LLMs-Universal-Life-Science-and-Clinical-Skills- alignment-io

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T=$(mktemp -d) && git clone --depth=1 https://github.com/mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- "$T" && mkdir -p ~/.claude/skills && cp -r "$T/Skills/Sequence_Analysis/alignment/alignment-io" ~/.claude/skills/mdbabumiamssm-llms-universal-life-science-and-clinical-skills-alignment-io && rm -rf "$T"

manifest: Skills/Sequence_Analysis/alignment/alignment-io/SKILL.md

source content

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 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:

read_file
run_shell_command

Alignment File I/O

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

Required Import

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

Single Alignment File

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

for alignment in AlignIO.parse('multi_alignment.sto', 'stockholm'):
    print(f'Alignment with {len(alignment)} sequences, length {alignment.get_alignment_length()}')

Read as List

alignments = list(AlignIO.parse('alignments.phy', 'phylip'))
print(f'Read {len(alignments)} alignments')

Writing Alignments

Write Single Alignment

AlignIO.write(alignment, 'output.fasta', 'fasta')

Write Multiple Alignments

alignments = [alignment1, alignment2, alignment3]
count = AlignIO.write(alignments, 'output.sto', 'stockholm')
print(f'Wrote {count} alignments')

Write to Handle

with open('output.aln', 'w') as handle:
    AlignIO.write(alignment, handle, 'clustal')

Format Conversion

Direct Conversion (Most Efficient)

AlignIO.convert('input.aln', 'clustal', 'output.phy', 'phylip')

With Alphabet Specification

AlignIO.convert('input.sto', 'stockholm', 'output.nex', 'nexus', molecule_type='DNA')

Manual Conversion (When Modification Needed)

alignment = AlignIO.read('input.aln', 'clustal')
# ... modify alignment ...
AlignIO.write(alignment, 'output.fasta', 'fasta')

Accessing Alignment Data

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

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

# 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

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

# 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)

alignment = AlignIO.read('pfam.sto', 'stockholm')

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

Clustal Format

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

Batch Processing Multiple Files

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

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.

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