/ 
CelegansInteractome
River stage zero No dependents
/ CelegansInteractome

NAME

CelegansInteractome - generates interactome graphs for a list of C.elegans genes

SYNOPSIS

use CelegansInteractome;
use GraphViz;

my $tmp = CelegansInteractome->new();
$tmp->load_interactome(
   wormbase_version    => $wormbase_version || "WS239",
   in_file             => $in_file,
   out_file            => $out_file,
   cleanup             => "0"
);

# print the interactome graph(s)
$tmp->graph_interactome();

DESCRIPTION

This object downloads an interaction table for C.elegans from WormBase (www.wormbase.org), then parses the downloaded data and builds a seperate interactome for each gene in a supplied list to return graphical files for each interactome. The supplied list of gene names, should be a text file with one entry per line using WormBase common names.

FEEDBACK

damienoh@gwu.edu

Mailing Lists

User feedback is an integral part of the evolution of this module. Send your comments and suggestions preferably to one of the mailing lists. Your participation is much appreciated.

Support

Please direct usage questions or support issues to: <damienoh@gwu.edu> Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the GitHub bug tracking system to help keep track of the bugs and their resolution. Bug reports can be submitted via the GitHub page:

https://github.com/dohalloran/CelegansInteractome/issues

AUTHORS - Damien OHalloran

Email: damienoh@gwu.edu

APPENDIX

The rest of the documentation details each of the object methods.

new()

Title   : new()
Usage   : my $tmp = CelegansInteractome->new();
Function: constructor routine
Returns : a blessed object
Args    : none

load_interactome()

Title   : load_interactome()
Usage   : my $tmp->load_interactome(
           wormbase_version    => $wb_version || "WS239",
           in_file             => $in_file,
           out_file            => $out_file,
           cleanup             => "0"
           );
Function: Populates the user data into $self hash
Returns : nothing returned
Args    : 
-wormbase_version, version of wormbase to get data from
-in_file, the name of the files containing a list of genes 
-out_file, name of the resulting graphical output file(s) 
-cleanup, option to delete tmp file: 1=yes, 0=no

graph_interactome()

Title   : graph_interactome()
Usage   : graph_interactome();
Function: starts a series of function calls beginning with a sub to download interactome data
Returns : the interactome data 
Args    : none

_parse_input()

Title   : _parse_input()
Usage   : _parse_input();
Function: replace tabs with commas in downloaded file for easy regex fetching
Returns : new txt with commas replacing tabs
Args    : none

_get_matches()

Title   : _get_matches()
Usage   : _get_matches();
Function: retrives all the interactome matches for each gene in the input file
Returns : new tmp txt file with list of matches
Args    : none

_sort_matches()

Title   : _sort_matches()
Usage   : _sort_matches();
Function: organizes matches from the _get_matches() subroutine into single lines
Returns : a new tmp txt file that contains a list of all macthes to each gene on single lines
Args    : none

_handle_graphs()

Title   : _handle_graphs()
Usage   : _handle_graphs();
Function: build arrays for GraphViz containing matches
Returns : a series of arrays are generated
Args    : none

_cleanup()

Title   : _cleanup()
Usage   : _cleanup();
Function: option to delete tmp files
Returns : nothing
Args    : 1=yes, 0=no

get_wormbase_version()

Title   : get_wormbase_version()
Usage   : my $get_wormbase_version= $tmp->get_wormbase_version();
Function: Retrieves the wormbase version used
Returns : A string of the version e.g. WS239
Args    : none

set_wormbase_version()

Title   : set_wormbase_version()
Usage   : my $set_wormbase_version = $tmp->set_wormbase_version("WS240");
Function: Populates the $self->{wormbase_version} property
Returns : $self->{wormbase_version}
Args    : the version as a string

get_out_file()

Title   : get_out_file()
Usage   : my $get_outfile = $tmp->get_out_file();
Function: Retrieves the output filename
Returns : A string containing filename
Args    : none

set_out_file()

Title   : set_out_file()
Usage   : my $set_output = $tmp->set_out_file("myOutPutFile");
Function: Populates the $self->{out_file} property
Returns : $self->{out_file}
Args    : name of the resulting graphical output file(s)

get_in_file()

Title   : get_in_file()
Usage   : my $get_in_file = $tmp->get_in_file();
Function: Retrieves the input filename
Returns : A string containing filename
Args    : none

set_in_file()

Title   : set_in_file()
Usage   : my $set_in_file= $tmp->set_in_file("myOutPutFile.txt");
Function: Populates the $self->{in_file} property
Returns : $self->{in_file}
Args    : name of the user provided input file

get_cleanup()

Title   : get_cleanup()
Usage   : my $get_cleanup = $tmp->get_cleanup();
Function: returns the value option for cleanup
Returns : 1 or 0
Args    : none

set_cleanup()

Title   : set_cleanup()
Usage   : my $set_cleanup = $tmp->set_cleanup("0");
Function: Populates the $self->{cleanup} property
Returns : $self->{cleanup}
Args    : a command to execute cleanup or not: 1=yes, 0=no