def main():
"""Print Reactome version in downloaded DAG."""
fout_py = 'src/reactomepy/data/reactome_version.py'
with open(fout_py, 'w') as prt:
prt_docstr_module('Reactome version in DAG', prt)
# CYPHER: MATCH (v:DBInfo) RETURN v
version = get_version(get_gdbdr())
prt.write('VERSION = {V}\n'.format(V=version))
prt_copyright_comment(prt)
print(' Version {V} WROTE: {PY}\n'.format(PY=fout_py, V=version))
def main():
"""Does this repo have the current version of the Reactome Knowledgebase?"""
# Reactome version from Content Service
obj = ContentService()
ver_curr = obj.get_version()
print('\n Current Reactome Knowledgebase Version:')
print(' {VER:3} <- Latest version from Content Service'.format(
VER=ver_curr))
# Reactome version from locally loaded Reactome DAG
ver_local = get_version(get_gdbdr())
print(
' {VER:3} <- version from locally loaded DAG'.format(VER=ver_local))
print(
' {VER:3} <- Version in this repo: src/reactomepy/data/reactome_version.py\n\n'
.format(VER=VERSION))
assert ver_local == ver_curr, 'VERSION: LOCAL DAG({A}) != CONTENT SERVICE({E})'.format(
E=ver_curr, A=ver_local)
assert VERSION == ver_curr, 'PLEASE DOWNLOAD THE MOST RECENT REACTOME KNOWLEDGEBASE'
assert obj.get_databasename() == 'reactome', 'UNEXPECTED DATABASE NAME'
assert isinstance(ver_curr, int), 'BAD VERSION VALUE'
def prt_referencedatabase():
"""Print all ReferenceDatabase in Reactome."""
fout_referencedatabase_py = 'src/reactomepy/data/referencedatabase2nt.py'
obj = ReferenceDatabases(get_gdbdr())
obj.wrpy_referencedatabase_nts(fout_referencedatabase_py)
def prt_disease():
"""Print all disease in Reactome."""
obj = Diseases(get_gdbdr())
fout_disease_py = 'src/reactomepy/data/disease_definitions.py'
obj.wrpy_disease2fld(fout_disease_py, 'definition', 'DISEASE2DEFN')
def main():
"""Save the participating molecules for each pathway into a Python module."""
fout_py = 'src/reactomepy/data/pwy/pwy2uniprot.py'
obj = PathwayMolecules(get_gdbdr())
obj.wrpy_pw2molecules(fout_py, 'UniProt')