Mercurial > repos > artbio > repenrich2

comparison RepEnrich2.py @ 8:567549a49eb2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit b3b166a8e991f49227e4888b8065b57cec0ba949
author artbio
date Thu, 25 Apr 2024 09:06:48 +0000
parents 61e0404f0d76
children 2b61c6407efb
comparison
equal deleted inserted replaced
7:61e0404f0d76 8:567549a49eb2
108 def run_bowtie(args): 108 def run_bowtie(args):
109 ''' 109 '''
110 write to files to save memory 110 write to files to save memory
111 ''' 111 '''
112 metagenome, fastqfile = args 112 metagenome, fastqfile = args
113 b_opt = "-k 1 -p 1 --quiet --no-hd" 113 b_opt = "-k 1 -p 1 --quiet --no-hd --no-unal"
114 command = shlex.split(f"bowtie2 {b_opt} -x {metagenome} {fastqfile}") 114 command = shlex.split(f"bowtie2 {b_opt} -x {metagenome} {fastqfile}")
115 bowtie_align = subprocess.run(command, check=True, 115 bowtie_align = subprocess.run(command, check=True,
116 capture_output=True, text=True).stdout 116 capture_output=True, text=True).stdout
117 bowtie_align = bowtie_align.rstrip('\r\n').split('\n') 117 bowtie_align = bowtie_align.rstrip('\r\n').split('\n')
118 with open(f"{metagenome}.reads", "a+") as readfile: 118 with open(f"{metagenome}.reads", "a+") as readfile:
146 for repname in metagenome_reads: 146 for repname in metagenome_reads:
147 for read in metagenome_reads[repname]: 147 for read in metagenome_reads[repname]:
148 repeats_by_reads[read].append(repname) 148 repeats_by_reads[read].append(repname)
149 for repname in repeats_by_reads: 149 for repname in repeats_by_reads:
150 repeats_by_reads[repname] = list(set(repeats_by_reads[repname])) 150 repeats_by_reads[repname] = list(set(repeats_by_reads[repname]))
151 # this repeats_by_reads dictionary is far too big
151 152
152 # 3 dictionnaries and 1 pointer variable to be populated 153 # 3 dictionnaries and 1 pointer variable to be populated
153 fractionalcounts = defaultdict(float) 154 fractionalcounts = defaultdict(float)
154 familyfractionalcounts = defaultdict(float) 155 familyfractionalcounts = defaultdict(float)
155 classfractionalcounts = defaultdict(float) 156 classfractionalcounts = defaultdict(float)