# Bio Alignment Msa Parsing

Parse and analyze multiple sequence alignments using Biopython.

- Repository: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills (3090 stars)
- Category: Engineering
- License: see repository
- Last updated: 2026-07-21
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-alignment-msa-parsing -g -a claude-code -y`
Codex: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-alignment-msa-parsing -g -a codex -y`
Cursor: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-alignment-msa-parsing -g -a cursor -y`
Gemini CLI: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-alignment-msa-parsing -g -a gemini-cli -y`

## Description

Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

## Version Compatibility

Reference examples tested with: BioPython 1.83+

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.

```python
from Bio import AlignIO
from Bio.Align import MultipleSeqAlignment
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
from collections import Counter
```

## Loading Alignments

**Goal:** Read an MSA file and inspect its dimensions.

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

```python
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
```python
seq_ids = [record.id for record in alignment]
```

### Get Sequences as Strings
```python
sequences = [str(record.seq) for record in alignment]
```

### Get Sequence by ID
```python
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
```python
for record in alignment:
    print(f'ID: {record.id}')
    print(f'Description: {record.description}')
    print(f'Annotations: {record.annotations}')
```

## Column-wise Analysis

The rest: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/blob/HEAD/skills/bio-alignment-msa-parsing/SKILL.md