mendelbrot 0.0.3

A really simple Pedigree Parser

mendelbrot

This library contains utility modules, used in both Talos and TalosAf - analysis tools created at the Centre for Population Genomics.

pedigree_parser

This is a simple pedigree parser, which provides a simple, minimal-dependency interface for parsing a Pedigree file.

This was developed as part of the broader Talos project, and as such can support standard 6-column pedigree files, as well as 7-column pedigree files which pack HPO terms into the final column. See the Usage documentation for more details

bcftools_intepreter

A wrapper to generate HGVS-compliant p. notation from BCFtools CSQ's amino_acid_change field.

This wrapper contains individual method and RegEx patterns to decipher long-form AA change Strings. These can be accessed directly (e.g. through mendelbrot.bcftools_interpreter.process_stop_gained()) or they can be accessed via a distributor method:

from mendelbrot.pedigree_parser import classify_change

neat_aa = classify_change('812L>812*', 'stop_gained')

neat_frameshift = classify_change('375VIGYECDCAAGFELIDRKTC..821>375V*', 'frameshift')

This wrapper only works for some consequence types (synonymous, missense, stop_gained, and frameshift). If it fails some corenr cases for any of these types, or new types are required, please raise an issue.