File I/O (pmaf.internal.io) - File I/O

This class is responsible for providing I/O functionality.

I/O Types (Classes)

class SequenceIO(seqsrc, ftype='auto', upper=False, **kwargs)[source]

Primary sequence data parser.

Constructor for SequenceIO.

Parameters

  • seqsrc (Union[Sequence[str], str, io.IOBase]) – Can be one of following: - Path to sequence FASTA file with defined format(ftype). - List of paths to sequence files with defined format(ftype). - String with sequence data in defined format(ftype). - Opened IO instance(must inherit IOBase

  • ftype (str) – Format of the sequence data like FASTA, FASTQ, etc. Default is “auto” - constructor will attempt to guess the type.

  • upper (bool) – Convert IUPAC bases to uppercase.

  • kwargs (Any) – Compatibility.