#!/usr/bin/env python import os,re,sys,string,commands,getopt,subprocess,glob from os import path #/disk/rdisk08/mhyleung/loreal_shotgun2/NovaSeq_new/decontam_output_genome/paired_completed/szy_test #LOR294C_S130_R1_001_kneaddata_paired_1_decontaminated.fastq.paired.fq.gz
#LOR294C_S130_R1_001_kneaddata_paired_1.fastq.gz #metawrap binning -o /home/mhyleung/workspace/loreal_shotgun2/NovaSeq_new/metawrap_assembly_R2/LOR303C -t 16 -a /home/mhyleung/workspace/loreal_shotgun2/NovaSeq_new/metawrap_assembly_R2/LOR303C_S134_R1_001_kneaddata_paired/LOR303C_final_assembly.fasta –maxbin2 –metabat2 –concoct /disk/rdisk08/mhyleung/loreal_shotgun2/NovaSeq_new/decontam_output_genome/paired_completed/szy_test/LOR303C_S134_R1_001_kneaddata_paired_*.fastq #host = subprocess.Popen([‘host’, target], stdout = subprocess.PIPE).communicate()[0] #p1 = subprocess.Popen([‘ping’, ‘-c 2′, host], stdout=subprocess.PIPE)
def main(): for d in os.listdir(‘/disk/rdisk08/mhyleung/loreal_shotgun2/NovaSeq_new/decontam_output_genome/paired_completed/szy_test’): #print(d) if re.search(“_1.fastq”, d): a = [] a = re.split(“_”,d) […]
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