Interfacing with other libraries

PyFAMSA is flexible over its inputs and outputs, and it is easy to integrate with other Python libraries from the bioinformatics ecosystem. This page lists some recipes on how to convert datatypes between these libraries to facilitate building a larger workflow.

Note

Feel free to open a pull request in the GitHub repository if you have some recipes you would like to add to the list!

PyHMMER

Converting a pyhmmer.easel.TextSequence to a pyfamsa.Sequence to pass to a pyfamsa.Aligner:

import pyfamsa
import pyhmmer

with pyhmmer.easel.SequenceFile("sequences.fasta") as f:
    text_seq = f.read()

sequence = pyfamsa.Sequence(id=text_seq.id, sequence=text_seq.sequence)

Converting a pyfamsa.Alignment to a pyhmmer.easel.TextMSA that can then be digitized and used with a pyhmmer.plan7.Builder to build a HMM:

import pyfamsa
import pyhmmer

aligner = pyfamsa.Aligner()
pyfamsa_alignment = aligner.align(sequences)

text_msa = pyhmmer.easel.TextMSA(
    name=b"alignment",
    sequences=[
        pyhmmer.easel.TextSequence(name=row.id, sequence=row.sequence)
        for row in pyfamsa_alignment
    ]
)

Converting a pyhmmer.easel.TextMSA loaded from a file or built from the PyHMMER API into a pyfamsa.Alignment, for instance to perform a profile-profile alignment with pyfamsa.Aligner.align_profiles:

import pyfamsa
import pyhmmer

with pyhmmer.easel.MSAFile("sequences.sto") as f:
    text_msa = f.read()

pyfamsa_alignment = pyfamsa.Alignment(
    pyfamsa.GappedSequence(id=id_, sequence=sequence)
    for id_, sequence in zip(text_msa.name, text_msa.aligned)
)

Pytrimal

Converting a pyfamsa.Alignment to a pytrimal.Alignment for trimming the generated alignment:

import pyfamsa
import pytrimal

aligner = pyfamsa.Aligner()
pyfamsa_alignment = aligner.align(sequences)

pytrimal_alignment = pytrimal.Alignment(
    names=[row.id for row in pyfamsa_alignment],
    sequences=[row.sequence for row in pyfamsa_alignment]
)

trimmer = pytrimal.AutomaticTrimmer()
trimmed_alignment = trimmer.trim(pytrimal_alignment)

PyCoMSA

Converting a pyfamsa.Alignment to pycomsa.MSA to write an alignment computed with FAMSA into a CoMSA file with compression:

import pycomsa
import pyfamsa

aligner = pyfamsa.Aligner()
pyfamsa_alignment = aligner.align(sequences)

pycomsa_msa = pycomsa.MSA(
    id="alignment",
    names=[row.id.decode() for row in pyfamsa_alignment],
    sequences=[row.sequence.decode() for row in pyfamsa_alignment]
)

with pycomsa.open("sequences.msac", "w", format="stockholm") as f:
    f.write(pycomsa_msa)

Biopython

Converting SeqRecord objects to pyfamsa.Sequence so they can be aligned:

import Bio.SeqIO
import pyfamsa

sequences = [
    pyfamsa.Sequence(id=record.id.encode(), sequence=bytes(record.seq))
    for record in Bio.SeqIO.parse("sequences.fa", "fasta"):
]

aligner = pyfamsa.Aligner()
pyfamsa_alignment = aligner.align(sequences)