def write_in_pe_format(self, filename):
check_dir(filename)
with open(filename, 'w') as f:
f.write(f"sequence={self.sequence}\n"
f"consensus={self.consensus}\n")
f.write("F3_5pos=-1\nF3_3pos=-1\nF2_5pos=-1\nF2_3pos=-1\nF1c_5pos=-1\nF1c_3pos=-1\nB3_5pos=-1\nB3_3pos=-1\n"
"B2_5pos=-1\nB2_3pos=-1\nB1c_5pos=-1\nB1c_3pos=-1\ntarget_range_type=0\ntarget_range_from=\n"
"target_range_to=")
def __run_gram_align(filename, outfile):
# checking directory of filename
check_dir(filename)
if ga_path:
program = ga_path
else:
program = "GramAlign"
command = program + " -i " + filename + " -o " + outfile + " -f 2"
print(command)
os.system(command)
def __run_muscle(filename, outfile):
# checking directory of filename
check_dir(filename)
if clustalo_path:
program = muscle_path
else:
program = "muscle"
command = program + " -in " + filename + " -out " + outfile
print(command)
os.system(command)
def __run_clustalo(filename, outfile):
# checking directory of filename
check_dir(filename)
if clustalo_path:
program = clustalo_path
else:
program = "clustalo"
command = program + " -i " + filename + " -o " + outfile
print(command)
os.system(command)
def __write_seqrec_to(self, filename, ignore_gaps=False, ignore_level=0.9):
"""
Private function for writing Seq consensus
:param filename: filename to write
:param coloring: 'c' or 'd'. First for coloring confidence, second for coloring deeps
:param ignore_gaps: boolean, True or False. Ignoring gaps with high level of confidence
(with confidence >= ignore_level)
:param ignore_level: float, level of ignoring gaps
"""
seq = self.__get_seq_consensus(ignore_gaps, ignore_level)
seq_rec = SeqRecord(seq)
check_dir(filename)
SeqIO.write(seq_rec, filename, "fasta")
def __write_html_to(self,
filename,
coloring="c",
ignore_gaps=False,
ignore_level=0.9):
"""
Private function for writing html consensus
:param filename: filename to write
:param coloring: 'c' or 'd'. First for coloring confidence, second for coloring deeps
:param ignore_gaps: boolean, True or False. Ignoring gaps with high level of confidence
(with confidence >= ignore_level)
:param ignore_level: float, level of ignoring gaps
"""
html_header = Extractor.extract_html_header(coloring)
html_body = self.__get_html_body(coloring, ignore_gaps, ignore_level)
check_dir(filename)
with open(filename, "w") as f:
f.write(html_header + html_body)
def write_to(self, filename):
check_dir(filename)
SeqIO.write(self.records, filename, "fasta")