Bio-Tradis

 view release on metacpan or  search on metacpan

lib/Bio/Tradis/CommandLine/AddTags.pm  view on Meta::CPAN

package Bio::Tradis::CommandLine::AddTags;
$Bio::Tradis::CommandLine::AddTags::VERSION = '1.4.5';
# ABSTRACT: Add given tags to the start of the sequence


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Cwd 'abs_path';
use Bio::Tradis::AddTagsToSeq;

has 'args'        => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str',      required => 1 );
has 'bamfile'     => ( is => 'rw', isa => 'Str',      required => 0 );
has 'help'        => ( is => 'rw', isa => 'Bool',     required => 0 );
has 'outfile'     => ( is => 'rw', isa => 'Str',      required => 0 );

has 'verbose'       => ( is => 'rw', isa => 'Bool', default => 0 );
has 'samtools_exec' => ( is => 'rw', isa => 'Str', default => 'samtools' );

sub BUILD {
    my ($self) = @_;

lib/Bio/Tradis/CommandLine/CheckTags.pm  view on Meta::CPAN

package Bio::Tradis::CommandLine::CheckTags;
$Bio::Tradis::CommandLine::CheckTags::VERSION = '1.4.5';
# ABSTRACT: Check for presence of tr tag in BAM file


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Cwd 'abs_path';
use Bio::Tradis::DetectTags;

has 'args'        => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str',      required => 1 );
has 'bamfile'        => ( is => 'rw', isa => 'Str', required => 0 );
has 'help'        => ( is => 'rw', isa => 'Bool', required => 0 );
has 'samtools_exec' => ( is => 'rw', isa => 'Str', default => 'samtools' );

sub BUILD {
    my ($self) = @_;
    
    my (
        $bamfile,	$help, $samtools_exec

lib/Bio/Tradis/CommandLine/FilterFastqTags.pm  view on Meta::CPAN

package Bio::Tradis::CommandLine::FilterFastqTags;
$Bio::Tradis::CommandLine::FilterFastqTags::VERSION = '1.4.5';
# ABSTRACT: Remove given tags from the start of the sequence


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Cwd 'abs_path';
use Bio::Tradis::FilterTags;

has 'args'        => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str',      required => 1 );
has 'fastqfile'   => ( is => 'rw', isa => 'Str',      required => 0 );
has 'tag'         => ( is => 'rw', isa => 'Str',      required => 0 );
has 'mismatch'    => ( is => 'rw', isa => 'Int',      required => 0, default => 0 );
has 'help'        => ( is => 'rw', isa => 'Bool',     required => 0 );
has 'outfile'     => ( is => 'rw', isa => 'Str',      required => 0 );

sub BUILD {
    my ($self) = @_;

lib/Bio/Tradis/CommandLine/PlotCombine.pm  view on Meta::CPAN

package Bio::Tradis::CommandLine::PlotCombine;
$Bio::Tradis::CommandLine::PlotCombine::VERSION = '1.4.5';
# ABSTRACT: Combine multiple plotfiles and generate updated statistics for the combined files


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Cwd 'abs_path';
use Bio::Tradis::CombinePlots;

has 'args'        => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str',      required => 1 );
has 'plotfile'    => ( is => 'rw', isa => 'Str',      required => 0 );
has 'output_dir'  => ( is => 'rw', isa => 'Str',      default  => 'combined' );
has 'help'        => ( is => 'rw', isa => 'Bool',     required => 0 );

sub BUILD {
    my ($self) = @_;

    my ( $plotfile, $output_dir, $help );

lib/Bio/Tradis/CommandLine/PlotTradis.pm  view on Meta::CPAN

package Bio::Tradis::CommandLine::PlotTradis;
$Bio::Tradis::CommandLine::PlotTradis::VERSION = '1.4.5';
# ABSTRACT: Generate plots as part of a tradis analysis


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Cwd 'abs_path';
use Bio::Tradis::TradisPlot;

has 'args'        => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str',      required => 1 );
has 'mappedfile'  => ( is => 'rw', isa => 'Str',      required => 0 );
has 'mapping_score' => ( is => 'rw', isa => 'Int', required => 0, default => 30);
has 'help'        => ( is => 'rw', isa => 'Bool',     required => 0 );
has 'outfile'     => ( is => 'rw', isa => 'Str',      required => 0, default => 'tradis.plot' );

sub BUILD {
    my ($self) = @_;

    my ( $mappedfile, $outfile, $mapping_score, $help );

lib/Bio/Tradis/CommandLine/RemoveFastqTags.pm  view on Meta::CPAN

package Bio::Tradis::CommandLine::RemoveFastqTags;
$Bio::Tradis::CommandLine::RemoveFastqTags::VERSION = '1.4.5';
# ABSTRACT: Remove given tags from the start of the sequence


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Cwd 'abs_path';
use Bio::Tradis::RemoveTags;

has 'args'        => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str',      required => 1 );
has 'fastqfile'   => ( is => 'rw', isa => 'Str',      required => 0 );
has 'tag'         => ( is => 'rw', isa => 'Str',      required => 0 );
has 'mismatch' => ( is => 'rw', isa => 'Int',  required => 0, default => 0 );
has 'help'     => ( is => 'rw', isa => 'Bool', required => 0 );
has 'outfile'  => ( is => 'rw', isa => 'Str',  required => 0 );

sub BUILD {
    my ($self) = @_;

lib/Bio/Tradis/CommandLine/RunMapping.pm  view on Meta::CPAN

package Bio::Tradis::CommandLine::RunMapping;
$Bio::Tradis::CommandLine::RunMapping::VERSION = '1.4.5';
# ABSTRACT: Perform mapping


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Cwd 'abs_path';
use Bio::Tradis::Map;

has 'args'        => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str',      required => 1 );
has 'fastqfile'   => ( is => 'rw', isa => 'Str',      required => 0 );
has 'reference'   => ( is => 'rw', isa => 'Str',      required => 0 );
has 'help'        => ( is => 'rw', isa => 'Bool',     required => 0 );
has 'refname' =>
  ( is => 'rw', isa => 'Str', required => 0, default => 'ref.index' );
has 'outfile' =>
  ( is => 'rw', isa => 'Str', required => 0, default => 'mapped.sam' );
has 'smalt' => ( is => 'rw', isa => 'Maybe[Int]', required => 0, default => 0 );
has 'smalt_k' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 );

lib/Bio/Tradis/CommandLine/TradisAnalysis.pm  view on Meta::CPAN

$Bio::Tradis::CommandLine::TradisAnalysis::VERSION = '1.4.5';
# ABSTRACT: Perform full tradis analysis


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Cwd qw(abs_path cwd);
use Bio::Tradis::RunTradis;
use Try::Tiny;

has 'args'        => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str',      required => 1 );
has 'fastqfile'   => ( is => 'rw', isa => 'Str',      required => 0 );
has 'tag'         => ( is => 'rw', isa => 'Maybe[Str]',      required => 0 );
has 'mismatch' => ( is => 'rw', isa => 'Int', required => 0, default => 0 );
has 'tagdirection' =>
  ( is => 'rw', isa => 'Str', required => 0, default => '3' );
has 'reference' => ( is => 'rw', isa => 'Str',  required => 0 );
has 'help'      => ( is => 'rw', isa => 'Bool', required => 0 );
has 'mapping_score' =>
  ( is => 'rw', isa => 'Int', required => 0, default => 30 );

lib/Bio/Tradis/CommandLine/TradisBam.pm  view on Meta::CPAN

$Bio::Tradis::CommandLine::TradisBam::VERSION = '1.4.5';
# ABSTRACT: Adds tags to sequences if tags are present


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Cwd 'abs_path';
use Bio::Tradis::DetectTags;
use Bio::Tradis::AddTagsToSeq;

has 'args'        => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str',      required => 1 );
has 'bamfile'     => ( is => 'rw', isa => 'Str',      required => 1 );
has 'outfile'     => (
    is       => 'rw',
    isa      => 'Str',
    required => 0,
);
has 'help' => ( is => 'rw', isa => 'Bool', required => 0 );
has 'verbose'       => ( is => 'rw', isa => 'Bool', default => 0 );
has 'samtools_exec' => ( is => 'rw', isa => 'Str', default => 'samtools' );

lib/Bio/Tradis/Parser/Cigar.pm  view on Meta::CPAN

package Bio::Tradis::Parser::Cigar;
$Bio::Tradis::Parser::Cigar::VERSION = '1.4.5';
# ABSTRACT: Take in a cigar string and output start and end relative to the reference sequence


use Moose;

has 'cigar'      => ( is => 'ro', isa => 'Str', required => 1 );
has 'coordinate' => ( is => 'ro', isa => 'Num', required => 1 );

has '_results' =>  (is      => 'ro', isa     => 'HashRef', lazy    => 1, builder => '_build__results');

sub _build__results
{
	my($self) = @_;
	my %results = ( start => 0, end => 0);
	my $current_coordinate = $self->coordinate;

	my @cigar_parts = $self->cigar =~ /(\d+[MIDNSHP=X])/g;
	for my $cigar_item (@cigar_parts)
	{