def align_bwa_pe_lib(command, index, reads_file1, reads_file2, work_dir, log, threads=1): log.info("Aligning paired-end library") log.info("Left reads: " + reads_file1) log.info("Right reads: " + reads_file2) log.info("Output directory: " + work_dir) if os.path.exists(work_dir): shutil.rmtree(work_dir) os.makedirs(work_dir) log_file = os.path.join(work_dir, "output.log") err_log_file = os.path.join(work_dir, "err_output") result = os.path.join(work_dir, "alignment.sam") log.info("Starting alignment of reads using bwa. See detailed log in " + log_file) log.info("Starting read alignment. See detailed log in " + log_file) support.universal_sys_call([ command, "mem", "-t", str(threads), "-S", "-M", index, reads_file1, reads_file2 ], log, result, err_log_file) log.info("Done. See result in " + result) return result
def align_bwa_pe_lib(command, index, reads_file1, reads_file2, work_dir, log, threads=1): log.info("Aligning paired-end library") log.info("Left reads: " + reads_file1) log.info("Right reads: " + reads_file2) log.info("Output directory: " + work_dir) if os.path.exists(work_dir): shutil.rmtree(work_dir) os.makedirs(work_dir) log_file = os.path.join(work_dir, "output.log") err_log_file = os.path.join(work_dir, "err_output") result = os.path.join(work_dir, "alignment.sam") log.info("Starting alignment of reads using bwa. See detailed log in " + log_file) log.info("Starting read alignment. See detailed log in " + log_file) support.universal_sys_call([ command, "mem", index, reads_file1, reads_file2, "-t", str(threads), "-S", "-M" ], log, result, err_log_file) log.info("Done. See result in " + result) return result
def index_bwa(command, log, reference, work_dir, algorithm = "is"): if os.path.exists(work_dir): shutil.rmtree(work_dir) os.makedirs(work_dir) log.info("Constructing bwa index") index = os.path.join(work_dir, "index") log_file = os.path.join(work_dir, "output.log") err_log_file = os.path.join(work_dir, "err_output") log.info(" ".join([command, "index", "-a", algorithm, "-p", index, reference])) support.universal_sys_call([command, "index", "-a", algorithm, "-p", index, reference], log, log_file, err_log_file) log.info("Index constructed.") return index
def index_bwa(command, log, reference, work_dir, algorithm="is"): if os.path.exists(work_dir): shutil.rmtree(work_dir) os.makedirs(work_dir) log.info("Constructing bwa index") index = os.path.join(work_dir, "index") log_file = os.path.join(work_dir, "output.log") err_log_file = os.path.join(work_dir, "err_output") log.info(" ".join( [command, "index", "-a", algorithm, "-p", index, reference])) support.universal_sys_call( [command, "index", "-a", algorithm, "-p", index, reference], log, log_file, err_log_file) log.info("Index constructed.") return index