alignment-io

Name: alignment-io
Author: GPTomics

1.1kstars185forks

How to install alignment-io?

gptomics/bioskills/alignment-io

$npx -y skills add GPTomics/bioSkills --skill alignment-io

Installs into the current project.

Summary

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.

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SKILL.md

1	## Version Compatibility
2
3	Reference examples tested with: BioPython 1.83+
4
5	Before using code patterns, verify installed versions match. If versions differ:
6	- Python: `pip show <package>` then `help(module.function)` to check signatures
7
8	If code throws ImportError, AttributeError, or TypeError, introspect the installed
9	package and adapt the example to match the actual API rather than retrying.
10
11	# Alignment File I/O
12
13	Read, write, and convert multiple sequence alignment files in various formats.
14
15	## Required Import
16
17	Goal: Load modules for reading, writing, and manipulating multiple sequence alignments.
18
19	Approach: Import AlignIO for file I/O and supporting classes for programmatic alignment construction.
20
21	```python
22	from Bio import AlignIO
23	from Bio.Align import MultipleSeqAlignment
24	from Bio.SeqRecord import SeqRecord
25	from Bio.Seq import Seq
26	```
27
28	## Format Coverage Map
29
30	Three Python libraries cover the alignment-format space, with overlapping but non-identical support. Pick by what is actually required.
31
32	\| Format \| `Bio.AlignIO` \| `Bio.Align` (modern) \| `pyhmmer.easel` \| Notes \|
33	\|--------\|---------------\|----------------------\|-----------------\|-------\|
34	\| Aligned FASTA \| R/W \| R/W \| R/W \| Most portable; loses annotations \|
35	\| Clustal \| R/W \| R/W \| R \| Clustal conservation marks NOT round-tripped \|
36	\| PHYLIP (interleaved/sequential/relaxed) \| R/W \| R/W \| R \| Strict 10-char names is silent footgun \|
37	\| Stockholm \| R/W \| R/W \| R/W \| Only format preserving GS/GR/GC/GF annotations \|
38	\| NEXUS \| R/W \| R/W \| -- \| MrBayes / PAUP* input \|
39	\| MAF (Multiple Alignment Format) \| R/W \| R/W \| -- \| UCSC whole-genome alignments \|
40	\| A2M / A3M \| -- (use `'fasta'` parser then post-process) \| -- \| R/W \| HMMER (a2m), HHsuite/ColabFold (a3m) \|
41	\| MSF (GCG) \| R \| -- \| -- \| GCG legacy \|
42	\| EMBOSS / Mauve XMFA / FASTA-m10 \| R \| partial \| -- \| One-way: read-only \|
43
44	Formats NOT in BioPython (use dedicated tools):
45
46	\| Format \| Tool \| Why \|
47	\|--------\|------\|-----\|
48	\| HAL \| progressiveCactus, halTools \| HDF5-backed multi-genome alignments at TB scale \|
49	\| chain / net \| UCSC Kent tools (`liftOver`, `chainNet`) \| Pairwise genome alignment \|
50	\| AXT \| BLASTZ / lastz native \| Pairwise alignment blocks \|
51	\| PSL \| UCSC Kent tools (`pslPretty`, `blat`) \| BLAT alignment summary \|
52	\| GFA / rGFA \| `vg`, `odgi`, `pggb`, gfatools \| Pangenome graph \|
53	\| GAF \| `vg surject`, `vg call` \| Graph alignment format (read-to-graph) \|
54
55	Recommend `Bio.Align` (modern API) over `Bio.AlignIO` (legacy) for new code; it returns `Alignment` objects with built-in `.counts()` and `.substitutions` properties. For multi-gigabyte Stockholm databases such as Pfam-A.full, `pyhmmer.easel.MSAFile` streams record-by-record where `Bio.AlignIO.parse` works but at higher per-record cost.
56
57	## Reading Alignments
58
59	"Read an alignment file" -> Parse an alignment file into an alignment object with sequences and metadata accessible.
60
61	Goal: Load alignment data from files in various formats (Clustal, PHYLIP, Stockholm, FASTA).
62
63	Approach: Use `AlignIO.read()` for single-alignment files or `AlignIO.parse()` for files containing multiple alignments.
64
65	### Single Alignment File
66	```python
67	from Bio import AlignIO
68
69	alignment = AlignIO.read('alignment.aln', 'clustal')
70	print(f'Alignment length: {alignment.get_alignment_length()}')
71	print(f'Number of sequences: {len(alignment)}')
72	```
73
74	### Multiple Alignments in One File
75	```python
76	for alignment in AlignIO.parse('multi_alignment.sto', 'stockholm'):
77	print(f'Alignment with {len(alignment)} sequences, length {alignment.get_alignment_length()}')
78	```
79
80	### Read as List
81	```python
82	alignments = list(AlignIO.parse('alignments.phy', 'phylip'))
83	print(f'Read {len(alignments)} alignments')
84	```
85
86	## Writing Alignments
87
88	Goal: Save alignment data to files in standard formats for downstream tools or archival.
89
90	Approach: Use `AlignIO.write()` with the target format specifier, supporting single or multiple alignments and file handles.
91
92	### Write Single Alignment
93	```python
94	AlignIO.write(alignment, 'output.fasta', 'fasta')
95	```
96
97	### Write Multiple Alignments
98	```python
99	alignments = [alignment1, alignment2, alignment3]
100	count = AlignIO.write(alignments, 'output.sto', 'stockholm')
101	print(f'Wrote {count} alignments')
102	```
103
104	### Write to Handle
105	```python
106	with open('output.aln', 'w') as handle:
107	AlignIO.write(alignment, handle, 'clustal')
108	```
109
110	## Format Conversion
111
112	"Convert alignment format" -> Transform an alignment file from one format to another (e.g., Clustal to PHYLIP).
113
114	Goal: Convert alignment files between formats for compatibility with different analysis tools.
115
116	Approach: Use `AlignIO.conve

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alignment-io

1.1kstars185forks

View on GitHub

How to install alignment-io?

gptomics/bioskills/alignment-io

$npx -y skills add GPTomics/bioSkills --skill alignment-io

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	## Version Compatibility
2
3	Reference examples tested with: BioPython 1.83+
4
5	Before using code patterns, verify installed versions match. If versions differ:
6	- Python: `pip show <package>` then `help(module.function)` to check signatures
7
8	If code throws ImportError, AttributeError, or TypeError, introspect the installed
9	package and adapt the example to match the actual API rather than retrying.
10
11	# Alignment File I/O
12
13	Read, write, and convert multiple sequence alignment files in various formats.
14
15	## Required Import
16
17	Goal: Load modules for reading, writing, and manipulating multiple sequence alignments.
18
19	Approach: Import AlignIO for file I/O and supporting classes for programmatic alignment construction.
20
21	```python
22	from Bio import AlignIO
23	from Bio.Align import MultipleSeqAlignment
24	from Bio.SeqRecord import SeqRecord
25	from Bio.Seq import Seq
26	```
27
28	## Format Coverage Map
29
30	Three Python libraries cover the alignment-format space, with overlapping but non-identical support. Pick by what is actually required.
31
32	\| Format \| `Bio.AlignIO` \| `Bio.Align` (modern) \| `pyhmmer.easel` \| Notes \|
33	\|--------\|---------------\|----------------------\|-----------------\|-------\|
34	\| Aligned FASTA \| R/W \| R/W \| R/W \| Most portable; loses annotations \|
35	\| Clustal \| R/W \| R/W \| R \| Clustal conservation marks NOT round-tripped \|
36	\| PHYLIP (interleaved/sequential/relaxed) \| R/W \| R/W \| R \| Strict 10-char names is silent footgun \|
37	\| Stockholm \| R/W \| R/W \| R/W \| Only format preserving GS/GR/GC/GF annotations \|
38	\| NEXUS \| R/W \| R/W \| -- \| MrBayes / PAUP* input \|
39	\| MAF (Multiple Alignment Format) \| R/W \| R/W \| -- \| UCSC whole-genome alignments \|
40	\| A2M / A3M \| -- (use `'fasta'` parser then post-process) \| -- \| R/W \| HMMER (a2m), HHsuite/ColabFold (a3m) \|
41	\| MSF (GCG) \| R \| -- \| -- \| GCG legacy \|
42	\| EMBOSS / Mauve XMFA / FASTA-m10 \| R \| partial \| -- \| One-way: read-only \|
43
44	Formats NOT in BioPython (use dedicated tools):
45
46	\| Format \| Tool \| Why \|
47	\|--------\|------\|-----\|
48	\| HAL \| progressiveCactus, halTools \| HDF5-backed multi-genome alignments at TB scale \|
49	\| chain / net \| UCSC Kent tools (`liftOver`, `chainNet`) \| Pairwise genome alignment \|
50	\| AXT \| BLASTZ / lastz native \| Pairwise alignment blocks \|
51	\| PSL \| UCSC Kent tools (`pslPretty`, `blat`) \| BLAT alignment summary \|
52	\| GFA / rGFA \| `vg`, `odgi`, `pggb`, gfatools \| Pangenome graph \|
53	\| GAF \| `vg surject`, `vg call` \| Graph alignment format (read-to-graph) \|
54
55	Recommend `Bio.Align` (modern API) over `Bio.AlignIO` (legacy) for new code; it returns `Alignment` objects with built-in `.counts()` and `.substitutions` properties. For multi-gigabyte Stockholm databases such as Pfam-A.full, `pyhmmer.easel.MSAFile` streams record-by-record where `Bio.AlignIO.parse` works but at higher per-record cost.
56
57	## Reading Alignments
58
59	"Read an alignment file" -> Parse an alignment file into an alignment object with sequences and metadata accessible.
60
61	Goal: Load alignment data from files in various formats (Clustal, PHYLIP, Stockholm, FASTA).
62
63	Approach: Use `AlignIO.read()` for single-alignment files or `AlignIO.parse()` for files containing multiple alignments.
64
65	### Single Alignment File
66	```python
67	from Bio import AlignIO
68
69	alignment = AlignIO.read('alignment.aln', 'clustal')
70	print(f'Alignment length: {alignment.get_alignment_length()}')
71	print(f'Number of sequences: {len(alignment)}')
72	```
73
74	### Multiple Alignments in One File
75	```python
76	for alignment in AlignIO.parse('multi_alignment.sto', 'stockholm'):
77	print(f'Alignment with {len(alignment)} sequences, length {alignment.get_alignment_length()}')
78	```
79
80	### Read as List
81	```python
82	alignments = list(AlignIO.parse('alignments.phy', 'phylip'))
83	print(f'Read {len(alignments)} alignments')
84	```
85
86	## Writing Alignments
87
88	Goal: Save alignment data to files in standard formats for downstream tools or archival.
89
90	Approach: Use `AlignIO.write()` with the target format specifier, supporting single or multiple alignments and file handles.
91
92	### Write Single Alignment
93	```python
94	AlignIO.write(alignment, 'output.fasta', 'fasta')
95	```
96
97	### Write Multiple Alignments
98	```python
99	alignments = [alignment1, alignment2, alignment3]
100	count = AlignIO.write(alignments, 'output.sto', 'stockholm')
101	print(f'Wrote {count} alignments')
102	```
103
104	### Write to Handle
105	```python
106	with open('output.aln', 'w') as handle:
107	AlignIO.write(alignment, handle, 'clustal')
108	```
109
110	## Format Conversion
111
112	"Convert alignment format" -> Transform an alignment file from one format to another (e.g., Clustal to PHYLIP).
113
114	Goal: Convert alignment files between formats for compatibility with different analysis tools.
115
116	Approach: Use `AlignIO.conve

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