ReddRadar
Agent skill
bio-write-sequences
Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when saving sequences, creating new sequence files, or outputting modified records.
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npx add-skill https://github.com/majiayu000/claude-skill-registry/tree/main/skills/data/write-sequences
SKILL.md
Write Sequences
Write SeqRecord objects to sequence files using Biopython's Bio.SeqIO module.
Required Import
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
Core Functions
SeqIO.write() - Write Records to File
Write one or more SeqRecord objects to a file.
SeqIO.write(records, 'output.fasta', 'fasta')
Parameters:
records- Single SeqRecord, list, or iterator of SeqRecordshandle- Filename (string) or file handleformat- Output format string
Returns: Number of records written (integer)
record.format() - Get Formatted String
Get a string representation without writing to file.
formatted = record.format('fasta')
print(formatted)
Creating SeqRecord Objects
Minimal SeqRecord
record = SeqRecord(Seq('ATGCGATCGATCG'), id='seq1')
Full SeqRecord
record = SeqRecord(
Seq('ATGCGATCGATCG'),
id='seq1',
name='sequence_one',
description='Example sequence for demonstration'
)
With Annotations (for GenBank output)
from Bio.SeqFeature import SeqFeature, FeatureLocation
record = SeqRecord(
Seq('ATGCGATCGATCG'),
id='seq1',
annotations={'molecule_type': 'DNA'}
)
record.features.append(
SeqFeature(FeatureLocation(0, 9), type='gene', qualifiers={'gene': ['exampleGene']})
)
Common Formats
| Format | String | Notes |
|---|---|---|
| FASTA | 'fasta' |
Most universal, sequence + header only |
| FASTQ | 'fastq' |
Requires quality scores in letter_annotations |
| GenBank | 'genbank' |
Requires annotations and molecule_type |
| EMBL | 'embl' |
Similar requirements to GenBank |
| Tab | 'tab' |
Simple ID + sequence tabular format |
Code Patterns
Write Single Record
record = SeqRecord(Seq('ATGC'), id='my_seq', description='test sequence')
SeqIO.write(record, 'output.fasta', 'fasta')
Write Multiple Records
records = [
SeqRecord(Seq('ATGC'), id='seq1'),
SeqRecord(Seq('GCTA'), id='seq2'),
SeqRecord(Seq('TTAA'), id='seq3')
]
count = SeqIO.write(records, 'output.fasta', 'fasta')
print(f'Wrote {count} records')
Write to File Handle
with open('output.fasta', 'w') as handle:
SeqIO.write(records, handle, 'fasta')
Write Modified Records
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
def uppercase_record(rec):
return SeqRecord(rec.seq.upper(), id=rec.id, description=rec.description)
records = SeqIO.parse('input.fasta', 'fasta')
modified = (uppercase_record(rec) for rec in records)
SeqIO.write(modified, 'output.fasta', 'fasta')
Append to Existing File
with open('output.fasta', 'a') as handle:
SeqIO.write(new_records, handle, 'fasta')
Write FASTQ with Quality Scores
record = SeqRecord(Seq('ATGCGATCG'), id='read1')
record.letter_annotations['phred_quality'] = [30, 30, 28, 25, 30, 30, 28, 25, 30]
SeqIO.write(record, 'output.fastq', 'fastq')
Write GenBank Format
record = SeqRecord(Seq('ATGCGATCGATCG'), id='SEQ001', name='example')
record.annotations['molecule_type'] = 'DNA'
record.annotations['topology'] = 'linear'
record.annotations['organism'] = 'Example organism'
SeqIO.write(record, 'output.gb', 'genbank')
Common Errors
| Error | Cause | Solution |
|---|---|---|
TypeError: SeqRecord expected |
Passed raw string/Seq | Wrap in SeqRecord object |
ValueError: missing molecule_type |
GenBank without annotations | Add record.annotations['molecule_type'] = 'DNA' |
ValueError: missing quality scores |
FASTQ without phred_quality | Add quality scores to letter_annotations |
ValueError: Sequences must all be the same length |
PHYLIP with unequal lengths | Pad or trim sequences first |
Format-Specific Requirements
FASTQ
Must have quality scores:
record.letter_annotations['phred_quality'] = [30] * len(record.seq)
GenBank/EMBL
Must have molecule_type:
record.annotations['molecule_type'] = 'DNA' # or 'RNA', 'protein'
PHYLIP
All sequences must be same length. IDs truncated to 10 characters.
Related Skills
- read-sequences - Read sequences before modifying and writing
- format-conversion - Direct format conversion without intermediate processing
- filter-sequences - Filter sequences before writing subset
- sequence-manipulation/seq-objects - Create SeqRecord objects to write
- alignment-files - For SAM/BAM output, use samtools/pysam
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