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metaphlan4folder.py
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metaphlan4folder.py
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#!/usr/bin/env python3
import sys
import os
import re
import glob
import subprocess
digits = re.compile(r'(\d+)')
def tokenize(filename):
return tuple(int(token) if match else token
for token, match in
((fragment, digits.search(fragment))
for fragment in digits.split(filename)))
folder = sys.argv[1] #working folder
g=sys.argv[2] #output folder
fmt=sys.argv[3]
db=sys.argv[4]
threads=sys.argv[5]
type1 = "rel_ab_w_read_stats"
filelist=glob.glob(folder)
filelist.sort(key=tokenize)
p0=subprocess.Popen("mkdir -p %s" %g,shell=True).wait()
p2=subprocess.Popen("module load bowtie2", shell=True).wait()
print(filelist)
for i in filelist:
print(i)
name =i.split("/")[-1]
outname=g+"/"+name+".txt"
p1=subprocess.Popen(f"metaphlan {i} -o {outname} --input_type {fmt} --nproc {threads} -t {type1} --tax_lev a --no_map --bt2_ps very-sensitive-local --min_alignment_len 50 --bowtie2db {db} -x mpa_vOct22_CHOCOPhlAnSGB_202212 --tmp_dir ./ --add_viruses --mpa3",shell=True).wait()