def MemeParser(lines, allowed_ids=[]):
"""Returns a MotifResults object given a MEME results file.
"""
warnings = []
#Create MotifResults object
meme_motif_results = MotifResults()
#Get main block and alphabet
main_block, alphabet = getDataBlock(lines)
#Add alphabet to MotifResults object
meme_motif_results.MolType = alphabet
#Get command line summary block and module blocks
command_block, module_blocks = getCommandModuleBlocks(main_block)
if command_block:
#Extract command line data and put in dict
parameters_list = extractCommandLineData(command_block)
#Add parameters dict to MotifResults object parameters
meme_motif_results.Parameters = parameters_list
#make sure modules were found
if len(module_blocks) > 0:
#Get Summary of motifs block
summary_block = getSummaryBlock(module_blocks[-1])
#Extract summary data and get summary_dict
summary_dict = extractSummaryData(summary_block)
seq_names = list(summary_dict['CombinedP'].keys())
if allowed_ids:
remap_dict, warning = make_remap_dict(seq_names, allowed_ids)
if warning:
warnings.append(warning)
sd = {}
for k, v in list(summary_dict['CombinedP'].items()):
sd[remap_dict[k]] = v
summary_dict['CombinedP'] = sd
else:
remap_dict = dict(list(zip(seq_names, seq_names)))
#Add summary dict to MotifResults object
meme_motif_results.Results = summary_dict
#Add warnings to MotifResults object
meme_motif_results.Results['Warnings'] = warnings
#Get blocks for each module
module_blocks = getModuleDataBlocks(module_blocks)
#Extract modules and put in MotifResults.Modules list
for module in module_blocks:
meme_motif_results.Modules.append(extractModuleData(module,\
alphabet,remap_dict))
for module in meme_motif_results.Modules:
meme_motif_results.Motifs.append(Motif(module))
return meme_motif_results
def MemeParser(lines, allowed_ids=[]):
"""Returns a MotifResults object given a MEME results file.
"""
warnings = []
#Create MotifResults object
meme_motif_results = MotifResults()
#Get main block and alphabet
main_block, alphabet = getDataBlock(lines)
#Add alphabet to MotifResults object
meme_motif_results.MolType = alphabet
#Get command line summary block and module blocks
command_block, module_blocks = getCommandModuleBlocks(main_block)
if command_block:
#Extract command line data and put in dict
parameters_list = extractCommandLineData(command_block)
#Add parameters dict to MotifResults object parameters
meme_motif_results.Parameters = parameters_list
#make sure modules were found
if len(module_blocks) > 0:
#Get Summary of motifs block
summary_block = getSummaryBlock(module_blocks[-1])
#Extract summary data and get summary_dict
summary_dict = extractSummaryData(summary_block)
seq_names = summary_dict['CombinedP'].keys()
if allowed_ids:
remap_dict,warning = make_remap_dict(seq_names,allowed_ids)
if warning:
warnings.append(warning)
sd = {}
for k,v in summary_dict['CombinedP'].items():
sd[remap_dict[k]]=v
summary_dict['CombinedP']=sd
else:
remap_dict = dict(zip(seq_names,seq_names))
#Add summary dict to MotifResults object
meme_motif_results.Results = summary_dict
#Add warnings to MotifResults object
meme_motif_results.Results['Warnings']=warnings
#Get blocks for each module
module_blocks = getModuleDataBlocks(module_blocks)
#Extract modules and put in MotifResults.Modules list
for module in module_blocks:
meme_motif_results.Modules.append(extractModuleData(module,\
alphabet,remap_dict))
for module in meme_motif_results.Modules:
meme_motif_results.Motifs.append(Motif(module))
return meme_motif_results
