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1#!/usr/bin/python3 env
2# -*- coding: utf-8 -*-
3
4"""Qsub command generator
5    Author: Arup Ghosh 
6    Creation date: 17/07/2019
7    last modified: 18/07/2019
8    Email: arupneo2 [at] gmail.com
9"""
10import glob
11import os
12
13files=glob.glob("*.fastq.gz")
14nodes=open("nodefile","r").read().split()
15#print(nodes)
16def _qsubFormat(fq,node):
17    tool="/software/FastQC/fastqc -t 20 --outdir"
18    cwd = os.getcwd()
19    command="qsub -b y -q all.q@compute-0-{0} -N fastqc.{1} -e {1}_error.log -o {1}_cmd.log -V {3} {2}/test/ {2}/{1}".format(node,fq,cwd,tool)
20    return command
21
22#Assign one node to one file
23if len(files) >len(nodes):
24    #print("Split Jobs nodes {} files {}".format(len(nodes),len(files)))
25    #Split the files list based upon the following calculation
26    chunks=[files[i:i + 10] for i in range(0, len(files), 10)]
27    for block in chunks:
28        i=0
29        for fq in block:
30            i += 1
31            #fix for node no tarting at compute-0-2
32            nodeno = i+1
33            print(_qsubFormat(fq,nodeno))
34else:
35    #print("Don't split jobs nodes {} files {}".format(len(nodes),len(files)))
36    i=0
37    for fq in files:
38        i += 1
39        #fix for node no tarting at compute-0-2
40        nodeno = i+1
41        print(_qsubFormat(fq,nodeno))