io

Quality IO

FASTQ file reading and per-read quality analysis including base quality, GC content, adapter detection, and length distributions.

Contents

File	Purpose
fastq.py	FASTQ record parsing, per-base quality, GC content, adapter screening

Key Classes and Functions

Symbol	Description
FastqRecord	Dataclass for a single FASTQ read (header, sequence, quality)
read_fastq_records()	Iterator over FASTQ records from file path
analyze_fastq_quality()	Complete quality analysis of a FASTQ file
basic_statistics()	Read count, total bases, mean quality, mean length
per_base_quality()	Quality score distribution at each read position
per_sequence_quality()	Distribution of mean quality scores across reads
sequence_length_distribution()	Histogram of read lengths
gc_content_distribution()	Per-read GC content distribution
adapter_content()	Adapter sequence detection rates by position
overrepresented_sequences()	Identify frequently occurring subsequences

Usage

from metainformant.quality.io.fastq import read_fastq_records, analyze_fastq_quality

quality = analyze_fastq_quality("data/sample.fastq.gz", n_reads=10000)
for record in read_fastq_records("data/sample.fastq.gz", max_records=100):
    print(record.header, len(record.sequence))