bio-write-sequences

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 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

Goal: Construct in-memory sequence records suitable for writing to any format.

Approach: Create SeqRecord with at minimum a Seq and id. Add letter_annotations for FASTQ, annotations['molecule_type'] for GenBank/EMBL.

"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 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