def __init__(self, conf_file=None, init_conf=None):
"""
Initialization function, parse options from configuration file and verify their values.
All self.variables are initialized explicitly in init.
"""
# Create a example conf file if needed
if init_conf:
print("Create an example configuration file in the current folder")
write_example_conf()
sys.exit(0)
print("Initialize Quade")
# Parse the configuration file and verify the values of variables
try:
# Verify if conf file was given and is valid
assert conf_file, "A path to the configuration file is mandatory"
self._is_readable_file(conf_file)
self.conf = conf_file
# Define a configuration file parser object and load the configuration file
cp = ConfigParser.RawConfigParser(allow_no_value=True)
cp.read(self.conf)
# Quality section
self.minimal_qual = cp.getint("quality", "minimal_qual")
# Boolean flag of subindex presence
self.idx1 = True
self.idx2 = cp.getboolean("index", "index2")
self.mol1 = self.idx1 and cp.getboolean("index", "molecular1")
self.mol2 = self.idx2 and cp.getboolean("index", "molecular2")
# Positions of subindex
self.idx1_pos = {
"start":cp.getint("index", "index1_start")-1,
"end":cp.getint("index", "index1_end")}
self.idx2_pos = {
"start":0 if not self.idx2 else cp.getint("index", "index2_start")-1,
"end":0 if not self.idx2 else cp.getint("index", "index2_end")}
self.mol1_pos = {
"start":0 if not self.mol1 else cp.getint("index", "molecular1_start")-1,
"end":0 if not self.mol1 else cp.getint("index", "molecular1_end")}
self.mol2_pos = {
"start":0 if not self.mol2 else cp.getint("index", "molecular2_start")-1,
"end":0 if not self.mol2 else cp.getint("index", "molecular2_end")}
# List of fastq files
self.seq_R1 = cp.get("fastq", "seq_R1").split()
self.seq_R2 = cp.get("fastq", "seq_R2").split()
self.index_R1 = cp.get("fastq", "index_R1").split()
self.index_R2 = [] if not self.idx2 else cp.get("fastq", "index_R2").split()
# Init the class Sample with generic values (unconventional initialization)
Sample.CLASS_INIT(
write_undetermined = cp.getboolean("output", "write_undetermined"),
write_pass = cp.getboolean("output", "write_pass"),
write_fail = cp.getboolean("output", "write_fail"),
min_qual = self.minimal_qual)
# Samples are a special case, since the number of sections is variable
# Iterate only on sections starting by "sample"
for sample in [i for i in cp.sections() if i.startswith("sample")]:
# Create a autoreferenced Sample object and fuse index if needed
if self.idx2:
Sample(name=cp.get(sample, "name"), index=(cp.get(sample, "index1_seq")+cp.get(sample, "index2_seq")))
else:
Sample(name=cp.get(sample, "name"), index=cp.get(sample, "index1_seq"))
# Values are tested in a private function
self._test_values()
# Handle the many possible errors occurring during conf file parsing or variable test
except (ConfigParser.NoOptionError, ConfigParser.NoSectionError) as E:
print ("Option or section missing. Report to the template configuration file\n" + E.message)
sys.exit(1)
except (ValueError, AssertionError) as E:
print ("One of the value in the configuration file is not correct\n" + E.message)
sys.exit(1)
except (IOError) as E:
print ("One of the file is incorrect or unreadable\n" + E.message)
sys.exit(1)
