#!/usr/bin/env python

#=========================================================================

# This is OPEN SOURCE SOFTWARE governed by the Gnu General Public

# License (GPL) version 3, as described at www.opensource.org.

# Copyright (C)2017 William H. Majoros (martiandna@gmail.com).

#=========================================================================

from __future__ import (absolute_import, division, print_function,

unicode_literals, generators, nested_scopes, with_statement)

from builtins import (bytes, dict, int, list, object, range, str, ascii,

chr, hex, input, next, oct, open, pow, round, super, filter, map, zip)

# The above imports should allow this program to run in both Python 2 and

# Python 3. You might need to update your version of module "future".

import sys

import os

import ProgramName

from SlurmWriter import SlurmWriter

from Rex import Rex

rex=Rex()

ROOT="/home/bmajoros/PopSTARR/graham"

MEM=50000

NICE=500

jobName="TRIM"

maxParallel=1000

THREADS=31

TRIMMOMATIC="java -jar /data/reddylab/software/Trimmomatic-0.33/Trimmomatic-0.33/trimmomatic-0.33.jar PE"

#=========================================================================

# main()

#=========================================================================

if(len(sys.argv)!=5):

exit(ProgramName.get()+" <adapters.fasta> <fastq-in> <fastq-out> <full-path-to-slurms>\n")

(adaptersFasta,fastqIn,fastqOut,slurmDir)=sys.argv[1:]

files=os.listdir(fastqIn)

writer=SlurmWriter()

for file in files:

if(not rex.find("(.*[_-])R1([_-].*)\.fastq.gz",file)): continue

file1=file

file2=rex[1]+"R2"+rex[2]+".fastq.gz"

cmd=TRIMMOMATIC+" -threads "+str(THREADS)+" -phred33 "+\

fastqIn+"/"+file1+" "+fastqIn+"/"+file2+" "+\

fastqOut+"/"+rex[1]+"_FWD_paired.fq.gz "+\

fastqOut+"/"+rex[1]+"_FWD_unpaired.fq.gz "+\

fastqOut+"/"+rex[1]+"_REV_paired.fq.gz "+\

fastqOut+"/"+rex[1]+"_REV_unpaired.fq.gz "+\

"ILLUMINACLIP:"+adaptersFasta+\

":2:30:10:8:TRUE HEADCROP:1 LEADING:30 TRAILING:30 "+\

"SLIDINGWINDOW:4:15 MINLEN:36"

writer.addCommand("cd "+ROOT+"\n"+cmd)

writer.nice(NICE) # turns on "nice" (sets it to 100 by default)

writer.mem(MEM)

writer.threads(THREADS)

writer.setQueue("new,all")

writer.writeArrayScript(slurmDir,jobName,maxParallel,

"#SBATCH --exclude=x2-01-1,x2-01-2,x2-01-3,x2-01-4,x2-02-1,x2-02-2,x2-02-3,x2-02-4,x2-03-1 ")