geetduggal / refdetect

Simple python module for reference file detection on the DNAnexus platform

refdetect module

Given an input bam file path or file ID, this module allows a DNAnexus user to obtain the reference file ID on the platform.

Currently supported genomes

This list is intended to expand, but we currently focus on these genomes:

• GRCh37 (b37)
• GRCh37 (hs37d5)
• hg18
• hg19 (UCSC)
• GRCh38

Please see https://wiki.dnanexus.com/Scientific-Notes/human-genome for more information on the distinctions between the GRCh37s.

Installation

python setup.py install

Examples

From command line within module directory:

refdetect <bam file on platform>

In a python script:

import refdetect

ref_file_id = refdetect.get_reference_id("<bam file on platform>")

If a reference is not found a Python exception will be thrown.

Adding a new reference to the module

$ refdetect <BAM file on platform> --refname=b37 --refid=file-XXX

In a python script:

import refdetect

ref_file_id = refdetect.write_ref_metadata("<bam file on platform>", "b37", "file-XXX")

Contributors

• Alpha Diallo
• Geet Duggal
• Marcus Kinsella
• Maria Simbirsky