metanetwork Files

These scripts were used to analyse sequence similarity networks as accurately described in Fondi et al. 2015 (Genome Biology and Evolution, submitted for pubblication). They were not meant to be of general use althought we are currently working to make all the codes as much generalizable as possible. For suggestions, queries and any help in general please contact marco.fondi at unifi.it

General requirements:

These codes relies on the availability of the following Perl modules:
Statistics::R 
LWP::Simple
metamod (available for download in this SourceForge folder. To be decompressed before usage);
Term::ANSIColor
List::Util 'shuffle'
Statistics::Basic


Detailed description:

- Blast2Netno20.pl
 
This script converts a list of tabular blast output files into network files. Supported output formats include Gephi and Cytoscape. 
Usage: perl Blast2Netno20.pl <list of fasta files>
Fasta files should be named consecutively (in this case 1.parsed4, 2.parsed4 and so on). Changing the naming scheme of the files requires changing the script at lines 38, 39 and 85 accordingly.


- Contigs2NetConnectedOnly.pl 
This script was used to maintain only connected nodes in the contigs networks.
Usage: perl Contigs2NetConnectedOnly.pl <list of fasta files>
Fasta files should be named consecutively (in this case 1.parsed4, 2.parsed4 and so on). Changing the naming scheme of the files requires changing the script at lines 38, 39 and 85 accordingly.

- GetHabitatCoherence.pl	
This script was used to infer the coherence of each network cluster in terms of the habitat of the embedded nodes.
Usage: perl GetHabitatCoherence.pl  <list of cluster file names> <nodes attribute file>
Input file should be a list of *.cc cluster files (Connected Compondents) and an atrribute file should be provided in the format:

node1_name	habitat
node2_name	habitat
node3_name	habitat
....

- GetMoleculeCoherence.pl	
This script was used to infer the coherence of each network cluster in terms of the informative molecule of the embedded nodes.
Usage: perl GetMoleculeCoherence.pl  <list of cluster file names> <nodes attribute file>
Input file should be a list of *.cc cluster files (Connected Compondents) and an atrribute file should be provided in the format:

node1_name	molecule
node2_name	molecule
node3_name	molecule
....

- ComputeCentralities.pl
This script was used to compute centralities metrics on the original networks.
Usage: perl ComputeCentralities.pl  <input network in igraph format>
Input network file should be in the ncol igraph format


- RandomizeCentralities.pl
This script was used to compute centralities metrics on randomized networks.
Usage: perl ComputeCentralities.pl  <input network in igraph format> <Number of randomizations>
Default N. of randomizations is 1000
Input network file should be in the ncol igraph format

- GetClusterICCC.pl
this script was used to compute Intra Cluster Clustering Coefficient at for diffent values of Inflation Values (ranging from <min inflation value> to <max inflation value> with a step of <inflation value step>)
 Usage: erl GetClusterICCC.pl <inputfile> <min inflation value> <max inflation value> <inflation value step>
MCL sohuld be performed in advance on the input graph and MCL output files named as reported at line 63 of this script (ClustresOnly.<inputfile>.<inflation value>)


- ComputePrecisionRecall.pl
This script was used to compute Precision, Recall and Accuracy on the original metagenome network
Usage: perl ComputePrecisionRecall.pl <input file> <Reference file>
Two arguments required,  <input file> is the cluster file from MCL output, <Reference file is the reference list containing the nodes number and their classes in the form:

node1_name	habitat
node2_name	habitat
node3_name	habitat
....

Current habitats implemented in the script are:

wwat
unknown
swast
soil
sea
other
iwater
biotrans
air
biorem

- ComputePrecisionRecallRND.pl
This script was used to compute Precision, Recall and Accuracy on (N=<number of shuffled networks to be re-built>) randomly re-shuffled network metagenome network. Avrage Precision, Recall and Accuracy are produced as outputs, together with std.
Usage: perl ComputePrecisionRecall.pl <input file> <Reference file> <number of shuffled networks to be re-built>

node1_name	habitat
node2_name	habitat
node3_name	habitat
....

Current habitats implemented in the script are:

wwat
unknown
swast
soil
sea
other
iwater
biotrans
air
biorem