run_cra_batch.py

import sys
import os
import shutil
import zipfile

from aux import lsftools, mailtools

"""RUNS BATCH, not sure if this works"""

def stop(iFilesDir):
    shutil.rmtree(iFilesDir)
    exit(0)


iZip = None
oFile = None
tDir = "tmp/"
eAddress = None

try:
    iZip = sys.argv[1]
    oFile = sys.argv[2]
    eAddress = sys.argv[3]
except IndexError:
    print "Too Few Arguments for run_cra_batch.py \n"
    exit(1)

if "@" not in eAddress:
    print "Invalid email given to run_cra_batch.py \n"
    exit(1)

if not os.path.isdir(tDir):
    print "Invalid temporary directory\n"
    exit(1)

if not os.path.exists(iZip):
    print "Invalid input fasta\n"
    exit(1)

logfil = "logs/" + os.path.basename(iZip) + ".log"

try:
    os.remove(logfil)
except OSError:
    pass

try:
    os.remove(oFile)
except OSError:
    pass



zeroj_param = .9
cdhit_param_thresh = .7
cdhit_param_flength = .8
min_len_param = 30
max_len_param = 30000
ff_param_thresh = .7
ff_param_flength = .8
ms_check = False
xs_tolerance = 0

no_fasta = False
no_simple = False
no_len = False
no_comp = False
no_red = False
no_fusfis = False



if len(sys.argv) > 4:
    if "-0j" in sys.argv[4:]:
        zeroj_param = float(sys.argv[sys.argv.index("-0j")+1])
    if "-ct" in sys.argv[4:]:
        cdhit_param_thresh = float(sys.argv[sys.argv.index("-ct")+1])
    if "-cl" in sys.argv[4:]:
        cdhit_param_flength = float(sys.argv[sys.argv.index("-cl")+1])
    if "-min" in sys.argv[4:]:
        min_len_param = int(sys.argv[sys.argv.index("-min")+1])
    if "-max" in sys.argv[4:]:
        max_len_param = int(sys.argv[sys.argv.index("-max")+1])
    if "-fft" in sys.argv[4:]:
        ff_param_thresh = float(sys.argv[sys.argv.index("-fft")+1])
    if "-ffl" in sys.argv[4:]:
        ff_param_flength = float(sys.argv[sys.argv.index("-ffl")+1])
    if "-ms" in sys.argv[4:]:
        ms_check = True
    if "-xs" in sys.argv[4:]:
        xs_tolerance = int(sys.argv[sys.argv.index("-xs")+1])
    # if "-nofasta" in sys.argv[5:]: #not recommended
    #     no_fasta = True
    # if "-nosimple" in sys.argv[5:]: #not recommended
    #     no_simple = True
    if "-nolen" in sys.argv[4:]:
        no_len = True
    if "-nocomp" in sys.argv[4:]:
        no_comp = True
    if "-nored" in sys.argv[4:]:
        no_red = True
    if "-noff" in sys.argv[4:]:
        no_fusfis = True


iFilesDir = None

if ".zip" in iZip:
    zip_ref = zipfile.ZipFile(iZip, 'r')
    iFilesDir = iZip.split(".zip")[0]
    zip_ref.extractall(os.path.dirname(os.path.realpath(iZip)))
else:
    iFilesDir = iZip

iFiles = os.listdir(iFilesDir)
for x in range(len(iFiles)):
    iFile = iFiles[x]
    iFiles[x] = iFilesDir + "/" + iFile

print iFiles

finCSVWriter = open(oFile, "w")

finCSVWriter.write("FileName,Original")
finCSVWriter.write(",Fasta")
if not no_len:
    finCSVWriter.write(",Length")
if not no_comp:
    finCSVWriter.write(",Complexity")
if not no_red:
    finCSVWriter.write(",Redundancy")
if not no_fusfis:
    finCSVWriter.write(",Ff")
finCSVWriter.write(",CrapScore\n")

finCSVWriter.close()


commands = []
for iFile in iFiles:
    params = iFile + " /dev/null /dev/null " + oFile + " " + eAddress + " 0"
    print params
    for a in sys.argv[4:]:
        params += " " + a
    commands.append("python run_cra_less_verbose.py " + params)
    
lsftools.run_job_set(commands, wait=True, dont_clean=True, bsub_output="/dev/null", bsub_error="/dev/null")

para_str = ""
if "-h" in sys.argv[4:]:
    para_str = "-0j " + str(zeroj_param) + " -ct " + str(cdhit_param_thresh) + " -cl " + str(cdhit_param_flength) + " -min " + str(min_len_param) + " -max " + str(max_len_param) + " -fft " + str(ff_param_thresh) + " -ffl " + str(ff_param_flength) + " -xs " + str(xs_tolerance)
    if ms_check:
        parastr += " -ms"
    if no_len:
        parastr += " -nolen"
    if no_fasta:
        parastr += " -nofasta"
    if no_red:
        parastr += " -nored"
    if no_fusfis:
        parastr += " -noff"
else:
    for a in sys.argv[1:]:
        if a[0] == "-":
            para_str += "<br>" + a
        else:
            para_str += " " + a


print oFile
mailtools.send_email("We ran CRAP version 2.0 [BATCH] on files in " + iZip + "<br>Here is a list of parameters used: <br>" + para_str + '<br>', eAddress, [oFile])
# if ".zip" in iZip:
#     stop(iFilesDir)