NAME
BoutrosLab::TSVStream::Format::VCF::RoleSYNOPSIS
Collection of roles that implement VCF format capable objects. This role provides the common attributes for VCF format. It also supplies methods that allow a VCF object act as a AnnovarInput object.
DESCRIPTION
These roles are combined with an IO/Base role to provide one of the two standard variants (Fixed and Dyn - depending upon whether you wish to allow only the default set of fields or to allow additional trailing fields following the default ones.)
See BoutrosLab::TSVStream::Format::Human::Fixed for an example.
Class Attributes
_fields
The _fields attribute is required by the IO roles to determine which fields are to be read or written. In this case, the fields are chrom, start, end, ref, and alt, which are described as attributes below.
Attributes
chrom
The chrom attribute provides the name of the chromosome that is being specified. There are different names used for different species of organism; and for different ways of processing the same organism; so this attribute is provided in a separate role.
pos
The pos attribute is an integer that provide the start position within the chromosome that is being described.
id
The id attribute is a string, not yet supported (in this module} for any specific use.
ref
alt
The ref and alt attributes describe amino acid sequences. They can either contain the string '-', or a sequence of acids ('A', 'C', 'G', and 'T' of at most 500 acids. (E.G.: CGATCGAT)
qual
filter
info
The qual, filter, and ifno attributes are strings, not yet supported (in this module} for any specific use.
_reader_args
_writer_args
info
The _reader_args and _writer_args attributes are internal settings. They cause the reader and writer be given special args required for handling VCF format files properly.
WRAPPER ROLES
BoutrosLab::TSVStream::Format::VCF::Role::AsAnnovarInputChr
BoutrosLab::TSVStream::Format::VCF::Role::AsAnnovarInputNoChr
These wrapper roles provide a wrapper around the basic VCF role that allows a vcf format record to be used as if it were an AnnovarInput (or AnnovarInput...NoChr) format record. This is done by providing start, end, and chr methods that match the attributes that are normally present in an AnnovarInput record.
start
end
The start and end attributes are integers that provide the start and end position within the chromosome that is being described. The start value is just a synonym for the pos attribute. The end attribute is computed from the pos value and the length of the ref attribute.
chr
The chr attribute is the chrom attribute with a leading 'chr' string either forced or removed.
SEE ALSO
- BoutrosLab::TSVStream::Format
-
This describes how IO-capable objects (such as ones created using a subrole of this role) are defined.
- BoutrosLab::TSVStream::IO
-
This describes of how readers and writers convert objects to or from a text stream.
- - BoutrosLab::TSVStream::Format::VCF::Fixed
- - BoutrosLab::TSVStream::Format::VCF::Dyn
-
These are the two variants for the object specification for VCF objects. Those are the modules that you will typically use and refer to in your program.
Fixed/Dyn specifies whether only the standard fields are expected, or if a dynamic list of additional fields may occur.
AUTHOR
John Macdonald - Boutros Lab
ACKNOWLEDGEMENTS
Paul Boutros, Phd, PI - Boutros Lab
The Ontario Institute for Cancer Research