NAME
bff_pxf_simulator: A script that creates a JSON array of random BFF/PXF
SYNOPSIS
bff_pxf_simulator [-options]
Options:
-f|format Format [>bff|pxf]
-n|number Number of individuals
-diseases Number of [1]
-phenotypicFeatures IDEM
-treatments IDEM
-max-diseases-pool To narrow the selection to N first array elements
-max-phenotypicFeatures-pool IDEM
-max-treatments-pool IDEM
-o|output Output file [individuals.json]
-external-ontologies YAML file with ontologies for diseases, phenotypicFeatures and treatments
-random-seed Initializes pseudorandom number sequences for reproducible results (int)
Generic Options;
-debug Print debugging (from 1 to 5, being 5 max)
-h|help Brief help message
-man Full documentation
-v|verbose Verbosity on
-V|version Print versionDESCRIPTION
A script that creates a JSON array of random BFF/PXF
SUMMARY
A script that creates a JSON array of random BFF/PXF
INSTALLATION
$ cpanm --sudo --installdeps .System requirements
* Ideally a Debian-based distribution (Ubuntu or Mint), but any other (e.g., CentOs, OpenSuse) should do as well.
* Perl 5 (>= 5.10 core; installed by default in most Linux distributions). Check the version with "perl -v"
* 1GB of RAM.
* 1 core (it only uses one core per job).
* At least 1GB HDD.HOW TO RUN BFF-PXF-SIMULATOR
The software runs without any argument and assumes defaults. If you want to change some pearmeters please take a look to the synopsis
Examples:
$ ./bff_pxf_simulator -f pxf # BFF with 100 samples
$ ./bff_pxf_simulator -f pxf -n 1000 -o pxf.json # PXF with 1K samples and saved to pxf.json
$ ./bff_pxf_simulator -phenotypicFeatures 10 # BFF with 100 samples and 10 pF eachCOMMON ERRORS AND SOLUTIONS
* Error message: Foo
Solution: Bar
* Error message: Foo
Solution: BarAUTHOR
Written by Manuel Rueda, PhD. Info about CNAG can be found at https://www.cnag.crg.eu.
COPYRIGHT AND LICENSE
This PERL file is copyrighted. See the LICENSE file included in this distribution.