deepbiop.utils¶

Classes¶

`GenomicInterval`	A segment is a genomic interval defined by a chromosome, a start position and an end position.
`PslAlignment`
`CompressedType`	Represents different types of file compression formats.
`SequenceFileType`	Represents different types of sequence file formats.

Functions¶

`check_compressed_type`(path)	Check the compression type of a file.
`generate_unmaped_intervals`(input, total_length)
`highlight_targets`(sequence, targets[, text_width])
`majority_voting`(labels, window_size)
`parse_psl_by_qname`(file_path)	Parse PSL file by query name.
`remove_intervals_and_keep_left`(seq, intervals)

Module Contents¶

class deepbiop.utils.GenomicInterval¶

A segment is a genomic interval defined by a chromosome, a start position and an end position. The start position is inclusive and the end position is exclusive.

property start: int¶

Return type:: int

property end: int¶

Return type:: int

property chr: str¶

Return type:: str

overlap(other)¶

Parameters:: other (GenomicInterval)
Return type:: bool

__repr__()¶

Return type:: str

class deepbiop.utils.PslAlignment¶

property qname: str¶

Return type:: str

property qsize: int¶

Return type:: int

property qstart: int¶

Return type:: int

property qend: int¶

Return type:: int

property qmatch: int¶

Return type:: int

property tname: str¶

Return type:: str

property tsize: int¶

Return type:: int

property tstart: int¶

Return type:: int

property tend: int¶

Return type:: int

property identity: float¶

Return type:: float

__repr__()¶

Return type:: str

class deepbiop.utils.CompressedType¶

Bases: enum.Enum

Represents different types of file compression formats.

This enum is used to identify and handle various compression formats commonly used for files. It can be used in Python through the deepbiop.utils module.

# Variants

Uncompress - Uncompressed/raw file format
Gzip - Standard gzip compression (.gz files)
Bgzip - Blocked gzip format, commonly used in bioinformatics
Zip - ZIP archive format
Bzip2 - bzip2 compression format
Xz - XZ compression format (LZMA2)
Zstd - Zstandard compression format
Unknown - Unknown or unrecognized compression format

Uncompress = Ellipsis¶

Gzip = Ellipsis¶

Bgzip = Ellipsis¶

Zip = Ellipsis¶

Bzip2 = Ellipsis¶

Xz = Ellipsis¶

Zstd = Ellipsis¶

Unknown = Ellipsis¶

class deepbiop.utils.SequenceFileType¶

Bases: enum.Enum

Represents different types of sequence file formats.

Fasta = Ellipsis¶

Fastq = Ellipsis¶

Unknown = Ellipsis¶

deepbiop.utils.check_compressed_type(path)¶

Check the compression type of a file.

Parameters:: path (str | os.PathLike | pathlib.Path) – Path to the file to check
Return type:: The compression type of the file (None, Gzip, Bzip2, Xz)
Raises:: IOError – If the file cannot be opened or read: