original_docstring: 
          Load the input parameters from the argparse object given as parameter
          :param options: a Argparse object
          
docstring: Load the input parameters from the argparse object given as parameter
docstring_tokens: Load the input parameters from the argparse object given as parameter
code: def load_parameters(self, options):
          """
          Load the input parameters from the argparse object given as parameter
          :param options: a Argparse object
          """
          self.allowed_missed = options.demultiplexing_mismatches
          self.allowed_kmer = options.demultiplexing_kmer
          self.overhang = options.demultiplexing_overhang
          self.min_length_trimming = options.min_length_qual_trimming
          self.trimming_rv = options.mapping_rv_trimming
          self.min_quality_trimming = options.min_quality_trimming
          self.clean = options.no_clean_up
          self.barcode_start = options.demultiplexing_start
          self.threads = options.threads
          self.verbose = options.verbose
          self.ids = os.path.abspath(options.ids)
          if options.ref_map is not None:
              self.ref_map = os.path.abspath(options.ref_map)
          if options.ref_annotation is not None:
              self.ref_annotation = os.path.abspath(options.ref_annotation)
          self.expName = options.expName
          self.htseq_mode = options.htseq_mode
          self.htseq_no_ambiguous = options.htseq_no_ambiguous
          self.qual64 = options.qual_64
          if options.contaminant_index is not None:
              self.contaminant_index = os.path.abspath(options.contaminant_index)
          # Load the given path into the system PATH
          if options.bin_path is not None and os.path.isdir(options.bin_path):
              os.environ["PATH"] += os.pathsep + options.bin_path
          if options.log_file is not None:
              self.logfile = os.path.abspath(options.log_file)
          self.fastq_fw = os.path.abspath(options.fastq_files[0])
          self.fastq_rv = os.path.abspath(options.fastq_files[1])
          if options.output_folder is not None and os.path.isdir(options.output_folder):
              self.output_folder = os.path.abspath(options.output_folder)
          else:
              self.output_folder = os.path.abspath(os.getcwd())
          if options.temp_folder is not None and os.path.isdir(options.temp_folder):
              self.temp_folder = os.path.abspath(options.temp_folder)
          else:
              self.temp_folder = tempfile.mkdtemp(prefix="st_pipeline_temp")
          self.umi_allowed_mismatches = options.umi_allowed_mismatches
          self.umi_start_position = options.umi_start_position
          self.umi_end_position = options.umi_end_position
          self.keep_discarded_files = options.keep_discarded_files
          self.remove_polyA_distance = options.remove_polyA
          self.remove_polyT_distance = options.remove_polyT
          self.remove_polyG_distance = options.remove_polyG
          self.remove_polyC_distance = options.remove_polyC
          self.remove_polyN_distance = options.remove_polyN
          self.filter_AT_content = options.filter_AT_content
          self.filter_GC_content = options.filter_GC_content
          self.disable_multimap = options.disable_multimap
          self.disable_clipping = options.disable_clipping
          self.umi_cluster_algorithm = options.umi_cluster_algorithm
          self.min_intron_size = options.min_intron_size
          self.max_intron_size = options.max_intron_size
          self.umi_filter = options.umi_filter
          self.umi_filter_template = options.umi_filter_template.upper()
          self.compute_saturation = options.compute_saturation
          self.include_non_annotated = options.include_non_annotated
          self.inverse_trimming_rv = options.inverse_mapping_rv_trimming
          self.two_pass_mode = options.star_two_pass_mode
          self.strandness = options.strandness
          self.umi_quality_bases = options.umi_quality_bases
          self.umi_counting_offset = options.umi_counting_offset
          self.taggd_metric = options.demultiplexing_metric
          self.taggd_multiple_hits_keep_one = options.demultiplexing_multiple_hits_keep_one
          self.taggd_trim_sequences = options.demultiplexing_trim_sequences
          self.adaptor_missmatches = options.homopolymer_mismatches
          self.star_genome_loading = options.star_genome_loading
          self.star_sort_mem_limit = options.star_sort_mem_limit
          self.disable_barcode = options.disable_barcode
          self.disable_trimming = options.disable_trimming
          self.disable_mapping = options.disable_mapping
          self.disable_annotation = options.disable_annotation
          self.transcriptome = options.transcriptome
          self.disable_umi = options.disable_umi
          self.transcriptome = options.transcriptome
          if options.saturation_points is not None:
              self.saturation_points = [int(p) for p in options.saturation_points]
          # Assign class parameters to the QA stats object
          attributes = inspect.getmembers(self, lambda a: not (inspect.isroutine(a)))
          attributes_filtered = [a for a in attributes if not (a[0].startswith('__') and a[0].endswith('__'))]
          # Assign general parameters to the qa_stats object
          qa_stats.input_parameters = attributes_filtered
          qa_stats.annotation_tool = "htseq-count {}".format(getHTSeqCountVersion())
          qa_stats.demultiplex_tool = "Taggd {}".format(getTaggdCountVersion())
          qa_stats.pipeline_version = version_number
          qa_stats.mapper_tool = getSTARVersion()
code_tokens: def load_parameters ( self , options ) : self . allowed_missed = options . demultiplexing_mismatches self . allowed_kmer = options . demultiplexing_kmer self . overhang = options . demultiplexing_overhang self . min_length_trimming = options . min_length_qual_trimming self . trimming_rv = options . mapping_rv_trimming self . min_quality_trimming = options . min_quality_trimming self . clean = options . no_clean_up self . barcode_start = options . demultiplexing_start self . threads = options . threads self . verbose = options . verbose self . ids = os . path . abspath ( options . ids ) if options . ref_map is not None : self . ref_map = os . path . abspath ( options . ref_map ) if options . ref_annotation is not None : self . ref_annotation = os . path . abspath ( options . ref_annotation ) self . expName = options . expName self . htseq_mode = options . htseq_mode self . htseq_no_ambiguous = options . htseq_no_ambiguous self . qual64 = options . qual_64 if options . contaminant_index is not None : self . contaminant_index = os . path . abspath ( options . contaminant_index ) if options . bin_path is not None and os . path . isdir ( options . bin_path ) : os . environ [ "PATH" ] += os . pathsep + options . bin_path if options . log_file is not None : self . logfile = os . path . abspath ( options . log_file ) self . fastq_fw = os . path . abspath ( options . fastq_files [ 0 ] ) self . fastq_rv = os . path . abspath ( options . fastq_files [ 1 ] ) if options . output_folder is not None and os . path . isdir ( options . output_folder ) : self . output_folder = os . path . abspath ( options . output_folder ) else : self . output_folder = os . path . abspath ( os . getcwd ( ) ) if options . temp_folder is not None and os . path . isdir ( options . temp_folder ) : self . temp_folder = os . path . abspath ( options . temp_folder ) else : self . temp_folder = tempfile . mkdtemp ( prefix = "st_pipeline_temp" ) self . umi_allowed_mismatches = options . umi_allowed_mismatches self . umi_start_position = options . umi_start_position self . umi_end_position = options . umi_end_position self . keep_discarded_files = options . keep_discarded_files self . remove_polyA_distance = options . remove_polyA self . remove_polyT_distance = options . remove_polyT self . remove_polyG_distance = options . remove_polyG self . remove_polyC_distance = options . remove_polyC self . remove_polyN_distance = options . remove_polyN self . filter_AT_content = options . filter_AT_content self . filter_GC_content = options . filter_GC_content self . disable_multimap = options . disable_multimap self . disable_clipping = options . disable_clipping self . umi_cluster_algorithm = options . umi_cluster_algorithm self . min_intron_size = options . min_intron_size self . max_intron_size = options . max_intron_size self . umi_filter = options . umi_filter self . umi_filter_template = options . umi_filter_template . upper ( ) self . compute_saturation = options . compute_saturation self . include_non_annotated = options . include_non_annotated self . inverse_trimming_rv = options . inverse_mapping_rv_trimming self . two_pass_mode = options . star_two_pass_mode self . strandness = options . strandness self . umi_quality_bases = options . umi_quality_bases self . umi_counting_offset = options . umi_counting_offset self . taggd_metric = options . demultiplexing_metric self . taggd_multiple_hits_keep_one = options . demultiplexing_multiple_hits_keep_one self . taggd_trim_sequences = options . demultiplexing_trim_sequences self . adaptor_missmatches = options . homopolymer_mismatches self . star_genome_loading = options . star_genome_loading self . star_sort_mem_limit = options . star_sort_mem_limit self . disable_barcode = options . disable_barcode self . disable_trimming = options . disable_trimming self . disable_mapping = options . disable_mapping self . disable_annotation = options . disable_annotation self . transcriptome = options . transcriptome self . disable_umi = options . disable_umi self . transcriptome = options . transcriptome if options . saturation_points is not None : self . saturation_points = [ int ( p ) for p in options . saturation_points ] attributes = inspect . getmembers ( self , lambda a : not ( inspect . isroutine ( a ) ) ) attributes_filtered = [ a for a in attributes if not ( a [ 0 ] . startswith ( '__' ) and a [ 0 ] . endswith ( '__' ) ) ] qa_stats . input_parameters = attributes_filtered qa_stats . annotation_tool = "htseq-count {}" . format ( getHTSeqCountVersion ( ) ) qa_stats . demultiplex_tool = "Taggd {}" . format ( getTaggdCountVersion ( ) ) qa_stats . pipeline_version = version_number qa_stats . mapper_tool = getSTARVersion ( )
short_docstring: Load the input parameters from the argparse object given as parameter
short_docstring_tokens: Load the input parameters from the argparse object given as parameter
comment: """
          Load the input parameters from the argparse object given as parameter
          :param options: a Argparse object
          """$SEP$# Load the given path into the system PATH$SEP$# Assign class parameters to the QA stats object$SEP$# Assign general parameters to the qa_stats object