ngs_tools.fastq.Fastq

Module Contents

Classes

Fastq

Class that represents a FASTQ file.

exception ngs_tools.fastq.Fastq.FastqError

Bases: Exception

Common base class for all non-exit exceptions.

class ngs_tools.fastq.Fastq.Fastq(path: str, mode: typing_extensions.Literal[r, w] = 'r')

Bases: ngs_tools.utils.FileWrapper

Class that represents a FASTQ file.

read() → ngs_tools.fastq.Read.Read

Read a single FASTQ entry.

Returns:

The next read as a Read instance

Raises:

• FastqError – If the file was not opened for reading, or the file was closed.

• StopIteration – When there are no more entries to read.

write(entry: ngs_tools.fastq.Read.Read)

Write a single FASTQ entry.

Parameters:

entry – Read instance to write to the FASTQ

Raises:

FastaError – If the file was not opened for writing, or the file was closed.