def main():
input_database_basename = sys.argv[1]
output_database_basename = sys.argv[2]
input_data = ffindex.read_data(input_database_basename + ".ffdata")
input_index = ffindex.read_index(input_database_basename + ".ffindex")
fh = open(output_database_basename + ".cs219", "wb")
total_length = 0
nr_sequences = len(input_index)
line_break = bytearray("\n", "utf-8")[0]
for entry in input_index:
entry_data = ffindex.read_entry_data(entry, input_data)
for i in range(len(entry_data)):
if entry_data[i] == line_break:
entry_data = entry_data[(i + 1):]
break
total_length += len(entry_data)
fh.write(bytearray(">" + entry.name + "\n", "utf-8"))
fh.write(entry_data)
fh.close()
fh = open(output_database_basename + ".cs219.sizes", "w")
fh.write(str(nr_sequences) + " " + str(total_length))
fh.close()
def check_a3m_format(db_basename, force_mode):
entries = ffindex.read_index(db_basename+"_a3m.ffindex")
data = ffindex.read_data(db_basename+"_a3m.ffdata")
corrupted_alignments = set()
for entry in entries:
lines = ffindex.read_lines(entry, data)
alignment = a3m.A3M_Container()
try:
alignment.read_a3m_from_lines(lines)
except:
corrupted_alignments.add(entry.name)
sys.stderr.write("Warning: A3M "+entry.name+" is corrupted!\n")
if len(corrupted_alignments) == 0:
return
if force_mode:
tmp_dir = tempfile.mkdtemp()
try:
sys.stderr.write("WARNING: remove corrupted a3m's!\n")
corrupted_index_file = os.path.join(tmp_dir, "corrupted.dat")
write_set_to_file(corrupted_alignments, corrupted_index_file)
for suffix in ["a3m", "cs219", "hhm"]:
remove_files_from_index(corrupted_index_file, db_basename+"_"+suffix+".ffindex")
sort_database(db_basename+"_"+suffix+".ffdata", db_basename+"_"+suffix+".ffindex")
optimize_database(db_basename+"_"+suffix+".ffdata", db_basename+"_"+suffix+".ffindex")
finally:
shutil.rmtree(tmp_dir)
else:
sys.stderr.write("You may try to use the option --force to fix the database!\n")
def main():
import sys
parser = arg()
args = parser.parse_args(sys.argv[1:])
data = read_data(args.data)
index = read_index(args.index)
dataset = extract_data(data, index, args.ev, args.cov, args.sim, args.max_len)
write_results(dataset, args.out_file)
def main():
import sys
parser = arg()
args = parser.parse_args(sys.argv[1:])
data = read_data(args.data)
index = read_index(args.index)
dataset = extract_data(data, index, args.ev, args.cov, args.sim,
args.max_len)
write_results(dataset, args.out_file)
def main():
data = ffindex.read_data(sys.argv[1])
entries = ffindex.read_index(sys.argv[2])
e = ffindex.get_entry_by_name('BAPNUNABA.a3m', entries)
for entry in [e]:
print(entry.name)
if (entry.length == 1):
print("skip: " + entry.name)
continue
entry_data = ffindex.read_entry_data(entry, data)
alis = read_alignment_matrices(entry.length, entry_data)
for ali in alis.alignments:
print(ali.alignment_start_matrix)
def main():
data = ffindex.read_data(sys.argv[1])
entries = ffindex.read_index(sys.argv[2])
e = ffindex.get_entry_by_name('BAPNUNABA.a3m', entries)
for entry in [e]:
print(entry.name)
if(entry.length == 1):
print("skip: "+entry.name)
continue
entry_data = ffindex.read_entry_data(entry, data)
alis = read_alignment_matrices(entry.length, entry_data)
for ali in alis.alignments:
print(ali.alignment_start_matrix)
def get_large_a3ms(a3m_base_path):
entries = ffindex.read_index(a3m_base_path+"_a3m.ffindex")
data = ffindex.read_data(a3m_base_path+"_a3m.ffindex")
large_alignments = set()
for entry in entries:
lines = ffindex.read_lines(entry, data)
alignment = a3m.A3M_Container()
try:
alignment.read_a3m_from_lines(lines)
if alignment.get_number_sequences() > 50:
large_alignments.add(entry.name)
except:
sys.stderr.write("Warning: A3M "+entry.name+" is corrupted!\n")
return large_alignments
def get_large_a3ms(a3m_base_path):
entries = ffindex.read_index(a3m_base_path + "_a3m.ffindex")
data = ffindex.read_data(a3m_base_path + "_a3m.ffindex")
large_alignments = set()
for entry in entries:
lines = ffindex.read_lines(entry, data)
alignment = a3m.A3M_Container()
try:
alignment.read_a3m_from_lines(lines)
if alignment.get_number_sequences() > 50:
large_alignments.add(entry.name)
except:
sys.stderr.write("Warning: A3M " + entry.name + " is corrupted!\n")
return large_alignments
def check_a3m_format(db_basename, force_mode):
entries = ffindex.read_index(db_basename + "_a3m.ffindex")
data = ffindex.read_data(db_basename + "_a3m.ffdata")
corrupted_alignments = set()
for entry in entries:
lines = ffindex.read_lines(entry, data)
alignment = a3m.A3M_Container()
try:
alignment.read_a3m_from_lines(lines)
except:
corrupted_alignments.add(entry.name)
sys.stderr.write("Warning: A3M " + entry.name + " is corrupted!\n")
if len(corrupted_alignments) == 0:
return
if force_mode:
tmp_dir = tempfile.mkdtemp()
try:
sys.stderr.write("WARNING: remove corrupted a3m's!\n")
corrupted_index_file = os.path.join(tmp_dir, "corrupted.dat")
write_set_to_file(corrupted_alignments, corrupted_index_file)
for suffix in ["a3m", "cs219", "hhm"]:
remove_files_from_index(
corrupted_index_file,
db_basename + "_" + suffix + ".ffindex")
sort_database(db_basename + "_" + suffix + ".ffdata",
db_basename + "_" + suffix + ".ffindex")
optimize_database(db_basename + "_" + suffix + ".ffdata",
db_basename + "_" + suffix + ".ffindex")
finally:
shutil.rmtree(tmp_dir)
else:
sys.stderr.write(
"You may try to use the option --force to fix the database!\n")
#!/usr/bin/env python
import ffindex
import sys
input_file = sys.argv[1]
output_file = sys.argv[2]
entries = ffindex.read_index(input_file + ".ffindex")
data = ffindex.read_data(input_file + ".ffdata")
with open(output_file, "w") as fh:
for entry in entries:
size = int(ffindex.read_entry_data(entry, data).decode("utf-8"))
if size < 51:
fh.write(entry.name + "\n")
def main():
import sys
parser = arg()
args = parser.parse_args(sys.argv[1:])
tmp_dir = tempfile.mkdtemp()
tmp = os.path.join(tmp_dir, tmp_dir.split("/")[-1])
tmp_graph = tmp + ".graph"
if args.verbose:
DEBUG = True
entries = read_index(args.mat_index)
data = read_data(args.mat_data)
# load predictions
predictions = read_predictions(args.predictions)
# process list (input for map)
block_size = args.block
current_block = 1
pool = Pool(args.cpu)
for block_start in range(0, len(entries), block_size):
block_end = min(len(entries), block_start + block_size)
block = entries[block_start:block_end]
print ("Processing Block {cb} ({bs}-{be})".format(cb=current_block, bs=block_start, be=block_end))
plist = list()
for entry in block:
query = entry.name.split(".")[0]
if (entry.length == 1):
print ("skip: "+ entry.name)
continue
entry_data = read_entry_data(entry, data)
alis = read_alignment_matrices(entry.length, entry_data)
for ali in alis.alignments:
template = ali.template
#print (query + '->' + template)
if query == template:
print ("Skipping {0} (Self alignmnent).".format(template))
break
prob = ali.alignment_probability / float(100)
if prob < args.p_low:
if DEBUG:
print ("Not adding {q} - {t}. Prob(query, template) < P_low.".format(q=query, t=template))
break
#if query == 'corrupt_mat' and template =='WEWKIWABA':
# import pdb; pdb.set_trace()
pred = dict()
pred[query] = predictions[query]
pred[template] = predictions[template]
# check whether all matrices contain values
if (len(ali.alignment_start_matrix) == 0) or (len(ali.alignment_end_matrix) == 0) or (len(ali.alignment_posterior_matrix) == 0):
print ('! Warning detected empty matrices! Skipping '+ query + '->' + template)
else:
plist.append((AlignmentMatrix(query, template, prob, pred, ali.alignment_end_matrix, ali.alignment_start_matrix, ali.alignment_posterior_matrix), args.p_low, args.cov))
# Uncomment to debug!
if args.verbose:
processed_data = list()
for process in plist:
chunck = wrapper(process)
processed_data.append(chunck)
else:
processed_data = pool.map(wrapper, plist)
results = list(filter(lambda x: x != None, processed_data))
mode = "a" if block_start > 0 else "w"
print ("Writing Block {cb}.".format(cb=current_block))
write_results(tmp_graph, results, mode)
current_block += 1
graph = read_graph(tmp_graph)
with open(args.output, 'w') as out_fh:
for initial_node in graph:
for terminal_node in graph[initial_node]:
out_fh.write('{inn}\t{on}\t{prob}\n'.format(inn = initial_node, on = terminal_node, prob = graph[initial_node][terminal_node]))