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
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):
gibbs_motif_results.Motifs.append(Motif(module))
gibbs_motif_results.Alphabet=module.Alphabet
return gibbs_motif_results
if __name__ == "__main__":
from sys import argv, exit
print "Running..."
if len(argv) != 2:
print "Usage: gibbs.py <gibbs out file>"
exit(1)
mr = GibbsParser(open(argv[1]), 24)
print mr
