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()
Exemple #2
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 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
Exemple #4
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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