def illumina_files(runobj): utils = PipelneUtils() start = time.time() # illumina_files_demultiplex_only(runobj) illumina_files = IlluminaFiles(runobj) if runobj.do_perfect: # illumina_files.perfect_reads() script_file_name = illumina_files.perfect_reads_cluster() utils.run_until_done_on_cluster(script_file_name) else: # illumina_files.partial_overlap_reads() # pass # TODO: test utils.run_until_done_on_cluster(illumina_files.partial_overlap_reads_cluster()) script_file_name = illumina_files.partial_overlap_reads_cluster() utils.run_until_done_on_cluster(script_file_name) script_file_name = illumina_files.filter_mismatches_cluster() utils.run_until_done_on_cluster(script_file_name) # illumina_files.filter_mismatches() # illumina_files.uniq_fa() script_file_name = illumina_files.uniq_fa_cluster() utils.run_until_done_on_cluster(script_file_name) # illumina_chimera(runobj) elapsed = (time.time() - start) print "illumina_files time = %s" % str(elapsed)
def illumina_files_demultiplex_only(runobj): start = time.time() illumina_files = IlluminaFiles(runobj) illumina_files.open_dataset_files() illumina_files.split_files(compressed = runobj.compressed) elapsed = (time.time() - start) print "illumina_files demultiplex only time = %s" % str(elapsed)
def illumina_files_demultiplex_only(runobj): logger.debug("Start Demultiplex Illumina files by index/run_key/lane") start = time.time() illumina_files_inst = IlluminaFiles(runobj) illumina_files_inst.open_dataset_files() illumina_files_inst.split_files(compressed = runobj.compressed) elapsed = (time.time() - start) logger.debug("illumina_files demultiplex only time = %s" % str(elapsed))
def illumina_files(runobj): logger.debug("Start Overlap, filter and unique reads") utils = PipelneUtils() start = time.time() # illumina_files_demultiplex_only(runobj) illumina_files_inst = IlluminaFiles(runobj) if runobj.do_perfect: # illumina_files_inst.perfect_reads() script_file_name = illumina_files_inst.merge_perfect() utils.run_until_done_on_cluster(script_file_name) script_file_name = illumina_files_inst.trim_primers_perfect() utils.run_until_done_on_cluster(script_file_name) else: # illumina_files_inst.partial_overlap_reads() # pass # TODO: test utils.run_until_done_on_cluster(illumina_files_inst.partial_overlap_reads_cluster()) # TODO: add cutting to 251 script_file_name = illumina_files_inst.partial_overlap_reads_cluster() utils.run_until_done_on_cluster(script_file_name) script_file_name = illumina_files_inst.filter_mismatches_cluster() utils.run_until_done_on_cluster(script_file_name) # illumina_files_inst.filter_mismatches() # illumina_files_inst.uniq_fa() script_file_name = illumina_files_inst.uniq_fa_cluster() utils.run_until_done_on_cluster(script_file_name) # illumina_chimera(runobj) elapsed = (time.time() - start) logger.debug("illumina_files time = %s" % str(elapsed))
def illumina_files(runobj): start = time() # if os.uname()[1] == 'ashipunova.mbl.edu': # import shutil # shutil.rmtree('/Users/ashipunova/BPC/py_mbl_sequencing_pipeline/test/data/fastq/illumina_files_test/output/analysis/') illumina_files = IlluminaFiles(runobj) illumina_files.split_files(compressed=runobj.compressed) illumina_files.perfect_reads() illumina_files.uniq_fa() elapsed = time() - start print "illumina_files time = %s" % str(elapsed)
def illumina_files_demultiplex_only(runobj): logger.debug("Start Demultiplex Illumina files by index/run_key/lane") start = time.time() illumina_files_inst = IlluminaFiles(runobj) illumina_files_inst.open_dataset_files() illumina_files_inst.split_files(compressed=runobj.compressed) elapsed = (time.time() - start) logger.debug("illumina_files demultiplex only time = %s" % str(elapsed))
def illumina_files(runobj): start = time() illumina_files = IlluminaFiles(runobj) illumina_files.open_dataset_files() illumina_files.split_files(compressed = runobj.compressed) if runobj.do_perfect: illumina_files.perfect_reads() else: illumina_files.partial_overlap_reads() illumina_files.filter_mismatches() illumina_files.uniq_fa() elapsed = (time() - start) print "illumina_files time = %s" % str(elapsed)