NAME

BoutrosLab::TSVStream::Format

SYNOPSIS

This namespace hierarchy contains classes that define a useful
object that also embeds the ability to create a reader or
writer.

DESCRIPTION

Classes in this namespace provide a set of useful attributes, etc. as any normal class. But they also consume one of the roles:

BoutrosLab::TSVStream::IO::Role::Fixed
BoutrosLab::TSVStream::IO::Role::Dyn

which allows them to create a reader (or writer) object that can read from (or write to) a stream or file, converting the text of the stream to (or from) an object of this class.

A class that consumes ...::IO::Role::Fixed deals with streams which contain only the fixed defined fields for this class (as specified by the class attribute _class).

A class that consumes ...::IO::Role::Dyn deals with streams which contain the fixed defined fields for this class (as specified by the class attribute _class), but on each line the fixed attributes are followed by a number of dynamic fields.

The stream format is a series of lines. Each line consists of a number of fields, separated by a tab character. The first line is (usually) a text line that has the field names as the contents of each field. (The field names are validated on reading to verify match the definition of the object.) The remaining lines of the stream consist of fields that contain data. The first fields contain data for each of the attributes defined by the object (in the order defined by the object). This data is validated using the type specification for those attributes. For Dyn objects, remaining fields contain text data for additional contents. The number and content of these dynamic fields are determined at run-time - there must be a consistant number of fields throughout an entire stream, but the validity of the content cannot be determined automatically (because each stream can have a different set of dynamic fields, so there is no way for the code to know in advance how to validate them).

SEE ALSO

BoutrosLab::TSVStream::Format::AnnovarInput::Human::Fixed

BoutrosLab::TSVStream::Format::AnnovarInput::Human::Dyn

BoutrosLab::TSVStream::Format::AnnovarInput::HumanNoChr::Fixed

BoutrosLab::TSVStream::Format::AnnovarInput::HumanNoChr::Dyn

These modules provide an example of how to write a module able to read/write TSV stream text. You can use them as templates either for adding a new module under this hierarchy, or for writing your own TSV capable objects that are not added to this namespace.

They provide objects that use AnnovarInput file format for the text form, and restrict the chrosome values to ones appropriate to humans.

BoutrosLab::TSVStream::Format::None::Dyn

A class with no fixed fields, but only dynamic fields. This is useful for dealing with dynamic TSV streams where you don't know the stream contents, or for fixed field formats where you don't want to have to create an object to define the fields - and you are able to simply treat the field contents as unconstrained text.

There is no point in defining the corresponding ...::None::Fixed module since that would only deal with objects having no attributes, converting them to/from streams containing only empty lines.

AUTHOR

John Macdonald - Boutros Lab

ACKNOWLEDGEMENTS

Paul Boutros, Phd, PI - Boutros Lab

The Ontario Institute for Cancer Research