scdynomics.utils.ref

Genome reference for scDynOmics

author: jy

Classes

Maker([gff_path, tf_list_path, load_path, ...])

Load in GFF file and parse gene records Annotate TFs based on a given list and mitochrondrial genes based on Chromosome name

class scdynomics.utils.ref.Maker(gff_path: str = None, tf_list_path: str = None, load_path: str = None, gene_types: dict = {'gene': None, 'ncRNA_gene': None, 'pseudogene': None}, trans_structure_types: dict = {'exon': None, 'five_prime_UTR': None, 'three_prime_UTR': None}, cds_types: dict = {'CDS': None}, remove_non_coding: bool = True, remove_weird: bool = True, exempt_chr: dict = {'MT': True, 'X': True, 'Y': True}, promoter_tss_upstream: int = 1500, promoter_tss_downstream: int = 500)

Bases: object

Load in GFF file and parse gene records Annotate TFs based on a given list and mitochrondrial genes based on Chromosome name

Weird genes (not on standard chromosomes or mitochrondria) are removed by default

__init__(gff_path: str = None, tf_list_path: str = None, load_path: str = None, gene_types: dict = {'gene': None, 'ncRNA_gene': None, 'pseudogene': None}, trans_structure_types: dict = {'exon': None, 'five_prime_UTR': None, 'three_prime_UTR': None}, cds_types: dict = {'CDS': None}, remove_non_coding: bool = True, remove_weird: bool = True, exempt_chr: dict = {'MT': True, 'X': True, 'Y': True}, promoter_tss_upstream: int = 1500, promoter_tss_downstream: int = 500)

load_epdnew_tss(path: str)

Load in EPDnew TSS data

WARNING: Due to the inconsistency with ENSEMBL GFF Not using this function for now

output_dict(save_path: str = None) → dict

Output gene dict

output_gex_index(skip_mt: bool = False, save_path: str = None)

Output Index(Gene) for Gene Expression Matrix AnnData