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 as 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)
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
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 as 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)
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
#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)
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
for module in mr.Modules:
print module.ID
print str(module)
#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)
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
for module in mr.Modules:
print module.ID
print str(module)
