fastseqio 0.2.3

A package for reading and writing fasta/fastq files

Documentation: https://openbioseq.github.io/fastseqio/

fastseqio

fastseqio is a Python library for fast reading and writing of FASTA/FASTQ files. It supports plain text and gzip-compressed files (.gz) and provides a small, practical API centered on:

• seqioFile: file reader/writer
• Record: sequence record object

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Installation

pip install fastseqio

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Quick Start

Read records (FASTA/FASTQ auto-detection)

from fastseqio import seqioFile

with seqioFile("test-data/test2.fa", "r") as f:
    for record in f:
        print(record.name, record.sequence)

Write FASTA

from fastseqio import seqioFile

with seqioFile("out.fa", "w") as f:
    f.writeFasta("seq1", "ACGGGGGGGTTTT")
    f.writeFasta("seq2", "TTTTCCCCAAAAG")

Write FASTQ

from fastseqio import seqioFile

with seqioFile("out.fq", "w") as f:
    f.writeFastq("read1", "ACGT", "IIII")

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File API (seqioFile)

Create a file handle

seqioFile(path: str, mode: 'r' | 'w' = 'r', compressed: bool = False)

• path: input/output file path. Use "-" for stdin/stdout.
• mode:
  • "r": read mode
  • "w": write mode
• compressed: force gzip mode when needed (for example when path="-").

Notes:

• If path ends with .gz, compression is enabled automatically.
• Iteration consumes the file sequentially. To re-read from the beginning, call reset().

Read methods

• readOne() → read next record (auto format)
• readFasta() → read next FASTA record
• readFastq() → read next FASTQ record
• for record in file: → iterate with readOne() internally

All read methods return Record or None at end-of-file.

Write methods

• writeFasta(name, sequence, comment=None)
• writeFastq(name, sequence, quality, comment=None)
• writeOne(name, sequence, quality=None, comment=None)
  • writes FASTA when quality is not provided
  • writes FASTQ when quality is provided
• writeRecord(record, fastq=False)

Validation:

• For FASTQ, sequence length must equal quality length.

Writer options

file.set_write_options(
    lineWidth=80,  # optional; when provided it must be > 0
    includeComments=True,  # optional
    baseCase="upper",  # optional: "upper" or "lower"
)

Utilities and properties

• reset() → rewind file to beginning
• fflush() → flush write buffer
• close() → close file
• readable / writable
• size → file size in bytes
• offset → current byte offset

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Record API (Record)

Create a record

from fastseqio import Record

record = Record("seq1", "ACGGGG", quality=None, comment="example")

Fields

• record.name
• record.sequence
• record.quality
• record.comment
• record.length (same as len(record))

Sequence helpers

• record.upper(inplace=False)
• record.lower(inplace=False)
• record.reverse(inplace=False)
• record.subseq(start, length)
• record.hpc() (homopolymer compression)
• record.kmers(k) (iterator of k-mers)

Example:

from fastseqio import Record

r = Record("id", "AAACCCGGGTTT")
print(r.hpc())  # ACGT
print(list(r.kmers(4)))  # ['AAAC', 'AACC', ...]

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Gzip Example

from fastseqio import seqioFile

# Compression auto-detected by .gz suffix
with seqioFile("reads.fa.gz", "w") as w:
    w.writeFasta("seq1", "ACGTACGT")

with seqioFile("reads.fa.gz", "r") as r:
    for rec in r:
        print(rec.name)

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Recommended Usage Pattern

Use context managers (with seqioFile(...) as f) so files are always closed correctly.