Summary This source did not publish a separate summary. Review SKILL.md before using the skill.
Version Compatibility
Reference examples tested with: BioPython 1.83+, pysam 0.22+, samtools 1.19+
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.
Write Sequences
"Write sequences to a file" → Serialize SeqRecord objects into a formatted sequence file.
Python: SeqIO.write() (BioPython)
R: writeXStringSet() (Biostrings)
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
Goal: Construct in-memory sequence records suitable for writing to any format.
Approach: Create
SeqRecord
Seq
id
letter_annotations
annotations['molecule_type']
"Create a sequence record from scratch" → Wrap a Seq string in a SeqRecord with metadata fields.
Python: SeqRecord(Seq(...), id=...) (BioPython)
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 Goal: Transform sequences in-memory and write the modified versions to a new file.
Approach: Parse input, apply transformation via generator, write output. Using a generator avoids loading all records into memory.
"Modify sequences and save" → Parse records, transform each, write to new file with SeqIO.write().
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 expectedPassed raw string/Seq Wrap in SeqRecord object ValueError: missing molecule_typeGenBank without annotations Add record.annotations['molecule_type'] = 'DNA' ValueError: missing quality scoresFASTQ without phred_quality Add quality scores to letter_annotations ValueError: Sequences must all be the same lengthPHYLIP 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 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
