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