]>

=item *

Felipe R. C. dos Santos <[e-mail]>

=item *

Helena B. Conceição <[e-mail]>

=item *

Rodrigo Barreiro <[e-mail]>

=item *

Gabriela Guardia <[e-mail]>

=item *

Fernanda Orpinelli <[e-mail]>

=item *

Rafael Mercuri <[e-mail]>

=item *

Rodrigo Barreiro <[e-mail]>

=item *

Pedro A. F. Galante <[e-mail]>

=back

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2023 by Teaching and Research Institute from Sírio-Libanês Hospital.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007

=cut