def check_filenames(self, file_name, outfile, outfile_tag):
"""
file_name name
check if it exist
overwrite or not
if os.path.exists( self.cwd+self.name_only ):
if os.path.exists( full_file_path ):
"""
# if file_name.find(self.wdir) > -1:
# self.file_name = file_name
# else:
# self.file_name = self.wdir + file_name
if outfile is None:
prefix = path_utils.remove_ext(file_name)
if outfile_tag is not None:
outfile = prefix + outfile_tag
# print "mm", self.filename
# if filename.find(self.wdir) > -1:
# self.filename = filename
# else:
# self.filename = self.wdir + filename
self.infile = path_utils.check_wdir_prefix(self.wdir, file_name)
self.outfile = path_utils.check_wdir_prefix(self.wdir, outfile)
def check_outfile_filename(self, infile, records, outfile):
"""
infile name
check if it exist
if yes, append <namebase>.#
if os.path.exists( self.cwd+self.name_only ):
if os.path.exists( full_file_path ):
"""
if infile == None and records == None:
raise TypeError("Neither Blast infile nor records variable exists!!! ")
elif infile is None:
now = datetime.datetime.now()
namebase = now.strftime("%Y.%m.%d_%H.%M")
elif records is None:
self.infile = path_utils.check_wdir_prefix(self.wdir, infile)
namebase = None
else:
raise TypeError("Blast infile and records both exist! Pick one!")
if outfile is not None:
if outfile.endswith(".csv"):
location = outfile.rfind(".")
outfile = outfile[0:location]
self.outfile = path_utils.check_wdir_prefix(self.wdir, outfile)
elif namebase is None:
self.outfile = path_utils.remove_ext(self.infile) + ".blast"
else:
self.outfile = self.wdir + namebase
self.header = os.path.basename(self.outfile)
if not os.path.exists(self.outfile + ".csv"):
self.outfile = self.outfile + ".csv"
else:
version = 1
while os.path.exists(self.outfile + ".%s.csv" % version):
version = version + 1
# print "#####",self.outfile, location
self.outfile = self.outfile + ".%s.csv" % version
def check_outfile_filename(self, outfile, outfile_tag):
"""
infile name
check if it exist
overwrite or not
if os.path.exists( self.cwd+self.name_only ):
if os.path.exists( full_file_path ):
"""
if outfile is None:
prefix = path_utils.remove_ext(self.infile)
outfile = prefix + outfile_tag
outfile = path_utils.check_wdir_prefix(self.wdir, outfile)
return outfile
def generate_default_outfile_name(self, infile, outfile_tag):
prefix = path_utils.remove_ext(infile)
outfile = prefix + outfile_tag
outfile = path_utils.check_wdir_prefix(self.all_setting.get("wdir"), outfile)
return outfile
