comparison ALFA/ALFA_wrapper.py @ 30:1c9cea51dc24 draft

Uploaded

29:c8acc8808b52

def get_input2_args(reads_list, format):
    n = len(reads_list)
    if n%2 != 0:
        exit_and_explain('Problem with pairing reads filename and reads label')
    input2_args='-i'
    k = 1
    reads_filenames = [''] * (n/2)
    reads_labels = [''] * (n/2)
    for i in range(0, n, 2):
        reads_filenames[k] = reads_list[i].split('__fname__')[1]
        reads_labels[k] = reads_list[i+1].split('__label__')[1]

def merge_count_files(reads_labels):
    merged_count_file = open('count_file.txt', 'wb')
    for i in range(0, len(reads_labels)):
        current_count_file = open(reads_labels[i] + '.categories_counts', 'r')
        merged_count_file.write('##LABEL: %s\n\n' % reads_label[i])
        merged_count_file.write(current_count_file.read())
        merged_count_file.write('__________________________________________________________________\n')
        current_count_file.close()
    merged_count_file.close()
    return 'count_file.txt'

30:1c9cea51dc24

def get_input2_args(reads_list, format):
    n = len(reads_list)
    if n%2 != 0:
        exit_and_explain('Problem with pairing reads filename and reads label')
    input2_args='-i'
    k = 0
    reads_filenames = [''] * (n/2)
    reads_labels = [''] * (n/2)
    for i in range(0, n, 2):
        reads_filenames[k] = reads_list[i].split('__fname__')[1]
        reads_labels[k] = reads_list[i+1].split('__label__')[1]

def merge_count_files(reads_labels):
    merged_count_file = open('count_file.txt', 'wb')
    for i in range(0, len(reads_labels)):
        current_count_file = open(reads_labels[i] + '.categories_counts', 'r')
        merged_count_file.write('##LABEL: %s\n\n' % reads_labels[i])
        merged_count_file.write(current_count_file.read())
        merged_count_file.write('__________________________________________________________________\n')
        current_count_file.close()
    merged_count_file.close()
    return 'count_file.txt'