def parser(self, log_file):
"""
@summary : Parse the command results to add information in log_file.
@log_file : [str] Path to the sample process log file.
"""
# Parse output
FH_output_seq = SequenceFileReader.factory(self.output_seq)
nb_cleaned = 0
for record in FH_output_seq:
nb_cleaned += 1
FH_output_seq.close()
# Write result
FH_log = Logger(log_file)
FH_log.write('Results:\n')
FH_log.write("\tnb seq with 3' primer : " + str(nb_cleaned) + '\n')
FH_log.close()
def parser(self, log_file):
"""
@summary : Parse the command results to add information in log_file.
@log_file : [str] Path to the sample process log file.
"""
# Parse output
FH_output_seq = SequenceFileReader.factory( self.output_seq )
nb_cleaned = 0
for record in FH_output_seq:
nb_cleaned += 1
FH_output_seq.close()
# Write result
FH_log = Logger( log_file )
FH_log.write( 'Results:\n' )
FH_log.write( "\tnb seq with 3' primer : " + str(nb_cleaned) + '\n' )
FH_log.close()
def get_seq_length(input_file, size_separator=None):
"""
@summary: Returns the number of sequences by sequences lengths.
@param input_file: [str] The sequence file path.
@param size_separator: [str] If it exists the size separator in sequence ID.
@return: [dict] By sequences lengths the number of sequence.
"""
nb_by_length = dict()
FH_seq = SequenceFileReader.factory(input_file)
for record in FH_seq:
nb_seq = 1
if size_separator is not None:
nb_seq = int(record.id.rsplit(size_separator, 1)[-1])
seq_length = len(record.string)
if not nb_by_length.has_key(str(seq_length)):
nb_by_length[str(seq_length)] = 0
nb_by_length[str(seq_length)] += nb_seq
FH_seq.close()
return nb_by_length
def get_seq_length( input_file, size_separator=None ):
"""
@summary: Returns the number of sequences by sequences lengths.
@param input_file: [str] The sequence file path.
@param size_separator: [str] If it exists the size separator in sequence ID.
@return: [dict] By sequences lengths the number of sequence.
"""
nb_by_length = dict()
FH_seq = SequenceFileReader.factory( input_file )
for record in FH_seq:
nb_seq = 1
if size_separator is not None:
nb_seq = int(record.id.rsplit(size_separator, 1)[-1])
seq_length = len(record.string)
if not nb_by_length.has_key(str(seq_length)):
nb_by_length[str(seq_length)] = 0
nb_by_length[str(seq_length)] += nb_seq
FH_seq.close()
return nb_by_length
# Get observation sequences
observation_id_by_seq = dict()
FH_seeds = FastaIO(args.seeds_fasta)
for record in FH_seeds:
if record.string in observation_id_by_seq:
raise Exception("The OTU '" +
observation_id_by_seq[record.string] + "' and '" +
record.id + "' have the same sequence.")
observation_id_by_seq[record.string] = record.id.split(";size=")[0]
FH_seeds.close()
# Get centroids of observation
reference_by_observation_id = dict()
for file in args.reads:
FH_reads = SequenceFileReader.factory(file)
for record in FH_reads:
if record.string in observation_id_by_seq:
observation_id = observation_id_by_seq[record.string]
reference_id = re.search("reference=([^\s]+)",
record.description).group(1)
if observation_id not in reference_by_observation_id:
reference_by_observation_id[observation_id] = reference_id
elif len(reference_by_observation_id[observation_id].split(
",")) > len(reference_id.split(",")):
reference_by_observation_id[observation_id] = reference_id
FH_reads.close()
if len(observation_id_by_seq) != len(reference_by_observation_id):
missing = list()
for seed_seq in observation_id_by_seq:
if observation_id_by_seq[
# Get observation sequences
nb_observations = 0
observation_ids_by_seq = dict()
FH_seeds = FastaIO(args.input)
for record in FH_seeds:
nb_observations += 1
if record.string not in observation_ids_by_seq:
observation_ids_by_seq[record.string] = list()
observation_ids_by_seq[record.string].append(record.id)
FH_seeds.close()
# Get centroids (the real centroid and indentical sequences) ID by observation
observation_ids_by_centroid_id = dict()
for file in args.trimmed_reads:
FH_reads = SequenceFileReader.factory(file)
for record in FH_reads:
record_seq = record.string.replace("-", "").replace(".", "")
if record_seq in observation_ids_by_seq:
observation_ids_by_centroid_id[record.id] = observation_ids_by_seq[record_seq]
FH_reads.close()
# Get reference by observation
reference_by_observation_id = dict()
for file in args.reads:
FH_reads = SequenceFileReader.factory(file)
for record in FH_reads:
if record.id in observation_ids_by_centroid_id:
observation_ids = observation_ids_by_centroid_id[record.id]
reference_id = re.search("reference=([^\s]+)", record.description).group(1)
for current_obs_id in observation_ids: