def __init__(self, file_path, header_only = False):
self._header_info = HeaderInfo()
self._entry_list = DiffEntryList()
self.from_genome_diff_file(file_path, header_only)
class GenomeDiff:
#Constructors:
def __init__(self): pass
def __init__(self, file_path, header_only = False):
self._header_info = HeaderInfo()
self._entry_list = DiffEntryList()
self.from_genome_diff_file(file_path, header_only)
def __getitem__(self, type):
return self._entry_list[type]
#Getters.
def entry_list(self):
return self._entry_list
def header_info(self):
return self._header_info
def ref_sequence_file_names(self):
ret_val = list()
for ref_seq in self._header_info.ref_seqs:
ret_val.append(os.path.basename(ref_seq))
return ret_val
def ref_sequence_file_paths(self, downloads_dir = "02_Downloads"):
tokens = self._header_info.ref_seqs
ref_seq_paths = list()
for token in tokens:
kvp = token.split(":")
file_name = os.path.basename(kvp[1])
if not file_name.endswith(".gbk"):
file_name = "{}.gbk".format(file_name)
file_path = os.path.join(downloads_dir, file_name)
ref_seq_paths.append(file_path)
assert ref_seq_paths
return ref_seq_paths
def from_genome_diff_file(self, file_path, header_only):
self._header_info.file_path = file_path
self._header_info.file_name = os.path.basename(file_path)
self._header_info.run_name = os.path.basename(file_path).split('.')[0]
fp = open(file_path, 'r')
#Hander header info.
lines = fp.readlines()
assert string.find(lines.pop(0), "#=GENOME_DIFF") == 0
for line in lines:
if string.find(line, "#=") != 0:
lines.append(line)
break
if (line.startswith("#=REFSEQ")):
self._header_info.ref_seqs.append(line.split()[1])
elif (line.startswith("#=READSEQ")):
self._header_info.read_seqs.append(line.split()[1])
elif (line.startswith("#=TITLE")):
self._header_info.run_name = line.split()[1]
else:
tokens = line.lstrip("#=").split()
if tokens:
key = tokens.pop(0)
value = " ".join(tokens) if len(tokens) > 0 else "?"
self._header_info.other[key] = value
line = fp.readline()
if header_only: return
#Handle diff entries.
for line in lines:
if line.startswith("#"): continue
line = line.rstrip('\n')
if not line: continue
de = DiffEntry(line)
self._entry_list.append(de)
