Bio-Pipeline-Comparison

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META.yml  view on Meta::CPAN

  File::Copy: 0
  File::Find: 0
  File::Path: 0
  File::Temp: 0
  File::Which: 0
  Getopt::Long: 0
  IO::Zlib: 0
  Moose: 0
  Moose::Util::TypeConstraints: 0
  POSIX: 0
  Try::Tiny: 0
  Vcf4_0: 0
  VcfReader: 0
  base: 0
  strict: 0
  vars: 0
  warnings: 0
resources:
  homepage: http://www.sanger.ac.uk/
  repository: https://github.com/sanger-pathogens/Bio-Pipeline-Comparison.git
version: 1.123050

Makefile.PL  view on Meta::CPAN

    "File::Copy" => 0,
    "File::Find" => 0,
    "File::Path" => 0,
    "File::Temp" => 0,
    "File::Which" => 0,
    "Getopt::Long" => 0,
    "IO::Zlib" => 0,
    "Moose" => 0,
    "Moose::Util::TypeConstraints" => 0,
    "POSIX" => 0,
    "Try::Tiny" => 0,
    "Vcf4_0" => 0,
    "VcfReader" => 0,
    "base" => 0,
    "strict" => 0,
    "vars" => 0,
    "warnings" => 0
  },
  "VERSION" => "1.123050",
  "test" => {
    "TESTS" => "t/*.t t/Bio/Pipeline/Comparison/Generate/*.t t/Bio/Pipeline/Comparison/Report/*.t"

lib/Bio/Pipeline/Comparison/Report/InputParameters.pm  view on Meta::CPAN

package Bio::Pipeline::Comparison::Report::InputParameters;

# ABSTRACT: Take in a set of input parameters for the evalute pipeline functionality, validate them, then manipulate them into a usable set.


use Moose;
use Cwd;
use File::Temp;
use File::Copy;
use File::Basename;
use Try::Tiny;
use Bio::SeqIO;
use Bio::Pipeline::Comparison::Types;
use Bio::Pipeline::Comparison::Exceptions;
use Vcf;

has 'known_variant_filenames'    => ( is => 'rw', isa => 'ArrayRef', required => 1 );
has 'observed_variant_filenames' => ( is => 'rw', isa => 'ArrayRef', required => 1 );

has 'bgzip_exec' => ( is => 'ro', isa => 'Bio::Pipeline::Comparison::Executable', default => 'bgzip' );
has 'tabix_exec' => ( is => 'ro', isa => 'Bio::Pipeline::Comparison::Executable', default => 'tabix' );

lib/Bio/Pipeline/Comparison/Report/ParseVCFCompare.pm  view on Meta::CPAN

package Bio::Pipeline::Comparison::Report::ParseVCFCompare;

# ABSTRACT: Take in the output of VCF compare and return details about intersection of variants.


use Moose;
use Try::Tiny;
use Bio::Pipeline::Comparison::Types;
use Bio::Pipeline::Comparison::Exceptions;

has 'known_variant_filename'    => ( is => 'rw', isa  => 'Str', required => 1 );
has 'observed_variant_filename' => ( is => 'rw', isa  => 'Str', required => 1 );

has 'vcf_compare_exec'          => ( is => 'ro', isa  => 'Bio::Pipeline::Comparison::Executable', default => 'vcf-compare' );

has '_venn_diagram_regex'       => ( is => 'ro', isa  => 'Str', default => '^VN\t(\d+)\t([^\s]+)\s\(([\d\.]+)%\)(\t([^\s]+)\s\(([\d\.]+)%\))?$' );
has '_vcf_compare_fh'           => ( is => 'ro', lazy => 1, builder => '_build__vcf_compare_fh' );