File formats

Lightweight readers for FASTA and FASTQ, and a couple of format-validation helpers. These are plain, dependency-free classes — useful when you want to stream a file record-by-record without pulling in a heavier library.

FASTA

import pybio.data
f = pybio.data.Fasta("sequences.fasta")  # also accepts .gz and .bz2
while f.read():
    print(f.id, len(f.sequence))

read() returns False at end of file. f.id is the header line (everything after >, untouched — split on whitespace yourself if you only want the accession), f.sequence is the concatenated sequence with newlines stripped.

FASTQ

f = pybio.data.Fastq("reads.fastq.gz")
while f.read():
    print(f.id, f.sequence, f.quality)

Same read-loop pattern as Fasta. f.quality is the raw quality string, unconverted — use ord(c) yourself to get Phred scores, or see fastq_qminmax() below for a ready-made min/max helper.

Format checks

Two small helpers for validating files before you commit to processing them:

pybio.data.fasta_check("sequences.fasta")
# (True, "File in FASTA format")

pybio.data.fastq_qminmax("reads.fastq.gz")
# (qmin, qmax) — the min and max Phred quality ord() values found in the file

fasta_check(filename, allowed_chars=["A","C","T","G","N"]) reads the whole file and confirms every sequence uses only the allowed characters (and isn't empty), returning (False, reason) on the first violation. fastq_qminmax() scans a FASTQ file and returns the observed (qmin, qmax) quality ordinal range — useful for guessing a FASTQ's quality encoding (Phred+33 vs. Phred+64) before aligning.