call_fastqc(self.dir_info.second, self.dir_info.fastqc_output_dir)
except:
raise Exception("Couldn't deduplicate for mate " + self.name() + "! Please inspect the log file")
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 pipeline(self, clean_output_dir=True):
self.setup(clean_output_dir)
self.call_fastqc()
self.call_trim_galore()
self.call_bismark()
self.call_deduplicate()
##self.extract_methylation()
def clean(self):
raise NotImplementedError()
if __name__ == "__main__":
handler = MateHandler()
test_mate = handler.get_mate_by_name("S112_tag_6_GCCAAT_L003_14101")
pipeline = MatePipeline(test_mate)
pipeline.pipeline()
