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 <input.csv>        CSV file

     Options:
       -generate-primary-key          Generates a primary key if absent. Use --primary-key-name to set its name
       -primary-key-name <name>       Sets the name for the primary key. Must be a single, non-array field
       -sep, --separator <char>       Delimiter for CSV fields [;] (e.g., --sep $'\t' for tabs)
       -array-separator <char>        Delimiter for nested arrays [|] (e.g., --array-separator ';' for semicolons)
       -output-dir <directory>        Specify the directory where output files will be stored. If not specified, outputs will be placed in the same directory as the input file

     Generic Options:
       -debug <level>                 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

Numerous tools exist for CSV to JSON conversion, but our focus here was on creating JSON specifically for Pheno-Ranker. The script supports both basic CSV files and complex, comma-separated CSV files with nested fields, ensuring seamless Pheno-Ranker integration.

The script will create both a JSON file and the configuration file for Pheno-Ranker. Then, 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 requires a CSV file as the input and operates with default settings. By default, both the JSON file and the configuration file will be created in the same directory as the input file, and will share the same basename.

If you have columns with nested values make sure that you use --array-separator to define the delimiting character (default is "|").

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

 $ ./csv2pheno-ranker -i example.csv --generate-primary-key --primary-key-name ID  --output-dir /my-path --sep ';' --array-separator ','

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.