import pandas
from .processor import CTDProcessor, CTDChemicalDiseaseProcessor, \
CTDGeneDiseaseProcessor, CTDChemicalGeneProcessor
base_url = 'http://ctdbase.org/reports/'
urls = {
'chemical_gene': base_url + 'CTD_chem_gene_ixns.tsv.gz',
'chemical_disease': base_url + 'CTD_chemicals_diseases.tsv.gz',
'gene_disease': base_url + 'CTD_genes_diseases.tsv.gz',
}
processors = {
'chemical_gene': CTDChemicalGeneProcessor,
'chemical_disease': CTDChemicalDiseaseProcessor,
'gene_disease': CTDGeneDiseaseProcessor,
}
[docs]def process_from_web(subset, url=None):
"""Process a subset of CTD from the web into INDRA Statements.
Parameters
----------
subset : str
A CTD subset, one of chemical_gene, chemical_disease,
gene_disease.
url : Optional[str]
If not provided, the default CTD URL is used (beware, it usually
gives permission denied). If provided, the given URL is used to
access a tsv or tsv.gz file.
Returns
-------
CTDProcessor
A CTDProcessor which contains INDRA Statements extracted from the
given CTD subset as its statements attribute.
"""
if subset not in urls:
raise ValueError('%s is not a valid CTD subset.' % subset)
url = url if url else urls[subset]
return _process_url_or_file(url, subset)
[docs]def process_tsv(fname, subset):
"""Process a subset of CTD from a tsv or tsv.gz file into INDRA Statements.
Parameters
----------
fname : str
Path to a tsv or tsv.gz file of the given CTD subset.
subset : str
A CTD subset, one of chemical_gene, chemical_disease,
gene_disease.
Returns
-------
CTDProcessor
A CTDProcessor which contains INDRA Statements extracted from the
given CTD subset as its statements attribute.
"""
return _process_url_or_file(fname, subset)
def _process_url_or_file(path, subset):
df = pandas.read_csv(path, sep='\t', comment='#',
header=None, dtype=str, keep_default_na=False)
return process_dataframe(df, subset)
[docs]def process_dataframe(df, subset):
"""Process a subset of CTD from a DataFrame into INDRA Statements.
Parameters
----------
df : pandas.DataFrame
A DataFrame of the given CTD subset.
subset : str
A CTD subset, one of chemical_gene, chemical_disease,
gene_disease.
Returns
-------
CTDProcessor
A CTDProcessor which contains INDRA Statements extracted from the
given CTD subset as its statements attribute.
"""
if subset not in processors:
raise ValueError('%s is not a valid CTD subset.' % subset)
cp = processors[subset](df)
cp.extract_statements()
return cp