NAME

csv2pheno-ranker: A script to convert a CSV to an input suitable for Pheno-Ranker

SYNOPSIS

csv2pheno-ranker -i <input.csv> [-options]

     Arguments:
       -i|input                       CSV file

     Options:

       -generate-primary-key          Generates a primary key if absent. Use --primary-key-name to set its name.
       -primary-key-name              Sets the name for the primary key. Must be a single, non-array field.
       -sep|separator                 Delimiter character for CSV files [;] e.g., --sep $'\t'

     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

There are hundreds of online tools available for converting CSV to JSON, and we saw no need to reinvent the wheel. Our primary focus was on efficiently getting the job done, enabling seamless compatibility between CSV and Pheno-Ranker.

This script is designed to handle both simple CSV files without nested fields in columns, as well as more complex ones with nested fields, as long as they are comma-separated.

The script will create both a JSON file and the configuration file for Pheno-Ranker. You can run Pheno-Ranker as:

 $ pheno-ranker -r my_csv.json --config --my_csv_config.yaml

Note that we load all data in memory before dumping the JSON file. If you have a huge CSV (e.g.,>5M rows) please use a computer that has enough RAM.

SUMMARY

A script to convert a CSV to an input suitable for Pheno-Ranker

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 CSV2PHENO-RANKER

The software needs a csv as input file and assumes defaults. If you want to change some parameters please take a look to the synopsis.

Examples:

 $ ./csv2pheno-ranker -i example.csv
 
 $ ./csv2pheno-ranker -i example.csv --generate-primary-key --primary-key-name ID

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.