def MemeParser(lines):
"""Returns a MotifResults object given a MEME results file.
"""
# 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.Alphabet = 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)
# Add summary dict to MotifResults object
meme_motif_results.Results = summary_dict
# 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))
for module in meme_motif_results.Modules:
meme_motif_results.Motifs.append(Motif(module))
return meme_motif_results
def GibbsParser(lines, truncate_len=None, strict=True):
"""Returns a MotifResults object given a Gibbs Sampler results file.
- only works with results from command line version of Gibbs Sampler
"""
try:
#Get sequence and motif blocks
sequence_block, motif_block = get_sequence_and_motif_blocks(lines)
except Exception, e:
if strict:
raise e
else:
return None
#Create MotifResults object
gibbs_motif_results = MotifResults()
#Get sequence map
sequence_map = get_sequence_map(sequence_block)
#Get motif blocks
motif_blocks = get_motif_blocks(motif_block)
#Get modules
for module in motif_blocks:
if module[1] == 'No Motifs Detected':
print "No Modules detcted!!", module[0]
continue
for cur_smod in build_module_objects(module, sequence_map, truncate_len=truncate_len):
gibbs_motif_results.Modules.append(cur_smod)
module_ids_to_int(gibbs_motif_results.Modules)
print "Found:", len(gibbs_motif_results.Modules)
for ct, module in enumerate(gibbs_motif_results.Modules):
