Mercurial > repos > artbio > repenrich2

comparison RepEnrich2.py @ 5:08e50af788f7 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit b1761de76fd068b86a06d88e70c1ba1d8644e7b5
author artbio
date Sun, 21 Apr 2024 21:52:40 +0000
parents 4905a332a094
children 388a47ca4199
comparison
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4:c5bb2f9af708 5:08e50af788f7
113 line = line.split('\t') 113 line = line.split('\t')
114 counts[line[3]] += int(line[4]) 114 counts[line[3]] += int(line[4])
115 sumofrepeatreads += int(line[4]) 115 sumofrepeatreads += int(line[4])
116 print(f"Identified {sumofrepeatreads} unique reads that mapped to repeats.") 116 print(f"Identified {sumofrepeatreads} unique reads that mapped to repeats.")
117 117
118 # print unique mapper counts
119 with open("unique_mapper_counts.tsv", 'w') as fout:
120 fout.write("#element\tcount\n")
121 for count in sorted(counts):
122 fout.write(f"{count}\t{counts[count]}\n")
123
118 # multimapper parsing 124 # multimapper parsing
119 if not paired_end: 125 if not paired_end:
120 args_list = [(metagenome, fastqfile_1) for 126 args_list = [(metagenome, fastqfile_1) for
121 metagenome in repeat_list] 127 metagenome in repeat_list]
122 with ProcessPoolExecutor(max_workers=cpus) as executor: 128 with ProcessPoolExecutor(max_workers=cpus) as executor: