def from_formulas(reaction_strings,
arrow='<=>',
has_reaction_ids=False,
raise_exception=False):
"""
parses a list of reactions in KEGG format
Arguments:
reaction_strings - a list of reactions in KEGG format
arrow - the string used as the 'arrow' in each reaction (default: '<=>')
has_reaction_ids - a boolean flag indicating if there is a column of
reaction IDs (separated from the reaction with
whitespaces)
Return values:
S - a stoichiometric matrix
cids - the KEGG compound IDs in the same order as the rows of S
"""
try:
reactions = []
not_balanced_count = 0
for line in reaction_strings:
rid = None
if has_reaction_ids:
tokens = re.findall('(\w+)\s+(.*)', line.strip())[0]
rid = tokens[0]
line = tokens[1]
try:
reaction = KeggReaction.parse_formula(line, arrow, rid)
except KeggParseException as e:
logging.warning(str(e))
reaction = KeggReaction({})
if not reaction.is_balanced(fix_water=True,
raise_exception=raise_exception):
not_balanced_count += 1
logging.warning('Model contains an unbalanced reaction: ' +
line)
reaction = KeggReaction({})
reactions.append(reaction)
logging.debug('Adding reaction: ' + reaction.write_formula())
if not_balanced_count > 0:
warning_str = '%d out of the %d reactions are not chemically balanced' % \
(not_balanced_count, len(reaction_strings))
logging.debug(warning_str)
return KeggModel.from_kegg_reactions(reactions, has_reaction_ids)
except ValueError as e:
if raise_exception:
raise e
else:
logging.debug(str(e))
return None
def from_formulas(reaction_strings, arrow='<=>', has_reaction_ids=False,
raise_exception=False):
"""
parses a list of reactions in KEGG format
Arguments:
reaction_strings - a list of reactions in KEGG format
arrow - the string used as the 'arrow' in each reaction (default: '<=>')
has_reaction_ids - a boolean flag indicating if there is a column of
reaction IDs (separated from the reaction with
whitespaces)
Return values:
S - a stoichiometric matrix
cids - the KEGG compound IDs in the same order as the rows of S
"""
try:
reactions = []
not_balanced_count = 0
for line in reaction_strings:
rid = None
if has_reaction_ids:
tokens = re.findall('(\w+)\s+(.*)', line.strip())[0]
rid = tokens[0]
line = tokens[1]
try:
reaction = KeggReaction.parse_formula(line, arrow, rid)
except KeggParseException as e:
logging.warning(str(e))
reaction = KeggReaction({})
if not reaction.is_balanced(fix_water=True, raise_exception=raise_exception):
not_balanced_count += 1
logging.warning('Model contains an unbalanced reaction: ' + line)
reaction = KeggReaction({})
reactions.append(reaction)
logging.debug('Adding reaction: ' + reaction.write_formula())
if not_balanced_count > 0:
warning_str = '%d out of the %d reactions are not chemically balanced' % \
(not_balanced_count, len(reaction_strings))
logging.debug(warning_str)
return KeggModel.from_kegg_reactions(reactions, has_reaction_ids)
except ValueError as e:
if raise_exception:
raise e
else:
logging.debug(str(e))
return None
