/ 
Pheno-Ranker-0.03_1
River stage zero No dependents
/ bff-pxf-simulator:

NAME

bff-pxf-simulator: A script that creates a JSON array of simulated BFF/PXF

SYNOPSIS

bff-pxf-simulator [-options]

Options:
  -f|format                      Format [>bff|pxf]
  -n|number                      Number of individuals
  -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)

  -diseases                      Number of [1]
  -exposures                     IDEM
  -phenotypicFeatures            IDEM
  -procedures                    IDEM
  -treatments                    IDEM
  -max-[term]-pool               To narrow the selection to N first array elements.
  -max-ethnicity-pool            Each individual can have only 1 ethnicity. However, you can also set a fixed sample size for the pool

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 version

DESCRIPTION

This script generates a JSON array of simulated BFF/PXF data. The files can be created based on pre-loaded ontologies or by utilizing an external YAML file.

SUMMARY

A script that creates a JSON array of simulated BFF/PXF.

Implemented array terms:

BFF: diseases, exposures, interventionsOrProcedures, phenotypicFeatures, treatments.

procedures = interventionsOrProcedures

PXF: interventionsOrProcedures, medicalActions.procedure, medicalActions.treatment, phenotypicFeatures.

procedures = medicalActions.procedure

treatments = medicalActions.treatment

INSTALLATION

(only needed if you did not install Pheno-Ranker)

$ 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

When run without any arguments, the software will use default settings. To modify any parameters, please refer to the synopsis for guidance.

If you prefer not to include a specific term in the analysis, set its value to zero. For example:

--treatments 0

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 each

$ ./bff-pxf-simulator -diseases 0 -exposures 0 -procedures 0 -phenotypicFeatures 0 -treatments 0 # Only sex and ethnicity

COMMON ERRORS AND SOLUTIONS

* Error message: Foo
  Solution: Bar

* Error message: Foo
  Solution: Bar

AUTHOR

Written by Manuel Rueda, PhD. Info about CNAG can be found at https://www.cnag.eu.

COPYRIGHT AND LICENSE

This PERL file is copyrighted. See the LICENSE file included in this distribution.