src.features.dbsnp

Created on Wed Mar 3 10:54:15 2021

@author: Paolo Cozzi <paolo.cozzi@ibba.cnr.it>

class src.features.dbsnp.DBSNP(path, elem)

Bases: object

__init__(path, elem)

ass_component(elem)

ass_maploc(elem)

ass_snpstat(elem)

classmethod clean_tag(tag: str)

config = {('ExchangeSet', 'Rs', 'Assembly'): 'record_assembly', ('ExchangeSet', 'Rs', 'Assembly', 'Component'): 'ass_component', ('ExchangeSet', 'Rs', 'Assembly', 'Component', 'MapLoc'): 'ass_maploc', ('ExchangeSet', 'Rs', 'Assembly', 'SnpStat'): 'ass_snpstat', ('ExchangeSet', 'Rs', 'Create'): 'record_create', ('ExchangeSet', 'Rs', 'Sequence'): 'record_exemplar', ('ExchangeSet', 'Rs', 'Sequence', 'Observed'): 'record_observed', ('ExchangeSet', 'Rs', 'Ss'): 'record_ss', ('ExchangeSet', 'Rs', 'Ss', 'Sequence', 'Observed'): 'ss_observed', ('ExchangeSet', 'Rs', 'Ss', 'Sequence', 'Seq3'): 'ss_seq3', ('ExchangeSet', 'Rs', 'Ss', 'Sequence', 'Seq5'): 'ss_seq5', ('ExchangeSet', 'Rs', 'Update'): 'record_update'}

process_element(path, elem)

record_assembly(elem)

record_create(elem)

record_exemplar(elem)

record_observed(elem)

record_ss(elem)

record_update(elem)

recurse_children(path: list, elem: Element)

ss_observed(elem)

ss_seq3(elem)

ss_seq5(elem)

to_dict()

src.features.dbsnp.process_rs_elem(elem: Element)

src.features.dbsnp.read_dbSNP(path: str)

src.features.dbsnp.search_chip_snps(snp, handle='AGR_BS')