modos.genomics.formats

Classes

GenomicFileSuffix

Enumeration of all supported genomic file suffixes.

Functions

read_pysam(path[, region])

Automatically instantiate a pysam file object from input path and passes any additional kwarg to it.

Module Contents

class modos.genomics.formats.GenomicFileSuffix

Bases: tuple, enum.Enum

Enumeration of all supported genomic file suffixes.

CRAM = ('.cram',)

BAM = ('.bam',)

SAM = ('.sam',)

VCF = ('.vcf', '.vcf.gz')

BCF = ('.bcf',)

FASTA = ('.fasta', '.fa')

FASTQ = ('.fastq', '.fq')

classmethod from_path(path)

Parameters:

path (pathlib.Path)

Return type:

GenomicFileSuffix

get_index_suffix()

Return the supported index suffix related to a genomic filetype

Return type:

str

to_htsget_endpoint()

Return the htsget endpoint for a genomic file type

Return type:

str

modos.genomics.formats.read_pysam(path, region=None, **kwargs)

Automatically instantiate a pysam file object from input path and passes any additional kwarg to it.

Parameters:

• path (pathlib.Path)

• region (Optional[modos.genomics.region.Region])

Return type:

Iterator[pysam.AlignedSegment | pysam.VariantRecord]