Version Compatibility

Reference examples tested with: BioPython 1.83+

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.

Paired-End FASTQ

"Work with my paired-end FASTQ files" → Iterate R1/R2 pairs in sync, filter both mates together, interleave/deinterleave files, and auto-detect paired file naming.

• Python: SeqIO.parse() with zip() iteration (BioPython)

Handle paired-end sequencing data (R1/R2 files) using Biopython.

Required Import

from Bio import SeqIO

Paired File Naming Conventions

Common patterns for paired files:

• sample_R1.fastq / sample_R2.fastq
• sample_1.fastq / sample_2.fastq
• sample_R1_001.fastq / sample_R2_001.fastq

Iterate Pairs Together

Basic Paired Iteration

r1_records = SeqIO.parse('reads_R1.fastq', 'fastq')
r2_records = SeqIO.parse('reads_R2.fastq', 'fastq')

for r1, r2 in zip(r1_records, r2_records):
    print(f'R1: {r1.id}, R2: {r2.id}')
    print(f'Lengths: {len(r1.seq)}, {len(r2.seq)}')

Verify Pair Matching

def iterate_pairs(r1_file, r2_file, format='fastq'):
    r1_records = SeqIO.parse(r1_file, format)
    r2_records = SeqIO.parse(r2_file, format)

    for r1, r2 in zip(r1_records, r2_records):
        # Strip /1, /2 or .1, .2 suffixes for comparison
        r1_base = r1.id.rsplit('/', 1)[0].rsplit('.', 1)[0]
        r2_base = r2.id.rsplit('/', 1)[0].rsplit('.', 1)[0]
        if r1_base != r2_base:
            raise ValueError(f'Pair mismatch: {r1.id} vs {r2.id}')
        yield r1, r2

for r1, r2 in iterate_pairs('reads_R1.fastq', 'reads_R2.fastq'):
    process_pair(r1, r2)