Introduction

The main purpose of MutationInfo is to simplify the process of locating a variant in a dataset (i.e. of sequences or variants) that is aligned in a human reference genome (for example hg19 or hg38). It mainly wraps a collection of existing tools with a simple interface.

Example:

from MutationInfo import MutationInfo
mi = MutationInfo()

# RS variant
print mi.get_info('rs53576')
{'chrom': '3', 'notes': '', 'source': 'UCSC',
'genome': 'hg19', 'offset': 8804371L, 'alt': 'G', 'ref': 'A'}

# HGVS variant
print mi.get_info('NM_000367.2:c.-178C>T')
{'chrom': '6', 'notes': '', 'source': 'counsyl_hgvs_to_vcf',
'genome': 'hg19', 'offset': 18155397, 'alt': 'A', 'ref': 'G'}

How it works

MutationInfo tries to infer the position, reference and alternative of a variant through the following pipeline:

  • If the variant is in rs format, then
  • If the variant is in HGVS then:

    • Try to parse the variant with the biocommon/hgvs parser.

    • If the parse fails then look if the variant contains some common mistakes in HGVS formatting. Correct if possible and then try again. For example remove parenthesis in the following variant: NM_001042351.1:-1923(A>C)

    • If parse still fails then make a request to the mutalyzer.nl . For example NT_005120.15:c.IVS1-72T>G is parsed only from mutalyzer but not from biocommons/hgvs

    • If neither of these methods are able to parse the variant then return None.

    • If biocommons/hgvs parses the variant then use the variantmapper method to locate the location of the variant in the reference assembly.

    • If this method fails then use the pyhgvs package and the hgvs_to_vcf method to convert the variant in a VCF entry.

    • If this method fails then use Mutalyzer’s Position Converter

    • if this method fails then use the Mutalyzer’s Name Checker which generates a genomic description of the variant. Then perform a blat search) with this variant (see below).

    • If both methods from Mutalyzer fail (for example M61857.1:c.121A>G crashes mutalyzer!) then:
      • Download the FASTA sequence of the trascript of the variant from NCBI database.
      • If the position of the variant is in coding (c.) coordinates then convert to genomic (g.) coordinates. To do that, we use the Coordinate mapper addition of biopython.
      • Perform a blat search) from UCSC. This methods performs an alignment search of the fasta sequence in the reference assembly. In case this succeeds then report the location of the variant in the reference genome.

    • If this method fails then search the LOVD database.

    • If all the aforementioned methods fail then return None

Installation

Note

Important! Requires 13 GB of disk space.

To install MutationInfo, download the latest release from https://github.com/kantale/MutationInfo/releases , uncompress and run:

python setup.py install

Then the first time you instantiate the MutationInfo class, it installs all required datasets:

from MutationInfo import MutationInfo
mi = MutationInfo()

Installation in Ubuntu

Before installing in Ubuntu Linux, make sure that the following packages / tools are installed:

sudo apt-get update
sudo apt-get install git
sudo apt-get install gcc python-dev libpq-dev python-pip python-mysqldb-dbg

wget https://bootstrap.pypa.io/ez_setup.py -O - | sudo python

Test Installation

To verify that everything works fine run: python test.py in test/ directory. The output after the long log messages should be:

----------------------------------------------------------------------
Ran 6 tests in 21.923s

OK

Troubleshooting

Possible problems from installing / running MutationInfo are: