def search(self):
if self.app.pargs.product is None:
print("Argument --product must be provided")
exit(1)
result = products.search(self.app.pargs.product)
if len(result) > 0:
print(result[['name', 'formula', 'mass', 'search_rank']])
else:
print("No results found")
def __translate_product_to_universal_reactions_model_metabolite(self, product, database):
if isinstance(product, Metabolite):
return product
elif isinstance(product, str):
search_result = products.search(product)
notice("Found %d compounds that match query '%s'" % (len(search_result), product))
self.__display_product_search_result(search_result)
notice("Choosing best match (%s) ... please interrupt if this is not the desired compound."
% search_result.name[0])
self.__display_compound(search_result.InChI[0])
return database.metabolites.get_by_id(search_result.index[0])
def translate_product_to_universal_reactions_model_metabolite(self, product, database):
if isinstance(product, Metabolite):
return product
elif isinstance(product, six.text_type) or isinstance(product, six.string_types):
search_result = products.search(product)
search_result = search_result.loc[[i for i in search_result.index if i in database.metabolites]]
if len(search_result) == 0:
raise KeyError("No compound matches found for query %s" % product)
notice("Found %d compounds that match query '%s'" % (len(search_result), product))
self.__display_product_search_result(search_result)
notice("Choosing best match (%s) ... please interrupt if this is not the desired compound."
% search_result.name.values[0])
self.__display_compound(search_result.InChI.values[0])
return database.metabolites.get_by_id(search_result.index[0])
def __translate_product_to_universal_reactions_model_metabolite(
self, product, database):
if isinstance(product, Metabolite):
return product
elif isinstance(product, str):
search_result = products.search(product)
notice("Found %d compounds that match query '%s'" %
(len(search_result), product))
self.__display_product_search_result(search_result)
notice(
"Choosing best match (%s) ... please interrupt if this is not the desired compound."
% search_result.name[0])
self.__display_compound(search_result.InChI[0])
return database.metabolites.get_by_id(search_result.index[0])
def translate_product_to_universal_reactions_model_metabolite(self, product, database):
if isinstance(product, Metabolite):
return product
elif isinstance(product, six.text_type) or isinstance(product, six.string_types):
search_result = products.search(product)
search_result = search_result.loc[[i for i in search_result.index if i in database.metabolites]]
if len(search_result) == 0:
raise KeyError("No compound matches found for query %s" % product)
notice("Found %d compounds that match query '%s'" % (len(search_result), product))
self.__display_product_search_result(search_result)
notice("Choosing best match (%s) ... please interrupt if this is not the desired compound."
% search_result.name.values[0])
self.__display_compound(search_result.InChI.values[0])
return database.metabolites.get_by_id(search_result.index[0])
def search(product):
"""Search for available products.
PRODUCT: The target product. You can search by name, InChI, and metanetx ID.
\b
Examples
--------
$ cameo search chebi:30838 # search for itaconate
"""
click.echo('Loading product database ...')
from cameo.api.products import products
click.echo('Searching product database ...')
result = products.search(product)
if len(result) > 0:
click.echo('The following products were found:')
click.echo(result[['name', 'formula', 'mass', 'InChI', 'search_rank']])
else:
click.echo("No products could be found that match the search query.")
def search(product):
"""Search for available products.
PRODUCT: The target product. You can search by name, InChI, and metanetx ID.
\b
Examples
--------
$ cameo search chebi:30838 # search for itaconate
"""
click.echo('Loading product database ...')
from cameo.api.products import products
click.echo('Searching product database ...')
result = products.search(product)
if len(result) > 0:
click.echo('The following products were found:')
click.echo(result[['name', 'formula', 'mass', 'InChI', 'search_rank']])
else:
click.echo("No products could be found that match the search query.")