boydgreenfield / codex

Perl library for working with the OneCodex api

Codex

Note: This is an unofficial module for interacting with the One Codex platform

A Perl module for consuming the One Codex API

Requires:

the Mojolicous web framework - link
the light-weight Mouse object framework - link

Description:

This module provides a wrapper around the One Codex REST api. It simplifies api calls by abstracting away the curl calls into simple method calls. It also provides Mouse objects for all of the api objects (Samples, Analyses, References etc), and typed Collections for working with sets of these objects. Allows for simple integration of the One Codex api into existing pipelines.

Installation:

```bash git clone https://github.com/mbiokyle29/codex/ cd codex perl MakeFile.PL sudo make sudo make install ```

Useage:

```perl use Codex;

Create instance, supplying your API key

my $codex = Codex->new(api_key => "API KEY");

Fetch a sample by sample id

returns a Codex::Sample object

my $sample = $codex->get_sample("SAMPLE ID");

Fetch all samples for authenticated user

returns a Codex::Collection object of type Sample

my $sample_collecion = $codex->get_samples;

Get all of the samples in the collection that are completed

my $array = $sample_collection->completed_samples # Returns an array of samples

Search the sample collection using a hash ref

the keys are the fields to search, values are what to match, can be regex

This searches the sample collection for all samples whos filename matches the regex

my $fasta_samples = $sample_collection->search( { filename => '.*.fasta$' } );

Process each sample

while(my $sample = $sample_collection->pop) { # Iterate through the samples }

upload a read file

my $uploaded_id = $codex->upload("my_sample_reads.fasta");

Download raw data

$codex->get_raw_analysis("SAMPLE ID");