def extract_and_assemble(bam_files, genome_file, white_list_file, output_dir, assembly_function_list,
subsample_nb_read=None,rg_ids=[], adapter_file=None, force_merge=False):
logging.info('processing %s'%output_dir)
logging.info("--------------------------")
logging.info("Extract the reads from bam")
logging.info("--------------------------")
list_consensus=RAD_bam_to_fastq.read_white_list(white_list_file)
RAD_bam_to_fastq.extract_reads_from_all_bam_files_set_of_consensus(bam_files, list_consensus=list_consensus,
output_dir=output_dir, all_read1_consensus_file=genome_file )
logging.info("--------------")
logging.info("Assemble read2")
logging.info("--------------")
RAD_assemble_read2.run_all_fastq_files(output_dir, assembly_function_list, 600, force_merge=force_merge,
subsample_nb_read=subsample_nb_read, rg_ids=rg_ids, adapter_file=adapter_file)
logging.info("----------------------------")
logging.info("Extract read groups from bam")
logging.info("----------------------------")
all_read_groups=get_readgroup_from_bam(bam_files)
logging.info("-------------------------------------")
logging.info("Align both reads back to the assembly")
logging.info("-------------------------------------")
RAD_smalt_align_reads_back_to_consensus.run_all_fastq_files(output_dir, all_read_groups=all_read_groups, snp_call=True)
logging.info("---------------------")
logging.info("Merge all the results")
logging.info("---------------------")
RAD_merge_results.merge_results(output_dir)
logging.info("------------------------------")
logging.info("Get the summary of the results")
logging.info("------------------------------")
RAD_summarize_assembly.run_all_summaries(output_dir)
def main():
#initialize the logging
utils_logging.init_logging(logging.INFO)
#Setup options
optparser=_prepare_optparser()
(options,args) = optparser.parse_args()
#verify options
arg_pass=_verifyOption(options)
if not arg_pass:
logging.warning(optparser.get_usage())
logging.critical("Non valid arguments: exit")
sys.exit(1)
if options.debug:
utils_logging.init_logging(logging.DEBUG)
utils_logging.init_logging(output_level=None,
log_file_name=os.path.join(options.output_dir,"extract_and_assemble.log"))
bam_files=[options.bam_files]
if len(args)>0:
bam_files.extend(args)
all_assembler_to_try = options.assembler_name.split(',')
assembly_function_list=[]
for assembler_name in all_assembler_to_try:
assembly_function=RAD_assemble_read2.get_assembly_function(assembler_name)
assembly_function_list.append(assembly_function)
command_runner.set_command_to_run_localy()
if options.rg_ids:
rg_ids=options.rg_ids.split()
else:
rg_ids=[]
extract_and_assemble(bam_files, options.read1_consensus_file, options.white_list_file, options.output_dir,
assembly_function_list, subsample_nb_read=options.subsample_nb_read, rg_ids=rg_ids,
adapter_file=options.adapter_file)
