genomicranges.io package¶

Submodules¶

genomicranges.io.gtf.parse_gtf(path, compressed, skiprows=None, comment='#')[source]¶

Read a GTF file as DataFrame.

Parameters:

path (str) – Path to the GTF file.
compressed (bool) – Whether the file is gzip compressed.
skiprows (Union[int, List[int]]) – Rows to skip if the gtf file has header.
comment (str) – Character indicating that the line should not be parsed. Defaults to “#”.

Returns:

Pandas DataFrame containing annotations from GTF.

genomicranges.io.gtf.read_gtf(file, skiprows=None, comment='#')[source]¶

Read a GTF file as GenomicRanges.

Parameters:

file (str) – Path to GTF file.
skiprows (Union[int, List[int]]) – Rows to skip if the gtf file has header.
comment (str) – Character indicating that the line should not be parsed. Defaults to “#”.

Return type:

GenomicRanges

Returns:

Genomic Ranges with annotations from the GTF file.

genomicranges.io.ucsc.access_gtf_ucsc(genome, type='refGene')[source]¶

Generate a path to a genome gtf file from UCSC, e.g. for hg19 genome.

Parameters:

genome (str) – Genome shortcode; e.g. hg19, hg38, mm10 etc.
type (Literal['refGene', 'ensGene', 'knownGene', 'ncbiRefSeq']) – Defaults to “refGene”.

Raises:

Exception, ValueError – When type does not match with a valid input.

Return type:

str

Returns:

The URI to the file.

genomicranges.io.ucsc.read_ucsc(genome, type='refGene')[source]¶

Load a genome annotation from UCSC as GenomicRanges.

Parameters:

genome (str) – Genome shortcode; e.g. hg19, hg38, mm10 etc.
type (Literal['refGene', 'ensGene', 'knownGene', 'ncbiRefSeq']) – Defaults to “refGene”.

Return type:

GenomicRanges

Returns:

The gene model from UCSC.