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In order to demonstrate one way of using the module, four example perl scripts are provided in the C<scripts/Code> directory. 
Each sample script utilises the module and uses/reuses subroutines in a pipeline fashion. The workflow suggested with the scripts is as follows:

B<User Input>: a textfile containing one gene ID per row. All gene IDs must belong to the same species. All gene IDs must be current Ensembl gene IDs.


=over

=item 1. B<Mine Direct Interactions.>

Generate a dataset of direct PPIs based on the input ID list. See example in C<getDirectInteractions.pl>

=item 2. B<Run the basic Interolog-Walk Pipeline.>

Generate dataset of projected putative PPIs following the paradigm explained earlier. Do some postprocessing on the dataset. See example in C<doInterologWalk.pl>

=item 3. B<Compute a prioritisation index for putative PPIs.>

Score the dataset obtained in (2.) using the dataset obtained in (1.) to normalise the score components values. See example in C<doScores.pl>

=item 4. B<Extract network and attributes for the two PPI datasets.>

For each of the two datasets obtained from (1) and (2) (putative PPIs) or from (1) and (3) (scored putative PPIs) extract a text file containing a network representation and 
two text files of node attributes. See example in C<doNets.pl>

=back


=head1 DEPENDENCIES 

C<Bio::Homology::InterologWalk> relies on the following prerequisite software:

=head2 1. Ensembl API

The Ensembl project is currently branched in two sub-projects:

=over

=item The Ensembl Vertebrates project 

This is of interest to you if you work with vertebrate genomes (although it also includes data from a few non-vertebrate common model organisms).
See http://www.ensembl.org/index.html for further details.

=item The Ensembl Genomes project 

This utilises the Ensembl software infrastructure (originally developed in the Ensembl Core project) to provide 
access to genome-scale data from non-vertebrate species. This is of interest to you if your species  is a non-vertebrate, or if
your species  is a vertebrate but you I<also want to obtain results mapped from non-vertebrates>. C<Bio::Homology::InterologWalk> at the moment officially supports
the B<metazoa> sub-site from the Ensembl Genomes Project (note that fungi, plants, protists might work however functionality has not been tested thoroughly). See http://metazoa.ensembl.org/index.html for further details.

=back 

Please obtain the APIs and set up the environment by following the steps described on the Ensembl Vertebrates API installation pages:

http://www.ensembl.org/info/docs/api/api_installation.html

or alternatively

http://www.ensembl.org/info/docs/api/api_cvs.html

B<NOTE 1 - > The Ensembl Vertebrate and Ensembl Genomes DB releases are usually not synchronised: an Ensembl Genomes DB release usually follows the corresponding Ensembl Vertebrates
release by a number of weeks. This means that if you install a bleeding-edge Ensembl Vertebrate API, while the corresponding Ensembl Vertebrate DB will exist, I<a matching EnsemblGenomes DB release might
not be available yet>: you will still be able to use C<Bio::Homology::InterologWalk> to run an orthology walk using exclusively Ensembl Vertebrate DBs, but you
will get an error if you try to choose an Ensembl Genomes databases. In such cases, please install the most recent API compatible with Ensembl Genomes Metazoa, from

http://metazoa.ensembl.org/info/docs/api/api_installation.html

or alternatively

http://metazoa.ensembl.org/info/docs/api/api_cvs.html

This option will not always use the most recent data, but will guarantee functionality across both Vertebrate and Metazoan genomes.

=back

B<NOTE 2 - >: All the API components  (C<ensembl>, C<ensembl-compara>, C<ensembl-variation>, C<ensembl-functgenomics>) must be installed.

B<NOTE 3 - >: The module has been tested on Ensembl Vertebrates API & DB v. 59-64 and EnsemblGenomes API & DB  v. 6-10.

=head2 2. Bioperl

Ensembl provides a customised Bioperl installation tailored to its API, v. 1.2.3. 
Should version 1.2.3 be no more available through Ensembl, please obtain release 1.6.x from CPAN. (while not officially supported by the
Ensembl Project it will work fine when using the API within the scope of the present module)

=head2 3. Additional Perl Modules

The following modules (including all dependencies) from CPAN are also required:

=over

=item 1. C<REST::Client>

=item 2. C<GO::Parser>

=item 3. C<DBD::CSV> (requires Perl DBI)

=item 4. C<String::Approx>

=back

I<See the README file for further information.>


=head1 INTERFACE

=cut


#################### main pod documentation ends ###################






#globals#############################
my $ENSEMBLIDFAILED;

our $ERREX            = '.04err';
our $OUTEX1           = '.01out';