alignment-io skill

---
name: bio-alignment-io
description: Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
tool_type: python
primary_tool: Bio.AlignIO
---

## 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.

# Alignment File I/O

Read, write, and convert multiple sequence alignment files in various formats.

## Required Import

**Goal:** Load modules for reading, writing, and manipulating multiple sequence alignments.

**Approach:** Import AlignIO for file I/O and supporting classes for programmatic alignment construction.

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

## Supported Formats

| Format | Extension | Read | Write | Description |
|--------|-----------|------|-------|-------------|
| `clustal` | .aln | Yes | Yes | Clustal W/X output |
| `fasta` | .fasta, .fa | Yes | Yes | Aligned FASTA |
| `phylip` | .phy | Yes | Yes | Interleaved PHYLIP |
| `phylip-sequential` | .phy | Yes | Yes | Sequential PHYLIP |
| `phylip-relaxed` | .phy | Yes | Yes | PHYLIP with long names |
| `stockholm` | .sto, .stk | Yes | Yes | Pfam/Rfam annotated |
| `nexus` | .nex | Yes | Yes | NEXUS format |
| `emboss` | .txt | Yes | No | EMBOSS tools output |
| `fasta-m10` | .txt | Yes | No | FASTA -m 10 output |
| `maf` | .maf | Yes | Yes | Multiple Alignment Format |
| `mauve` | .xmfa | Yes | No | progressiveMauve output |
| `msf` | .msf | Yes | No | GCG MSF format |

## Reading Alignments

**"Read an alignment file"** → Parse an alignment file into an alignment object with sequences and metadata accessible.

**Goal:** Load alignment data from files in various formats (Clustal, PHYLIP, Stockholm, FASTA).

**Approach:** Use `AlignIO.read()` for single-alignment files or `AlignIO.parse()` for files containing multiple alignments.

### Single Alignment File
```python
from Bio import AlignIO

alignment = AlignIO.read('alignment.aln', 'clustal')
print(f'Alignment length: {alignment.get_alignment_length()}')
print(f'Number of sequences: {len(alignment)}')
```

### Multiple Alignments in One File
```python
for alignment in AlignIO.parse('multi_alignment.sto', 'stockholm'):
    print(f'Alignment with {len(alignment)} sequences, length {alignment.get_alignment_length()}')
```

### Read as List
```python
alignments = list(AlignIO.parse('alignments.phy', 'phylip'))
print(f'Read {len(alignments)} alignments')
```

## Writing Alignments

**Goal:** Save alignment data to files in standard formats for downstream tools or archival.

**Approach:** Use `AlignIO.write()` with the target format specifier, supporting single or multiple alignments and file handles.

### Write Single Alignment
```python
AlignIO.write(alignment, 'output.fasta', 'fasta')
```

### Write Multiple Alignments
```python
alignments = [alignment1, alignment2, alignment3]
count = AlignIO.write(alignments, 'output.sto', 'stockholm')
print(f'Wrote {count} alignments')
```

### Write to Handle
```python
with open('output.aln', 'w') as handle:
    AlignIO.write(alignment, handle, 'clustal')
```

## Format Conversion

**"Convert alignment format"** → Transform an alignment file from one format to another (e.g., Clustal to PHYLIP).

**Goal:** Convert alignment files between formats for compatibility with different analysis tools.

**Approach:** Use `AlignIO.convert()` for direct one-step conversion, or read-modify-write for cases requiring intermediate manipulation.

### Direct Conversion (Most Efficient)
```python
AlignIO.convert('input.aln', 'clustal', 'output.phy', 'phylip')
```

### With Alphabet Specification
```python
AlignIO.convert('input.sto', 'stockholm', 'output.nex', 'nexus', molecule_type='DNA')
```

### Manual Conversion (When Modification Needed)
```python
alignment = AlignIO.read('input.aln', 'clustal')
# ... modify alignment ...
AlignIO.write(alignment, 'output.fasta', 'fasta')
```

## Accessing Alignment Data

**Goal:** Navigate and extract data from alignment objects including sequences, columns, and slices.

**Approach:** Use iteration, indexing, and column slicing on the alignment object.

```python
alignment = AlignIO.read('alignment.aln', 'clustal')

# Iterate over sequences
for record in alignment:
    print(f'{record.id}: {record.seq}')

# Access by index
first_seq = alignment[0]
last_seq = alignment[-1]

# Slice columns
column_slice = alignment[:, 10:20]  # Columns 10-19

# Get specific column
column = alignment[:, 5]  # Column 5 as string
```

## Working with Alignment Objects

### Get Alignment Properties
```python
alignment = AlignIO.read('alignment.aln', 'clustal')

length = alignment.get_alignment_length()
num_seqs = len(alignment)
seq_ids = [record.id for record in alignment]
```

### Slice Alignments
```python
# Get subset of sequences
subset = alignment[0:5]  # First 5 sequences

# Get subset of columns
trimmed = alignment[:, 50:150]  # Columns 50-149

# Combine slicing
region = alignment[0:5, 50:150]  # 5 sequences, columns 50-149
```

## Creating Alignments Programmatically

**Goal:** Build an alignment object from sequences defined in code rather than read from a file.

**Approach:** Construct SeqRecord objects with gap characters and wrap them in a MultipleSeqAlignment.

```python
from Bio.Align import MultipleSeqAlignment
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq

records = [
    SeqRecord(Seq('ACTGACTGACTG'), id='seq1'),
    SeqRecord(Seq('ACTGACT-ACTG'), id='seq2'),
    SeqRecord(Seq('ACTG-CTGACTG'), id='seq3'),
]
alignment = MultipleSeqAlignment(records)
AlignIO.write(alignment, 'new_alignment.fasta', 'fasta')
```

## Format-Specific Notes

### PHYLIP Format
```python
# Standard PHYLIP (10 char names, interleaved)
alignment = AlignIO.read('file.phy', 'phylip')

# Sequential PHYLIP
alignment = AlignIO.read('file.phy', 'phylip-sequential')

# Relaxed PHYLIP (allows longer names)
alignment = AlignIO.read('file.phy', 'phylip-relaxed')
```

### Stockholm Format (with Annotations)
```python
alignment = AlignIO.read('pfam.sto', 'stockholm')

# Access annotations
for record in alignment:
    print(record.id, record.annotations)
```

### Clustal Format
```python
# Clustal preserves conservation symbols in file but not when parsed
alignment = AlignIO.read('clustal.aln', 'clustal')
```

## Batch Processing Multiple Files

**Goal:** Convert a directory of alignment files from one format to another in bulk.

**Approach:** Glob for input files and iterate, reading each alignment and writing to the target format.

```python
from pathlib import Path

input_dir = Path('alignments/')
output_dir = Path('converted/')

for input_file in input_dir.glob('*.aln'):
    alignment = AlignIO.read(input_file, 'clustal')
    output_file = output_dir / f'{input_file.stem}.fasta'
    AlignIO.write(alignment, output_file, 'fasta')
```

## Alternative: Bio.Align Module I/O

**Goal:** Use the modern Bio.Align module for alignment I/O with access to newer features like counts and substitutions.

**Approach:** Use `Align.read()`, `Align.parse()`, and `Align.write()` which return `Alignment` objects instead of `MultipleSeqAlignment`.

The newer `Bio.Align` module provides its own I/O functions that return `Alignment` objects (instead of `MultipleSeqAlignment`). These support additional formats and provide access to modern alignment features.

```python
from Bio import Align

# Read single alignment (returns Alignment object)
alignment = Align.read('alignment.aln', 'clustal')

# Parse multiple alignments
for alignment in Align.parse('multi.sto', 'stockholm'):
    print(f'Alignment with {len(alignment)} sequences')

# Write alignment
Align.write(alignment, 'output.fasta', 'fasta')
```

### When to Use Which

| Use Case | Module |
|----------|--------|
| Legacy code, MultipleSeqAlignment needed | `Bio.AlignIO` |
| Modern features (counts, substitutions) | `Bio.Align` |
| Format conversion | Either works |
| Working with pairwise alignments | `Bio.Align` |

## Quick Reference: Common Operations

| Task | Code |
|------|------|
| Read single alignment | `AlignIO.read(file, format)` |
| Read multiple alignments | `AlignIO.parse(file, format)` |
| Write alignment(s) | `AlignIO.write(align, file, format)` |
| Convert format | `AlignIO.convert(in_file, in_fmt, out_file, out_fmt)` |
| Get length | `alignment.get_alignment_length()` |
| Get sequence count | `len(alignment)` |
| Slice columns | `alignment[:, start:end]` |

## Common Errors

| Error | Cause | Solution |
|-------|-------|----------|
| `ValueError: No records` | Empty file | Check file path and format |
| `ValueError: More than one record` | Multiple alignments with `read()` | Use `parse()` instead |
| `ValueError: Sequences different lengths` | Invalid alignment | Ensure all sequences same length |
| `ValueError: unknown format` | Unsupported format string | Check supported formats list |

## Related Skills

- pairwise-alignment - Create pairwise alignments with PairwiseAligner
- msa-parsing - Analyze alignment content and annotations
- msa-statistics - Calculate conservation and identity
- sequence-io/format-conversion - Convert sequence (non-alignment) formats