Library for applying haplotypes to reference DNA sequences
Daniel Standage, 2018
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.
pip3 install happer
To make sure the package installed correctly:
pip3 install pytest py.test --pyargs happer
happer requires Python version 3.
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
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