VNTRseekHelpers

Helper modules for reading input/output files produced by the VNTRseek pipeline.

So far, these modules are only used for reading .seq (input) and .vcf (output) files.

Basic usage

VNTRseek::Reader

Class used by a client to access one of [possibly] many file readers. A call to this class looks like:

my $file_reader = VNTRseek::Reader->get_file_reader($format, $file)

where $format is a string denoting the format (currently only "seq" and "vcf" are supported) and $file is the full or relative path to a file of that format. The file reader can then be used to access the file contents.

VNTRseek::Reader::seqF

my $seq_reader = VNTRseek::Reader->get_file_reader("seq", $file);
while (my $entry = $seq_reader->next_seq) {
    #...
    # See documentation on VNTRseek::Reader::seq
}

You can also call this module directly, without needing to use VNTRseek, but that is simply more convenient. Here's how a direct call to this module would look:

    my $seq_reader = VNTRseek::Reader::seqF->new(fh => $fh);

where $fh is an IO::File file handle.

VNTRseek::Reader::seq

This class is meant to be accessed via the VNTRseek::Reader::seqF module, but can be accessed directly to build such entries.

Apart from having built in accessors for the various fields in a .seq file record, you can also print a whole record at once, in a CSV format as follows:

# Prints line to STDOUT
print $seq_record;
# Prints line to file handle pointed to by $fh
print $fh $seq_record;

You can access specific parts of the record. Examples:

my $rid = $self->Repeatid;
my $start = $self->FirstIndex;
my $stop = $self->LastIndex;
my $cn = $self->CopyNumber;
my $name = $self->FastaHeader;
my $pattern = $self->Pattern;
my $percent_conserived = $self->Conserved;

VNTRseek::Reader::vcfF

my $vcf_reader = VNTRseek::Reader->get_file_reader("vcf", $file);
while (my $entry = $vcf_reader->next_var) {
    #...
    # See documentation on VNTRseek::Reader::var
}

You can also call this module directly, without needing to use VNTRseek::Reader, but that is simply more convenient. Here's how a direct call to this module would look:

    my $vcf_reader = VNTRseek::Reader::vcfF->new(fh => $fh);

where $fh is an IO::File file handle.

VNTRseek::Reader::var

This class is meant to be accessed via the VNTRseek::Reader::vcfF module, but can be accessed directly to build such entries.

Apart from having built in accessors for the various fields in a .vcf file record, you can also print a whole record at once, in a CSV format as follows:

my $vcf_record = $vcf_reader->next_var;
# Prints line to STDOUT
print $vcf_record;
# Prints line to file handle pointed to by $fh
print $fh $vcf_record;

You can access specific parts of the record. Examples:

my $rid = $vcf_record->Repeatid;
my $refseq = $vcf_record->RefSeq;
my @allele_seqs = @{ $vcf_record->AlleleSeqs };
my @alleles = @{ $vcf_record->Alleles };
my @rcounts = @{ $vcf_record->ReadCounts };
my @cgl = @{ $vcf_record->CopyGainLoss };

Note that AlleleSeqs (or the corresponding get_allele_seqs) does not include the reference sequence. If the genotype is homozygous reference (0/0), it will contain one sequence, '.'.

For convenience, accessors are available that return a list or a scalar, depending on the calling context:

my @cgl = $vcf_record->get_cgls;                 # Get the copy gain/loss as an array
my $cgl_str = $vcf_record->get_cgls;             # Get as a comma-separated string
my $cgl_str = $vcf_record->get_cgls(sep => "\t"); # Same, but use "\t" as the separator

Known issues

• VNTRseek::Reader::vcfF does not currently use the existing Perl VCF module, so it cannot properly validate VCF files. Really, this module should be a wrapper for VCF.pm.