def call_trim_galore(self):
try:
trimmer = TrimGalore(self.dir_info.first,
self.dir_info.second,
self.dir_info.trim_galore_output_dir)
run_shell_command(trimmer.generate_command())
except:
raise Exception("Couldn't trim galore for mate " + self.name() + "! Please inspect the log file")
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")
def merge_aligned_bams(self):
files = self.dir_info.list_aligned_bam_files()
output_file = self.dir_info.aligned_bam_path
if len(files) > 1:
command = samtools_merge_files_command(output_file, files)
print(command, file=self.log_file_handler)
run_shell_command(command, redirect_output_path=self.dir_info.analysis_log_path, append=True)
else:
print("Only one bam file, skipping merging", file = self.log_file_handler)
shutil.copyfile(files[0], output_file)
def call_bismark(self):
try:
bismark = BismarkAligner(self.dir_info.first_mate_trimmed_file_path,
self.dir_info.second_mate_trimmed_file_path,
self.dir_info.bismark_output_dir,
self.dir_info.bismark_output_dir)
command = bismark.generate_command()
run_shell_command(command)
except:
raise Exception("Couldn't use bismark for mate " + self.name() + ", please inspect the log file")
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 split_bam_by_chromosome(self):
input_file_path = self.latest_processed_file()
command = split_by_chromosome_command(input_file_path, self.dir_info.splitted_dir)
print(command, file=self.log_file_handler)
run_shell_command(command, redirect_output_path=self.dir_info.analysis_log_path, append=True)
def filter_quality(self):
input_file_path = self.latest_processed_file()
command = bamtools_clean_command(input_file_path, self.dir_info.filtered_bam_path)
print(command, file=self.log_file_handler)
run_shell_command(command, redirect_output_path=self.dir_info.analysis_log_path, append=True)
def call_deduplicate(self):
try:
command_str = deduplicate_bismark_command_str(self.dir_info.aligned_bam_path)
run_shell_command(command_str)
except:
raise Exception("Couldn't deduplicate for mate " + self.name + "! Please inspect the log file")
