alignmentrs
Quickly read and manipulate multiple sequence alignments in Python
Installation
pip install alignmentrs
Quickstart
Import alignment into Python
>>> import alignmentrs as rs
>>> aln = rs.Alignment.from_fasta('hiv.fna', 'HIV_alignment')
>>> aln
Alignment(nsamples=10, nsites=120, nmarkers=0)
>>> aln.sample_ids
['sample01', 'sample02', 'sample03', 'sample04', 'sample05', 'sample06'
'sample07', 'sample08', 'sample09', 'sample10']Select sites to remove from the alignment
>>> sites_to_remove = [i for i in range(120) if (i-2) % 3 != 0] # remove 1st and 2nd position in codon triplet
>>> aln.remove_sites(sites_to_remove, copy=False) # manipulate inplace, copy=True returns a new copy
Alignment(nsamples=10, nsites=40, nmarkers=0)Select sites to retain in the alignment
>>> sites_to_retain = list(range(2, 3, 120)) # third position in codon triplet
>>> aln.retain_sites(sites_to_retain, copy=False) # manipulate inplace, copy=True returns a new copy
Alignment(nsamples=10, nsites=40, nmarkers=0)Get a subset of samples and sites
>>> sub_aln = aln.subset(samples=['sample01', 'sample03', 'sample05'], sites=list(range(2, 3, 120)))
>>> sub_aln
Alignment(nsamples=3, nsites=40, nmarkers=0)
