def setJellyfish(self):
jellyfishpath, _ = QtWidgets.QFileDialog.getOpenFileName(self, "Select jellyfish File", filter='jellyfish')
if jellyfishpath:
jfversion = jellyfish.jfversion(jfbin=jellyfishpath)
QtWidgets.QMessageBox.information(self, "Jelly Fish", "Jelly Fish Version: %s" % jfversion)
if jfversion == 'None':
self.lineEdit_program_JFPath.setText(jellyfishpath)
self.label_program_JFversion.setText(jfversion)
self.label_program_JFversion.setStyleSheet("color:red")
else:
self.lineEdit_program_JFPath.setText(jellyfishpath)
self.label_program_JFversion.setText(jfversion)
self.label_program_JFversion.setStyleSheet("color:green")
self.jellyfishpath = jellyfishpath
def setJellyfish(self):
jellyfishpath, _ = QtWidgets.QFileDialog.getOpenFileName(
self, "Select jellyfish File", filter='jellyfish')
if jellyfishpath:
jfversion = jellyfish.jfversion(jfbin=jellyfishpath)
QtWidgets.QMessageBox.information(
self, "Jelly Fish", "Jelly Fish Version: %s" % jfversion)
if jfversion == 'None':
self.lineEdit_program_JFPath.setText(jellyfishpath)
self.label_program_JFversion.setText(jfversion)
self.label_program_JFversion.setStyleSheet("color:red")
else:
self.lineEdit_program_JFPath.setText(jellyfishpath)
self.label_program_JFversion.setText(jfversion)
self.label_program_JFversion.setStyleSheet("color:green")
self.jellyfishpath = jellyfishpath
def check_options(parser):
args = parser.parse_args()
# Start check bwa
if args.bwa:
if not os.path.exists(args.bwa):
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
bwaversion = bwa.bwaversion(args.bwa)
if bwaversion == 'None':
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
else:
bwapath = which('bwa')
if bwapath:
bwaversion = bwa.bwaversion(bwapath[0])
if bwaversion == 'None':
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
else:
args.bwa = bwapath[0]
else:
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
# End check bwa
# Start check jellyfish
if args.jellyfish:
if not os.path.exists(args.jellyfish):
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
jellyfishversion = jellyfish.jfversion(args.jellyfish)
if jellyfishversion == 'None':
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
else:
jellyfishpath = which('jellyfish')
if jellyfishpath:
jellyfishversion = jellyfish.jfversion(jellyfishpath[0])
if jellyfishversion == 'None':
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
else:
args.jellyfish = jellyfishpath[0]
else:
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
# End check jellyfish
if not os.path.exists(args.genome):
print("Can not locate genome file, please input genome file.\n")
parser.print_help()
sys.exit(1)
if not os.path.exists(args.input):
print("Can not locate input file, please input input file.\n")
parser.print_help()
sys.exit(1)
if args.homology > 100 or args.homology < 50:
print("Please set homology between 50 and 100.\n")
parser.print_help()
sys.exit(1)
if args.dtm > 37 or args.dtm < 0:
print("Please set dtm between 0 and 37.\n")
parser.print_help()
sys.exit(1)
if args.step < 1:
print("step must >1.\n")
parser.print_help()
sys.exit(1)
# Start check saved folder
if os.path.exists(args.saved):
if not args.docker:
print(args.saved, "exists. Everything in this folder will be remove. Press Y or N to continue: ")
while True:
char = getch()
if char.lower() in ("y", "n"):
print(char)
if char == 'n':
sys.exit(1)
break
else:
os.mkdir(args.saved)
# End check saved folder
# Print Checked information
print("#"*40)
print("bwa version:", args.bwa, bwaversion)
print("jellyfish version:", args.jellyfish, jellyfishversion)
print("genome file:", args.genome)
print("input file:", args.input)
print("5\' labeled R primer:", args.primer)
print("result output folder:", os.path.realpath(args.saved))
print("threads number:", args.threads)
print("homology:", args.homology)
print("dtm:", args.dtm)
print("#"*40)
return args
def check_options(parser):
args = parser.parse_args()
# Start check bwa
if args.bwa:
if not os.path.exists(args.bwa):
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
bwaversion = bwa.bwaversion(args.bwa)
if bwaversion == 'None':
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
else:
bwapath = which('bwa')
if bwapath:
bwaversion = bwa.bwaversion(bwapath[0])
if bwaversion == 'None':
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
else:
args.bwa = bwapath[0]
else:
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
# End check bwa
# Start check jellyfish
if args.jellyfish:
if not os.path.exists(args.jellyfish):
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
jellyfishversion = jellyfish.jfversion(args.jellyfish)
if jellyfishversion == 'None':
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
else:
jellyfishpath = which('jellyfish')
if jellyfishpath:
jellyfishversion = jellyfish.jfversion(jellyfishpath[0])
if jellyfishversion == 'None':
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
else:
args.jellyfish = jellyfishpath[0]
else:
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
# End check jellyfish
if not os.path.exists(args.genome):
print("Can not locate genome file, please input genome file.\n")
parser.print_help()
sys.exit(1)
if not os.path.exists(args.input):
print("Can not locate input file, please input input file.\n")
parser.print_help()
sys.exit(1)
if args.homology > 100 or args.homology < 50:
print("Please set homology between 50 and 100.\n")
parser.print_help()
sys.exit(1)
if args.dtm > 37 or args.dtm < 0:
print("Please set dtm between 0 and 37.\n")
parser.print_help()
sys.exit(1)
if args.step < 1:
print("step must >1.\n")
parser.print_help()
sys.exit(1)
# Start check saved folder
if os.path.exists(args.saved):
if not args.docker:
print(args.saved, "exists. Everything in this folder will be remove. Press Y or N to continue: ")
while True:
char = getch()
if char.lower() in ("y", "n"):
print(char)
if char == 'n':
sys.exit(1)
break
else:
os.mkdir(args.saved)
# End check saved folder
# Print Checked information
print("#"*40)
print("bwa version:", args.bwa, bwaversion)
print("jellyfish version:", args.jellyfish, jellyfishversion)
print("genome file:", args.genome)
print("input file:", args.input)
print("5\' labeled R primer:", args.primer)
print("result output folder:", os.path.realpath(args.saved))
print("threads number:", args.threads)
print("homology:", args.homology)
print("dtm:", args.dtm)
print("#"*40)
return args
def check_options(parser):
args = parser.parse_args()
# Start check bwa
if args.bwa:
if not os.path.exists(args.bwa):
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
bwaversion = bwa.bwaversion(args.bwa)
if bwaversion == 'None':
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
else:
bwapath = which('bwa')
if bwapath:
bwaversion = bwa.bwaversion(bwapath[0])
if bwaversion == 'None':
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
else:
args.bwa = bwapath[0]
else:
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
# End check bwa
# Start check jellyfish
if args.jellyfish:
if not os.path.exists(args.jellyfish):
print(
"Can not locate jellyfish, please input full path of jellyfish\n"
)
parser.print_help()
sys.exit(1)
jellyfishversion = jellyfish.jfversion(args.jellyfish)
if jellyfishversion == 'None':
print(
"Can not locate jellyfish, please input full path of jellyfish\n"
)
parser.print_help()
sys.exit(1)
else:
jellyfishpath = which('jellyfish')
if jellyfishpath:
jellyfishversion = jellyfish.jfversion(jellyfishpath[0])
if jellyfishversion == 'None':
print(
"Can not locate jellyfish, please input full path of jellyfish\n"
)
parser.print_help()
sys.exit(1)
else:
args.jellyfish = jellyfishpath[0]
else:
print(
"Can not locate jellyfish, please input full path of jellyfish\n"
)
parser.print_help()
sys.exit(1)
# End check jellyfish
if not os.path.exists(args.source):
print(
"Can not locate source genome (GenomeA) file, please input a source genome file.\n"
)
parser.print_help()
sys.exit(1)
if not os.path.exists(args.target):
print(
"Can not locate target genome (GenomeB) file, please input a target genome file.\n"
)
parser.print_help()
sys.exit(1)
if not os.path.exists(args.input):
print("Can not locate input file, please input input file.\n")
parser.print_help()
sys.exit(1)
# Start check saved folder
if os.path.exists(args.saved):
print(
args.saved,
"exists. Everything in this folder will be remove. Press Y or N to continue: "
)
while True:
char = getch()
if char.lower() in ("y", "n"):
print(char)
if char.lower() == 'n':
sys.exit(1)
break
else:
os.mkdir(args.saved)
# End check saved folder
# Print Checked information
print("#" * 40)
print("bwa version:", os.path.abspath(os.path.expanduser(args.bwa)),
bwaversion)
print("jellyfish version:",
os.path.abspath(os.path.expanduser(args.jellyfish)),
jellyfishversion)
print("source genome (GenomeA) file:",
os.path.abspath(os.path.expanduser(args.source)))
print("target genome (GenomeB) file:",
os.path.abspath(os.path.expanduser(args.target)))
print("input file:", os.path.abspath(os.path.expanduser(args.input)))
print("result output folder:", os.path.realpath(args.saved))
print("threads number:", args.threads)
print("#" * 40)
return args
def setprogramedefault(self):
machine = platform.machine()
system = platform.system()
jellyfishpath = 'bin/jellyfish/' + machine + '-' + system + '/bin/' + 'jellyfish'
bwapath = 'bin/bwa/' + machine + '-' + system + '/bwa'
# set default jellyfish path
if os.path.isfile(jellyfishpath):
self.jfversion = jellyfish.jfversion(jellyfishpath)
if not self.jfversion == 'None':
self.label_program_JFversion.setText(self.jfversion)
self.label_program_JFversion.setStyleSheet("color:green")
self.lineEdit_program_JFPath.setText(jellyfishpath)
self.jellyfishpath = jellyfishpath
else:
jellyfishpath = shutil.which("jellyfish")
if jellyfishpath:
self.jfversion = jellyfish.jfversion(jellyfishpath)
if not self.jfversion == 'None':
self.label_program_JFversion.setText(self.jfversion)
self.label_program_JFversion.setStyleSheet("color:green")
self.lineEdit_program_JFPath.setText(jellyfishpath)
self.jellyfishpath = jellyfishpath
# set default bwa path
if os.path.isfile(bwapath):
self.bwaversion = bwa.bwaversion(bwapath)
print(bwapath, self.bwaversion)
if not self.bwaversion == 'None':
self.label_program_Alnversion.setText(self.bwaversion)
self.lineEdit_program_AlnPath.setText(bwapath)
self.alignerpath = bwapath
self.aligner = 'BWA'
self.label_program_Alnversion.setStyleSheet("color:green")
else:
bwapath = shutil.which("bwa")
if bwapath:
self.bwaversion = bwa.bwaversion(bwapath)
print(bwapath, self.bwaversion)
if not self.bwaversion == 'None':
self.label_program_Alnversion.setText(self.bwaversion)
self.lineEdit_program_AlnPath.setText(bwapath)
self.alignerpath = bwapath
self.aligner = 'BWA'
self.label_program_Alnversion.setStyleSheet("color:green")
def check_options(parser):
args = parser.parse_args()
# Start check bwa
if args.bwa:
if not os.path.exists(args.bwa):
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
bwaversion = bwa.bwaversion(args.bwa)
if bwaversion == 'None':
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
else:
bwapath = which('bwa')
if bwapath:
bwaversion = bwa.bwaversion(bwapath[0])
if bwaversion == 'None':
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
else:
args.bwa = bwapath[0]
else:
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
# End check bwa
# Start check jellyfish
if args.jellyfish:
if not os.path.exists(args.jellyfish):
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
jellyfishversion = jellyfish.jfversion(args.jellyfish)
if jellyfishversion == 'None':
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
else:
jellyfishpath = which('jellyfish')
if jellyfishpath:
jellyfishversion = jellyfish.jfversion(jellyfishpath[0])
if jellyfishversion == 'None':
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
else:
args.jellyfish = jellyfishpath[0]
else:
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
# End check jellyfish
if not os.path.exists(args.genome):
print("Can not locate genome file, please input genome file.\n")
parser.print_help()
sys.exit(1)
if not os.path.exists(args.input):
print("Can not locate input file, please input input file.\n")
parser.print_help()
sys.exit(1)
if args.homology > 100 or args.homology < 50:
print("Please set homology between 50 and 100.\n")
parser.print_help()
sys.exit(1)
if args.dtm > 37 or args.dtm < -1:
# dtm = -1 skip calculate dtm
print("Please set dtm between 0 and 37.\n")
parser.print_help()
sys.exit(1)
if args.skipdtm == True:
args.dtm = -1
print("skip calculate dtm")
if args.length > 50:
args.dtm = -1
print("oligo length longer than 50nt, skip calculate dtm")
if args.step < 1:
print("step must >1.\n")
parser.print_help()
sys.exit(1)
# Start check saved folder
if os.path.exists(args.saved):
if not args.docker:
print("The output folder ",args.saved, " already exists.")
print('''
Press Y to use it for output files. Everything in this folder will be removed.
Press N and set -s/--saved to a different folder:
''')
while True:
char = getch()
if char.lower() in ("y", "n"):
print(char)
if char.lower() == 'n':
sys.exit(1)
break
else:
os.mkdir(args.saved)
# End check saved folder
# Print Checked information
print("#"*40)
print("bwa version:", args.bwa, bwaversion)
print("jellyfish version:", args.jellyfish, jellyfishversion)
print("genome file:", args.genome)
print("input file:", args.input)
print("5\' labeled R primer:", args.primer)
print("result output folder:", os.path.realpath(args.saved))
print("threads number:", args.threads)
print("homology:", args.homology)
print("dtm:", args.dtm)
if args.dtm == -1:
print("Warning: skip calculate dtm.")
print("#"*40)
return args
def check_options(parser):
args = parser.parse_args()
# Start check jellyfish
if args.jellyfish:
if not os.path.exists(args.jellyfish):
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
jellyfishversion = jellyfish.jfversion(args.jellyfish)
if jellyfishversion == 'None':
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
else:
jellyfishpath = which('jellyfish')
if jellyfishpath:
jellyfishversion = jellyfish.jfversion(jellyfishpath[0])
if jellyfishversion == 'None':
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
else:
args.jellyfish = jellyfishpath[0]
else:
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
# End check jellyfish
# check max min
if args.maxk < args.mink:
print("Error! Max kmer count is smaller than min kmer count!\n")
parser.print_help()
sys.exit(1)
# End check max min
# Check input file
if not os.path.exists(args.input):
print("Can not locate input file, please input input file.\n")
parser.print_help()
sys.exit(1)
# End check input file
return args
def check_options(parser):
args = parser.parse_args()
if args.jellyfish:
if not os.path.exists(args.jellyfish):
print(
"Can not locate jellyfish, please input full path of jellyfish\n"
)
parser.print_help()
sys.exit(1)
jellyfishversion = jellyfish.jfversion(args.jellyfish)
if jellyfishversion == 'None':
print(
"Can not locate jellyfish, please input full path of jellyfish\n"
)
parser.print_help()
sys.exit(1)
else:
jellyfishpath = which('jellyfish')
if jellyfishpath:
jellyfishversion = jellyfish.jfversion(jellyfishpath[0])
if jellyfishversion == 'None':
print(
"Can not locate jellyfish, please input full path of jellyfish\n"
)
parser.print_help()
sys.exit(1)
else:
args.jellyfish = jellyfishpath[0]
else:
print(
"Can not locate jellyfish, please input full path of jellyfish\n"
)
parser.print_help()
sys.exit(1)
if not os.path.exists(args.input):
print("Can not input file, please input probe file.\n")
parser.print_help()
sys.exit(1)
if args.mincount > args.maxcount:
print("min count %s is larger than max count %s" %
(args.mincount, args.maxcount))
parser.print_help()
sys.exit(1)
print("jellyfish version:", args.jellyfish, jellyfishversion)
print("input file:", args.input)
print("min count %s, max count %s" % (args.mincount, args.maxcount))
print("result output folder:", os.path.realpath(args.outfile))
return args
def check_options(parser):
args = parser.parse_args()
if args.jellyfish:
if not os.path.exists(args.jellyfish):
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
jellyfishversion = jellyfish.jfversion(args.jellyfish)
if jellyfishversion == 'None':
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
else:
jellyfishpath = which('jellyfish')
if jellyfishpath:
jellyfishversion = jellyfish.jfversion(jellyfishpath[0])
if jellyfishversion == 'None':
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
else:
args.jellyfish = jellyfishpath[0]
else:
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
# End check jellyfish
if not os.path.exists(args.genome):
print("Can not locate genome file, please input genome file.\n")
parser.print_help()
sys.exit(1)
if not os.path.exists(args.probe):
print("Can not locate probe file, please input genome file.\n")
parser.print_help()
sys.exit(1)
if args.input:
inputfiles = args.input.split(',')
for inputfile in inputfiles:
if not os.path.exists(inputfile):
print("Can not locate %s file.\n" % inputfile)
parser.print_help()
sys.exit(1)
elif args.jfile:
if not os.path.exists(args.jfile):
print("Can not locate %s file.\n" % args.jfile)
parser.print_help()
sys.exit(1)
else:
print("Can not locate input or jellyfish index file, please input jellyfish index or input file.\n")
parser.print_help()
sys.exit(1)
return args
def setprogramedefault(self):
machine = platform.machine()
system = platform.system()
jellyfishpath = 'bin/jellyfish/' + machine + '-' + system + '/bin/' + 'jellyfish'
bwapath = 'bin/bwa/' + machine + '-' + system + '/bwa'
# set default jellyfish path
if os.path.isfile(jellyfishpath):
self.jfversion = jellyfish.jfversion(jellyfishpath)
if not self.jfversion == 'None':
self.label_program_JFversion.setText(self.jfversion)
self.label_program_JFversion.setStyleSheet("color:green")
self.lineEdit_program_JFPath.setText(jellyfishpath)
self.jellyfishpath = jellyfishpath
else:
jellyfishpath = shutil.which("jellyfish")
if jellyfishpath:
self.jfversion = jellyfish.jfversion(jellyfishpath)
if not self.jfversion == 'None':
self.label_program_JFversion.setText(self.jfversion)
self.label_program_JFversion.setStyleSheet("color:green")
self.lineEdit_program_JFPath.setText(jellyfishpath)
self.jellyfishpath = jellyfishpath
# set default bwa path
if os.path.isfile(bwapath):
self.bwaversion = bwa.bwaversion(bwapath)
print(bwapath, self.bwaversion)
if not self.bwaversion == 'None':
self.label_program_Alnversion.setText(self.bwaversion)
self.lineEdit_program_AlnPath.setText(bwapath)
self.alignerpath = bwapath
self.aligner = 'BWA'
self.label_program_Alnversion.setStyleSheet("color:green")
else:
bwapath = shutil.which("bwa")
if bwapath:
self.bwaversion = bwa.bwaversion(bwapath)
print(bwapath, self.bwaversion)
if not self.bwaversion == 'None':
self.label_program_Alnversion.setText(self.bwaversion)
self.lineEdit_program_AlnPath.setText(bwapath)
self.alignerpath = bwapath
self.aligner = 'BWA'
self.label_program_Alnversion.setStyleSheet("color:green")
def check_options(parser):
args = parser.parse_args()
if args.bwa:
if not os.path.exists(args.bwa):
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
bwaversion = bwa.bwaversion(args.bwa)
if bwaversion == 'None':
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
else:
bwapath = subprocesspath.which('bwa')
if bwapath:
bwaversion = bwa.bwaversion(bwapath[0])
if bwaversion == 'None':
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
else:
args.bwa = bwapath[0]
else:
print("Can not locate bwa, please input full path of bwa\n")
parser.print_help()
sys.exit(1)
# End check bwa
# Start check jellyfish
if args.jellyfish:
if not os.path.exists(args.jellyfish):
print(
"Can not locate jellyfish, please input full path of jellyfish\n"
)
parser.print_help()
sys.exit(1)
jellyfishversion = jellyfish.jfversion(args.jellyfish)
if jellyfishversion == 'None':
print(
"Can not locate jellyfish, please input full path of jellyfish\n"
)
parser.print_help()
sys.exit(1)
else:
jellyfishpath = subprocesspath.which('jellyfish')
if jellyfishpath:
jellyfishversion = jellyfish.jfversion(jellyfishpath[0])
if jellyfishversion == 'None':
print(
"Can not locate jellyfish, please input full path of jellyfish\n"
)
parser.print_help()
sys.exit(1)
else:
args.jellyfish = jellyfishpath[0]
else:
print(
"Can not locate jellyfish, please input full path of jellyfish\n"
)
parser.print_help()
sys.exit(1)
# End check jellyfish
if args.samtools:
if not os.path.exists(args.samtools):
print(
"Can not locate samtools, please input full path of samtools\n"
)
parser.print_help()
sys.exit(1)
samtoolsversion = bwa.samtoolsversion(args.samtools)
if samtoolsversion == 'None':
print(
"Can not locate samtools, please input full path of samtools\n"
)
parser.print_help()
sys.exit(1)
else:
samtoolspath = subprocesspath.which('samtools')
if samtoolspath:
samtoolsversion = bwa.samtoolsversion(samtoolspath[0])
if samtoolsversion == 'None':
print(
"Can not locate samtools, please input full path of samtools\n"
)
parser.print_help()
sys.exit(1)
else:
args.samtools = samtoolspath[0]
else:
print(
"Can not locate samtools, please input full path of samtools\n"
)
parser.print_help()
sys.exit(1)
if args.bcftools:
if not os.path.exists(args.bcftools):
print(
"Can not locate bcftools, please input full path of bcftools\n"
)
parser.print_help()
sys.exit(1)
bcftoolsversion = bcftools.bcftoolsversion(args.bcftools)
if bcftoolsversion == 'None':
print(
"Can not locate bcftools, please input full path of bcftools\n"
)
parser.print_help()
sys.exit(1)
else:
bcftoolspath = subprocesspath.which('bcftools')
if bcftoolspath:
bcftoolsversion = bcftools.bcftoolsversion(bcftoolspath[0])
if bcftoolsversion == 'None':
print(
"Can not locate bcftools, please input full path of bcftools\n"
)
parser.print_help()
sys.exit(1)
else:
args.bcftools = bcftoolspath[0]
else:
print(
"Can not locate bcftools, please input full path of bcftools\n"
)
parser.print_help()
sys.exit(1)
if not os.path.exists(args.genome):
print("Can not locate genome file, please input genome file.\n")
parser.print_help()
sys.exit(1)
if not os.path.exists(args.probe):
print(
"Can not locate probe file, please input probe file which generate by Chorus2.\n"
)
parser.print_help()
sys.exit(1)
names = args.names.split(',')
reads1 = args.reads1.split(',')
reads2 = args.reads2.split(',')
if len(names) != len(reads1):
print("There are %s species (%s) but %s reads1 files (%s)" %
(len(names), names, len(reads1), reads1))
if len(names) != len(reads2):
print("There are %s species (%s) but %s reads2 files (%s)" %
(len(names), names, len(reads2), reads2))
for read1 in reads1:
# print(read1)
if not os.path.exists(read1):
print("Can not locate %s file.\n", read1)
parser.print_help()
sys.exit(1)
for read2 in reads2:
if not os.path.exists(read2):
print("Can not locate %s file.\n", read2)
parser.print_help()
sys.exit(1)
if os.path.exists(args.saved):
args.saved = os.path.realpath(args.saved)
print("The output folder ", args.saved, " already exists.")
print('''
Press Y to use it for output files. Everything in this folder will be removed.
Press N and set -s/--saved to a different folder:
''')
while True:
char = getch()
if char.lower() in ("y", "n"):
print(char)
if char.lower() == 'n':
sys.exit(1)
break
else:
args.saved = os.path.realpath(args.saved)
os.mkdir(args.saved)
if args.tmp:
tmpfolder = os.path.abspath(args.tmp)
else:
tmpfolder = os.path.abspath(os.path.join(args.saved, './tmp'))
print("tmp", args.tmp, tmpfolder)
args.tmp = tmpfolder
if os.path.exists(tmpfolder):
tmpfolder = os.path.realpath(tmpfolder)
print("The output folder ", tmpfolder, " already exists.")
print('''
Press Y to use it for output files. Everything in this folder will be removed.
Press N and set --tmp to a different folder:
''')
while True:
char = getch()
if char.lower() in ("y", "n"):
print(char)
if char.lower() == 'n':
sys.exit(1)
break
else:
args.tmp = tmpfolder
os.mkdir(tmpfolder)
print("#" * 40)
print("bwa version:", args.bwa, bwaversion)
print("jellyfish version:", args.jellyfish, jellyfishversion)
print("samtools version:", args.samtools, samtoolsversion)
print("bcftools version:", args.bcftools, bcftoolsversion)
print("genome file:", args.genome)
print("probe file:", args.probe)
print("out put folder:", args.saved)
for i in range(len(names)):
print(names[i], reads1[i], reads2[i])
return args
def check_options(parser):
args = parser.parse_args()
if args.jellyfish:
if not os.path.exists(args.jellyfish):
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
jellyfishversion = jellyfish.jfversion(args.jellyfish)
if jellyfishversion == "None":
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
else:
jellyfishpath = which("jellyfish")
if jellyfishpath:
jellyfishversion = jellyfish.jfversion(jellyfishpath[0])
if jellyfishversion == "None":
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
else:
args.jellyfish = jellyfishpath[0]
else:
print("Can not locate jellyfish, please input full path of jellyfish\n")
parser.print_help()
sys.exit(1)
if not os.path.exists(args.input):
print("Can not input file, please input probe file.\n")
parser.print_help()
sys.exit(1)
if args.mincount > args.maxcount:
print("min count %s is larger than max count %s" % (args.mincount, args.maxcount))
parser.print_help()
sys.exit(1)
print("jellyfish version:", args.jellyfish, jellyfishversion)
print("input file:", args.input)
print("min count %s, max count %s" % (args.mincount, args.maxcount))
print("result output folder:", os.path.realpath(args.outfile))
return args