NAME

Microarray::File - Perl objects for handling microarray file formats

SYNOPSIS

        use Microarray::File;

        my $array_file = microarray_text_file->new('/file');            # can pass just a filename...
        my $filehandle = $array_file->filehandle;                                       # ...and retrieve the filehandle

        my $array_file = microarray_text_file->new('/file',$Fh);        # or create the filehandle yourself

DESCRIPTION

Microarray::File provides functions for creating microarray file objects. The module includes functions for importing and sorting data for text files.

METHODS

Generic methods

file_name

Get or set the file name. If the filehandle is being set by Microarray::File, this needs to be the full path, otherwise can be any name.

get_header_keys, get_header_info

If the file type has a header of some kind, the method get_header_keys() will return a list of the keys parsed from the header. The method get_header_info() will return a hash of the header information, or if a key is passed it will return the relevant value.

get_source

Returns the file contents, as are.

microarray_text_file

The sub class microarray_text_file handles any standard text file. As with all text files, line endings are 'normalised'.

line_num

Returns the number of lines read

delimited_file

This is a text file with delimited cells, but not necessarily a straightforward 'spreadsheet' type format.

delimiter

Guesses and returns the delimiter type based on file name suffix. If '.csv', assumes a comma separated format, otherwise assumes a tab-delimited format.

get_data_fields

Returns the column headers as a hash. Both the column names and column numbers have keys, returning the corresponding value. i.e. if column 2 is called 'Name', then the data_fields hash has the following keys;

        2=>'Name'
        'Name'=>2

Clearly this falls down if any of the columns have a numerical name in the same range as the number of columns, but different values (i.e. column 2 is named '3'). Oh well.

get_column_id

Returns the column name from its column number, and vice versa

simple_delimited_file

This is a delimited file with a simple columnar 'spreadsheet' format and no header.

column_num

The number of columns

key_column

Get/set the column index of a column to use as a 'primary key'. If a column is not set, returns -1.

log_file methods

add_text

Add text to the log file

SEE ALSO

Microarray

AUTHOR

Christopher Jones, Gynaecological Cancer Research Laboratories, Institute for Women's Health, University College London.

http://www.instituteforwomenshealth.ucl.ac.uk/AcademicResearch/Cancer/trl

c.jones@ucl.ac.uk

COPYRIGHT AND LICENSE

Copyright 2008 by Christopher Jones, University College London

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.