Bio Write Sequences

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 SeqRecords
• handle - Filename (string) or file handle
• format - 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

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

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