Bio::Community::Role::Table - Role to read/write data tables and provide random access to their cells
package My::Package; use Moose; extends 'Bio::Root::IO'; with 'Bio::Community::Role::Table'; # Use the new(), _read_table(), _get_value(), _set_value(), _insert_line(), # _delete_col() and _write_table() # methods as needed # ... 1;
This role implements methods to read and write file structured as a table containing rows and columns. When reading a table from a file, an index is kept to provide random-access to any cell of the table. When writing a table to a file, cell data can also be given in any order. It is kept in memory until the file is written to disk.
Objects are constructed with the new() method. Since Table-consuming classes must inherit from Bio::Root::IO, all Bio::Root::IO options are accepted, e.g. -file, -fh, -string, -flush, etc. Other constructors are detailed in the APPENDIX.
Florent Angly florent.angly@gmail.com
User feedback is an integral part of the evolution of this and other Bioperl modules. Please direct usage questions or support issues to the mailing list, bioperl-l@bioperl.org, rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
If you have found a bug, please report it on the BioPerl bug tracking system to help us keep track the bugs and their resolution: https://redmine.open-bio.org/projects/bioperl/
Copyright 2011-2014 by Florent Angly <florent.angly@gmail.com>
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.1 or, at your option, any later version of Perl 5 you may have available.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Usage : my $delim = $in->delim; Function: When reading or writing a table, get or set the delimiter, i.e. the characters that delimit the columns of the table. The default is the tab character "\t". Args : A string Returns : A string
Usage : my $line_num = $in->start_line; Function: When reading a table, get or set the line number at which the table starts. The default is 1, i.e. the table starts at the first line of the file. This option is not used when writing a table, but see _write_table() for details. Args : A strictly positive number Returns : A strictly positive number
Usage : my $line_num = $in->end_line; Function: When reading a table, get or set the line number at which the table ends. If undef (the default), the table ends at the last line of the file. Args : A strictly positive number or undef Returns : A strictly positive number or undef
Usage : my $missing = $out->missing_string; Function: When reading a table, get or set the line number at which the table ends. If undef (the default), the table ends at the last line of the file. Args : A string, e.g. '', '0', 'n/a', '-' Returns : A string
Usage : my $txt = $in->_get_start_content; Function: After the table has been parsed, this returns everything before -start_line Args : A strictly positive number Returns : A strictly positive number
Usage : my $num_lines = $in->_get_max_line; Function: Get the number of lines in the table Args : None Returns : Positive integer
Usage : my $num_cols = $in->_get_max_col; Function: Get the number of columns in the table Args : None Returns : Positive integer
Usage : $in->_read_table; Function: Read the table in the file and index the position of its cells. Args : None Returns : 1 on success
Usage : my $value = $in->_get_value(1, 3); Function: Get the value of the cell given its position in the table (line and column). Args : A strictly positive integer for the line A strictly positive integer for the column Returns : A string for the value of the table at the given line and column or undef if line or column was out-of-bounds
Usage : $out->_set_value(1, 3, $value); Function: Set the element at the given line and column of the table. Args : A strictly positive integer for the line A strictly positive integer for the column A string for the value of the table at the given line and column Returns : 1 for success
Usage : $out->_insert_line(3, ['sample1', 3, 10.9, 'Mus musculus']); Function: Insert a line of values in the table, at the indicated line, shifting all other lines down. You can also append a line to the table by providing the maximum line number + 1. Args : A strictly positive integer for the line at which to insert An arrayref containing the values to insert (must match table width) Returns : 1 for success
Usage : $out->_delete_col(3); Function: Delete a column of the table. Args : A strictly positive integer for the column to delete. Returns : 1 for success
Usage : $out->_write_table; Function: Write the content of the cells in the table to a file. It is generally called automatically when closing the object. However, if you want header lines before or after the table, you can write them to file using the _print() method of Bio::Root::IO prior and after calling _write_table(). Args : None Returns : 1 on success
To install Bio::Community, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Community
CPAN shell
perl -MCPAN -e shell install Bio::Community
For more information on module installation, please visit the detailed CPAN module installation guide.