comparison RepEnrich2.py @ 5:08e50af788f7 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit b1761de76fd068b86a06d88e70c1ba1d8644e7b5

4:c5bb2f9af708

    line = line.split('\t')
    counts[line[3]] += int(line[4])
    sumofrepeatreads += int(line[4])
print(f"Identified {sumofrepeatreads} unique reads that mapped to repeats.")

# multimapper parsing
if not paired_end:
    args_list = [(metagenome, fastqfile_1) for
                 metagenome in repeat_list]
    with ProcessPoolExecutor(max_workers=cpus) as executor:

5:08e50af788f7

    line = line.split('\t')
    counts[line[3]] += int(line[4])
    sumofrepeatreads += int(line[4])
print(f"Identified {sumofrepeatreads} unique reads that mapped to repeats.")

# print unique mapper counts
with open("unique_mapper_counts.tsv", 'w') as fout:
    fout.write("#element\tcount\n")
    for count in sorted(counts):
        fout.write(f"{count}\t{counts[count]}\n")

# multimapper parsing
if not paired_end:
    args_list = [(metagenome, fastqfile_1) for
                 metagenome in repeat_list]
    with ProcessPoolExecutor(max_workers=cpus) as executor: