def __init__(self, upstream, downstream, ref_base=None, alt_answer=None,
mut_type=None, path_to_seq_file=None, seq_dir=None,
seq_filename = None):
self.seq_file = get_AB1_file.handle_seq_file(path_to_seq_file, seq_dir)
# if statement helps with the recursive function in match_with_seq_file(), otherwise the actual reverse complemented sequence is used as the seq_filename, which causes errors in get_het_calls when it tries to open a string instead of an actual file
self.seq_filename = path_to_seq_file if not seq_filename else seq_filename
self.upstream = upstream
self.downstream = downstream
self.seq_dir = seq_dir
self.mut_type = mut_type
self.alt_answer = alt_answer
self.ref_base = ref_base
def parse_file(*args):
''' Parse a file line by line into the get_seq function
'''
input_file, output_file, upstream, downstream, hg_version, \
seq_dir, reference, genome = args
# append all returned data to this list
all_scrapped_info = []
for line in [line.rstrip("\n").split("\t") for line in open(input_file)]:
seq_name = line[0]
var_pos = line[1]
logging.info("\n\n\t We are looking for {} in sample {}\n\n".format( var_pos, seq_name))
# Determine the type of mutation
mutation = line[2]
ref_base = line[2].split("/")[0]
alt_answer, mut_type = determine_mutation(mutation)
logging.debug(" We are looking for a {}\n".format(mutation))
# check each individual line of the file for CUSTOM ERRORS
error_check = reference.handle_argument_exception(var_pos)
# find a list of files with seq_name in its title.
seq_file = get_AB1_file.get_matching_seq_file(seq_name, seq_dir)
# produce seq & tab files for each matched file, otherwise return blank line
if seq_file:
convert = [get_AB1_file.handle_seq_file(x, seq_dir)
for x in seq_file]
else:
all_scrapped_info.append("\t".join((seq_name, var_pos, "-", "-", "-", "-", "-", "0")))
# intialise the check_sanger CompareSeq class for every found seq_file
sanger = [CompareSeqs(upstream, downstream, ref_base, alt_answer,
mut_type, x, seq_dir)
for x in seq_file]
# parse it all into get_seq()
sequence_info = [get_seq(seq_name, var_pos, mutation, reference,
hg_version, genome, x) for x in sanger]
logging.debug("Sequence Info: ".format(sequence_info))
# filter out sequences where no seq file was found
filtered_answers = [x for x in sequence_info if "-" != x[1].split("\t")[4]]
logging.debug("Filtered Answer: {}".format(filtered_answers))
# check if any of the filtered_answer list contains the het call of interest
found_answer = find_variant(filtered_answers, ref_base, alt_answer)
# if a het call was found in some of the matching seq files, then print and return its values. Otherwise, return no seq_file matched values
if found_answer:
print_out, answer = found_answer
print(print_out)
logging.debug("printing: {}".format(print_out))
all_scrapped_info.append(answer)
elif filtered_answers:
print_out, answer = filtered_answers[0]
print(print_out)
logging.debug("printing: {}".format(print_out))
# append each lines returned data to an emty list
all_scrapped_info.append(answer)
elif sequence_info:
print_out, answer = sequence_info[0]
print(print_out)
logging.debug("printing: {}".format(print_out))
all_scrapped_info.append(answer)
# reset variable for next line/iteration
found_answer = None
# return all scrapped data
return all_scrapped_info