happer

Daniel Standage, 2018
https://github.com/bioforensics/happer

happer is a minimal Python library for generating complete haplotype sequences. Given a reference sequence and haplotype alleles annotated in BED format, happer will mutate the reference and produce sequences to match the specified haplotypes.

Installation

To install:

pip3 install happer

To make sure the package installed correctly:

pip3 install pytest
py.test --pyargs happer

happer requires Python version 3.

Usage

Reference sequences must be provided in Fasta format, and haplotype alleles must be specified in BED format as follows. Alleles corresponding to different haplotypes at the locus are separated by a | character, so for example a diploid individual should have 2 |-separated alleles annotated at each locus, while a tetraploid would have 4 alleles. In the example below, the CCGA alleles are phased and represent one haplotype, while the TATG alleles are phased and represent another haplotype.

#SeqID    Start  End     Alleles
chr1     38827  38828   C|T
chr1     59288  59289   C|A
chr2     24771  24772   G|T
chr4     201191 201192  A|G

To invoke happer from the command line:

[standage@lappy ~]$ happer --out haploseqs.fasta refr.fasta alleles.bed

To invoke happer directly in Python:

>>> import happer
>>> seqfile = open('refr.fasta', 'r')
>>> alleles = open('alleles.bed', 'r')
>>> for label, haploseq in happer.mutate.mutate(seqfile, alleles):
...     # do whatever you'd like with the sequences