def extract_methylation(self):
for file_path in os.listdir(self.dir_info.splitted_dir):
file_path = os.path.join(self.dir_info.splitted_dir, file_path)
extractor = BismarkMethylationExtractor(file_path,
self.dir_info.bismark_methylation_extractor_output_dir,
ncores=45)
command = extractor.bismark_met_extractor_command()
# perform logging
print("*************************************", file=self.log_file_handler)
print("This is how the extractor will be called: ", file=self.log_file_handler)
print(command, file=self.log_file_handler)
print("", file=self.log_file_handler)
print("Logging extractor output to: " + extractor.log_file_path(), file=self.log_file_handler)
print("*************************************", file=self.log_file_handler)
print("", file=self.log_file_handler)
print("", file=self.log_file_handler)
# close log, because bismark likes to write to stderr and python doesnt' like it
self.log_file_handler.close()
# call thea actual command
output = run_shell_command(command)
# reopen log
self.log_file_handler = open(self.dir_info.analysis_log_path, mode='a')
def extract_methylation(self):
try:
extractor = BismarkMethylationExtractor(
self.dir_info.deduplicated_bam_path, self.dir_info.bismark_methylation_extractor_output_dir
)
command = extractor.bismark_met_extractor_command()
run_shell_command(command)
except:
raise Exception("Couldn't extract methylation for mate " + self.name + "! Please inspect the log file")
