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.