def split_fasta_file(input_file_path,
dest_dir,
prefix='part',
number_of_sequences_per_file=20000):
debug('%s; src: %s, dest dir: %s' % (my_name(), input_file_path, dest_dir))
input = SequenceSource(input_file_path)
parts = []
next_part = 1
part_obj = None
while input.next():
if (input.pos - 1) % number_of_sequences_per_file == 0:
sys.stderr.write('\rCreating part: ~ %s' % (pp(next_part)))
sys.stderr.flush()
if part_obj:
part_obj.close()
file_path = os.path.join(dest_dir, prefix + '-%08d' % next_part)
parts.append(file_path)
next_part += 1
part_obj = open(file_path, 'w')
part_obj.write('>%s\n' % input.id)
part_obj.write('%s\n' % input.seq)
if part_obj:
part_obj.close()
sys.stderr.write('\n')
return parts
def split_fasta_file(input_file_path, dest_dir, prefix = 'part', number_of_sequences_per_file = 20000):
debug('%s; src: %s, dest dir: %s' % (my_name(), input_file_path, dest_dir))
input = SequenceSource(input_file_path)
parts = []
next_part = 1
part_obj = None
while input.next():
if (input.pos - 1) % number_of_sequences_per_file == 0:
sys.stderr.write('\rCreating part: ~ %s' % (pp(next_part)))
sys.stderr.flush()
if part_obj:
part_obj.close()
file_path = os.path.join(dest_dir, prefix + '-%08d' % next_part)
parts.append(file_path)
next_part += 1
part_obj = open(file_path, 'w')
part_obj.write('>%s\n' % input.id)
part_obj.write('%s\n' % input.seq)
if part_obj:
part_obj.close()
sys.stderr.write('\n')
return parts
def split_file(ids_file,
source_file,
filtered_dest_file,
survived_dest_file,
type='fasta'):
"""splits reads in input file into two files based on ids_file
for read_id in input:
if read_id in list_of_ids:
--> filtered_dest_file
else:
--> survived dest_file
"""
debug('%s; src: "%s" (%s), filtered_dest: "%s", survived_dest: "%s"'\
% (my_name(), source_file, type, filtered_dest_file, survived_dest_file))
try:
ids_to_filter = set([id.strip() for id in open(ids_file).readlines()])
except IOError:
raise FilterError, 'Hit IDs file missing ("%s").' \
% (ids_to_filter)
if type == 'fasta':
STORE = lambda e, f: f.write('>%s\n%s\n' % (e.id, e.seq))
input = SequenceSource(source_file)
filtered_output = open(filtered_dest_file, 'w')
survived_output = open(survived_dest_file, 'w')
filtered_count, survived_count = 0, 0
while input.next():
if input.pos % 10000 == 0 or input.pos == 1:
sys.stderr.write('\rSplitting FASTA file: ~ %s' %
(pp(input.pos)))
sys.stderr.flush()
if input.id in ids_to_filter:
ids_to_filter.remove(input.id)
STORE(input, filtered_output)
filtered_count += 1
else:
STORE(input, survived_output)
survived_count += 1
sys.stderr.write('\n')
filtered_output.close()
survived_output.close()
debug('%s; done. of %s total reads, filtered: %s, survived: %s.'\
% (my_name(), pp(filtered_count + survived_count),\
pp(filtered_count), pp(survived_count)))
else:
raise UtilsError, "type '%s' is not implemented" % (type)
return True
def split_file(ids_file, source_file, filtered_dest_file, survived_dest_file, type = 'fasta'):
"""splits reads in input file into two files based on ids_file
for read_id in input:
if read_id in list_of_ids:
--> filtered_dest_file
else:
--> survived dest_file
"""
debug('%s; src: "%s" (%s), filtered_dest: "%s", survived_dest: "%s"'\
% (my_name(), source_file, type, filtered_dest_file, survived_dest_file))
try:
ids_to_filter = set([id.strip() for id in open(ids_file).readlines()])
except IOError:
raise FilterError, 'Hit IDs file missing ("%s").' \
% (ids_to_filter)
if type == 'fasta':
STORE = lambda e, f: f.write('>%s\n%s\n' % (e.id, e.seq))
input = SequenceSource(source_file)
filtered_output = open(filtered_dest_file, 'w')
survived_output = open(survived_dest_file, 'w')
filtered_count, survived_count = 0, 0
while input.next():
if input.pos % 10000 == 0 or input.pos == 1:
sys.stderr.write('\rSplitting FASTA file: ~ %s' % (pp(input.pos)))
sys.stderr.flush()
if input.id in ids_to_filter:
ids_to_filter.remove(input.id)
STORE(input, filtered_output)
filtered_count += 1
else:
STORE(input, survived_output)
survived_count += 1
sys.stderr.write('\n')
filtered_output.close()
survived_output.close()
debug('%s; done. of %s total reads, filtered: %s, survived: %s.'\
% (my_name(), pp(filtered_count + survived_count),\
pp(filtered_count), pp(survived_count)))
else:
raise UtilsError, "type '%s' is not implemented" % (type)
return True
