BoutrosLab::TSVStream::IO::Writer
This namespace hierarchy contains classes that can convert a series of objects compatible with some type into an output stream (file or handle).
Usually, a writer object is created indirectly, using a writer method of the target class (which it acquires by consuming the BoutrosLab::TSVStream::IO::Role::Fixed, or BoutrosLab::TSVStream::IO::Role::Dyn role).
Since most of the attributes and methods of writers are the same, this document describes them - there are differences between Fixed and Dyn writers which are distinguished below.
It is recommended that when there are multiple formats possible for a target class, they be implemented as a group of classes, where each class in the group implements its attributes able to coerce their value from any of the formats. If that is done, then a file in any of the formats (or even using a mixture of the formats) can be used as the text stream and a reader will automatically convert it to the format of the target class that the reader is associated with. Additionally, objects of any of the group of classes can be provided to a writer from any of the group and it will use the coercion to automatically convert to the desired format. So, you choose a reader that matches the format you wish to use for your programming code, and a writer for the format you wish for the output. The classes BoutrosLab::TSVStream::Format::AnnovarInput::Human and BoutrosLab::TSVStream::Format::AnnovarInput::NoChr provide an example of this.
my $writer = Some::Class->writer( # class => $class, # (required) class handle => $fd, # (optional if file provided) file => $file, # (optional if handle provided) append => 1, # (optional) append to file header => $str, # (optional) write skip dyn_fields => $ref, # (optional, Dyn only) extra_class_params => [...], # (optional) extra params for # creating new class objects );
The new method will usually be called indirectly from within the writer method of some other class. Such a writer method will provide its own class as the class argument to the new method, so the user calling the writer method does not need to provide it. The writer method will pass any arguments that the caller provides to it on to the new method. This document will refer to that other class as the related class.
At least one of the handle and file arguments must be provided. If only the file is provided, it will be opened for writing and the handle attribute will be initialized to that. If handle is provided, it must be an open handle to a readable stream. If errors are encountered during processing, the file (if provided) and line number are used in the diagnostic - which means that even if you are providing a handle, it can be useful to provide the file argument as well to make the diagnostics clearer (unless your users never make mistakes, of course).
If no handle is provided, the file is opened. By default, it is opened for normal write (overwriting any previous contents). However, if the optional append attribute is provided and has a true value, the file is instead opened for append. If the handle attribute is provided, this append attribute has no effect.
If header is provided, it can be 'write', or 'skip'. This controls what is done to the handle initially.
'write'
'skip'
If 'write' is specified, the field names are written as a header to the stream before any data. If 'skip' is specified, no header is written before any data records. The default is to 'write' the headers.
If the optional pre_headers attribute is provided, it must contain an arrayref contining a list of comment lines that are to be written before the header is written (if any).
For Dyn writers, the dyn_fields parameter can be passed to specify the field names for the dynamic fields. If not, and if headers are being written. then a default set of header names will be provided ('extra1', 'extra2', ...).
'extra1'
'extra2'
The extra_class_params attribute accepts a ref to a list of strings. These will be passed to the new method of the target class when a set of values has been read. This may be useful for some target classes. There is currently no generic use of this for writer.
The write method takes arguments. Usually, you will call it with a single object of the target class, and its fields will be written to the stream.
Alternatively, you can pass an object of a compatible class, an array ref or a list of values. These values will be validated converted (if possible) into the target class and then written (croaking if conversion fails).
The write_comments method takes an array ref containing lines to be written verbatim to the output stream. It is the caller's respopnsibility to ensure that these lines are formatted properly to match the commenting conventions for the targe TSVStream file type.
$writer->_croak("error message");
The _croak method is needed internally, but may also be useful in some cases by the code that uses the writer. It croaks with the supplied message, appending the filename and line number.
_croak
These are the two classes of writer - which read streams containing either only the fields of the consumed class (Fixed), or the fields of the consumed class followed by an additional dynamic set of fields (Dyn).
Describes the hierarchy of provided modules that define a set of attributes that are useful to move to/from a text stream.
A class that has no fixed fields, just dynamic fields. It is useful for processing one-off files where there is no value in going to the work of creating an entire class for that file format.
Describes the format of a text stream that a writer can read from.
John Macdonald - Boutros Lab
Paul Boutros, Phd, PI - Boutros Lab
The Ontario Institute for Cancer Research
To install BoutrosLab::TSVStream, copy and paste the appropriate command in to your terminal.
cpanm
cpanm BoutrosLab::TSVStream
CPAN shell
perl -MCPAN -e shell install BoutrosLab::TSVStream
For more information on module installation, please visit the detailed CPAN module installation guide.