bio-alignment-msa-parsing

Version Compatibility

Reference examples tested with: BioPython 1.83+, numpy 1.26+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

MSA Parsing and Analysis

Parse multiple sequence alignments to extract information, analyze content, and prepare for downstream analysis.

Required Import

Goal: Load modules for parsing, analyzing, and manipulating multiple sequence alignments.

Approach: Import AlignIO for reading, Counter for column analysis, and alignment classes for constructing modified alignments.

from Bio import AlignIO
from Bio.Align import MultipleSeqAlignment
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
from collections import Counter
import numpy as np
import pandas as pd

Optional for streaming and Easel-based weighting:

import pyhmmer

Loading Alignments

Goal: Read an MSA file and inspect its dimensions.

Approach: Use AlignIO.read() specifying the file and format.

from Bio import AlignIO

alignment = AlignIO.read('alignment.fasta', 'fasta')
print(f'{len(alignment)} sequences, {alignment.get_alignment_length()} columns')

Extracting Sequence Information

Get All Sequence IDs

seq_ids = [record.id for record in alignment]

Get Sequences as Strings

sequences = [str(record.seq) for record in alignment]

Get Sequence by ID

def get_sequence_by_id(alignment, seq_id):
    for record in alignment:
        if record.id == seq_id:
            return record
    return None

target = get_sequence_by_id(alignment, 'species_A')

Access Descriptions and Annotations

for record in alignment:
    print(f'ID: {record.id}')
    print(f'Description: {record.description}')
    print(f'Annotations: {record.annotations}')