Index

_

__init__() (minorg.annotation.Annotation method) (minorg.annotation.Attributes method) (minorg.annotation.GFF method) (minorg.blast.BlastHSP method) (minorg.blast.BlastNR method) (minorg.blast.BlastResult method) (minorg.dynamic_logger.CustomFormatter method) (minorg.dynamic_logger.DynamicFileHandler method) (minorg.dynamic_logger.DynamicFileLogger method) (minorg.dynamic_logger.DynamicFileLoggerBase method) (minorg.dynamic_logger.DynamicFileParasiticSingleLogger method) (minorg.dynamic_logger.DynamicMultiFileHandler method) (minorg.dynamic_logger.DynamicMultiFileLogger method) (minorg.dynamic_logger.GroupLogger method) (minorg.dynamic_logger.HiddenAttribute method) (minorg.dynamic_logger.HiddenMethod method) (minorg.dynamic_logger.HiddenProperty method) (minorg.dynamic_logger.MultiChild method) (minorg.dynamic_logger.MultiHandler method) (minorg.dynamic_logger.MultiHandlerBase method) (minorg.dynamic_logger.MultiLogger method) (minorg.dynamic_logger.PublicAwareLogger method) (minorg.dynamic_logger.PublicLogger method) (minorg.extend_reference.UserAnnotation method) (minorg.filter_grna.Masked method) (minorg.grna.CheckObj method) (minorg.grna.gRNAHit method) (minorg.grna.gRNAHits method) (minorg.grna.gRNASeq method) (minorg.grna.Target method) (minorg.index.IndexedFasta method) (minorg.index.IndexedFile method) (minorg.index.rFaidx method) (minorg.InputFormatError method) (minorg.InvalidFile method) (minorg.InvalidPath method) (minorg.log.MINORgLogger method) (minorg.mafftcommandline_add.MafftCommandline method) (minorg.minimum_set.CollapsedgRNA method) (minorg.minimum_set.gRNA method) (minorg.minimum_set.SetOfCollapsedgRNA method) (minorg.MINORg.MINORg method) (minorg.MINORg.PathHandler method) (minorg.MINORgCLI.MINORgCLI method) (minorg.MINORgError method) (minorg.minweight_sc.e method) (minorg.minweight_sc.e1 method) (minorg.minweight_sc.e2 method) (minorg.minweight_sc.Q method) (minorg.minweight_sc.Set method) (minorg.minweight_sc.SetOfSets method) (minorg.pam.PAM method) (minorg.parse_config.Lookup method) (minorg.parse_config.OptionParams method) (minorg.parse_config.Param method) (minorg.parse_config.Params method) (minorg.reference.AnnotatedFasta method) (minorg.reference.AnnotatedFeature method) (minorg.reference.InvalidFeatureID method) (minorg.UnreadableFile method)

__iter__() (minorg.annotation.GFF method) _annotated_features (minorg.reference.AnnotatedFasta attribute) _args (minorg.MINORgCLI.MINORgCLI attribute) _attr_fields (minorg.annotation.GFF attribute) _attr_mod (minorg.annotation.GFF attribute) _cached_coverage (minorg.grna.gRNAHits attribute) _checks (minorg.grna.CheckObj attribute) _chunk_lines (minorg.annotation.GFF attribute) _data (minorg.annotation.GFF attribute) _fmt (minorg.annotation.GFF attribute) _fname (minorg.annotation.GFF attribute) _gff (minorg.reference.AnnotatedFasta attribute) _grnahits (minorg.grna.gRNASeq attribute) _gRNAseqs (minorg.grna.gRNAHits attribute) _hit_id (minorg.grna.gRNAHit attribute) _hits (minorg.grna.gRNAHits attribute) _id (minorg.grna.gRNASeq attribute) (minorg.grna.Target attribute) _indexed_file (minorg.annotation.GFF attribute) _kwargs (minorg.annotation.GFF attribute) _memsave (minorg.annotation.GFF attribute) _quiet (minorg.annotation.GFF attribute) _range (minorg.grna.gRNAHit attribute) _raw_args (minorg.MINORgCLI.MINORgCLI attribute) _sense (minorg.grna.Target attribute) _seq (minorg.grna.gRNASeq attribute) (minorg.grna.Target attribute) _seqids (minorg.annotation.GFF attribute) _strand (minorg.grna.gRNAHit attribute) (minorg.grna.Target attribute) _string (minorg.annotation.GFF attribute) _target (minorg.grna.gRNAHit attribute)

A

AacCas12b (in module minorg.pam) aaccas12b (in module minorg.pam) accept_feature_unknown (minorg.MINORg.MINORg attribute) accept_invalid (minorg.MINORg.MINORg attribute) accept_invalid_field (minorg.MINORg.MINORg attribute) active_handler_names (minorg.dynamic_logger.GroupLogger property) active_handlers (minorg.dynamic_logger.GroupLogger property) add() (minorg.minimum_set.CollapsedgRNA method) (minorg.minweight_sc.SetOfSets method) add_background() (minorg.MINORg.MINORg method) add_child() (minorg.dynamic_logger.MultiChild method) add_entry() (minorg.annotation.GFF method) add_file() (minorg.dynamic_logger.DynamicMultiFileHandler method) (minorg.dynamic_logger.DynamicMultiFileLogger method) add_file_handler (minorg.dynamic_logger.DynamicFileParasiticSingleLogger property) add_file_handler() (minorg.dynamic_logger.DynamicMultiFileLogger method) (minorg.dynamic_logger.GroupLogger method) add_format() (minorg.dynamic_logger.GroupLogger method) add_grna() (minorg.minimum_set.SetOfCollapsedgRNA method) add_group() (minorg.dynamic_logger.DynamicFileParasiticSingleLogger method) (minorg.dynamic_logger.GroupLogger method) add_handler() (minorg.dynamic_logger.DynamicFileParasiticSingleLogger method) (minorg.dynamic_logger.MultiHandlerBase method) add_hit() (minorg.grna.gRNAHits method) add_logger (minorg.dynamic_logger.DynamicFileParasiticSingleLogger property) add_logger() (minorg.dynamic_logger.MultiLogger method) add_query() (minorg.MINORg.MINORg method) add_reference() (minorg.MINORg.MINORg method) add_seq() (minorg.grna.gRNAHits method) add_stream_handler (minorg.dynamic_logger.DynamicFileParasiticSingleLogger property) add_stream_handler() (minorg.dynamic_logger.GroupLogger method) addHandler() (minorg.dynamic_logger.DynamicFileParasiticSingleLogger method) (minorg.dynamic_logger.PublicLogger method) adj_feature_range() (minorg.reference.AnnotatedFeature method) adj_range() (minorg.grna.gRNAHit method) adj_subfeature_range() (minorg.reference.AnnotatedFeature method) adjusted_feature_ranges() (in module minorg.functions)

adjusted_pos() (in module minorg.functions) adjusted_ranges() (in module minorg.functions) align_reference() (minorg.MINORg.MINORg method) align_reference_and_targets() (minorg.MINORg.MINORg method) all_best_nr() (in module minorg.minimum_set) all_best_pos() (in module minorg.minimum_set) all_checks_passed() (minorg.grna.CheckObj method) all_handlers (minorg.dynamic_logger.GroupLogger property) (minorg.dynamic_logger.MultiHandlerBase property) all_not_empty() (minorg.minimum_set.SetOfCollapsedgRNA method) all_target_len_valid() (minorg.grna.gRNAHits method) all_valid_checks_passed() (minorg.grna.CheckObj method) aln_to_annotation() (in module minorg.extend_reference) annotated_fasta (minorg.reference.AnnotatedFeature attribute) annotated_feature() (minorg.reference.AnnotatedFasta method) AnnotatedFasta (class in minorg.reference) AnnotatedFeature (class in minorg.reference) Annotation (class in minorg.annotation) annotation (minorg.reference.AnnotatedFasta attribute) (minorg.reference.AnnotatedFeature attribute) annotations (minorg.MINORg.MINORg property) app() (in module minorg.console) append() (in module minorg.functions) append_time() (in module minorg.dynamic_logger) approx_min_SC() (in module minorg.minweight_sc) argmin() (in module minorg.minweight_sc) args (minorg.MINORgCLI.MINORgCLI property) assemblies (minorg.MINORg.MINORg property) assembly (minorg.reference.AnnotatedFasta attribute) assign_alias() (in module minorg.functions) assign_gRNAseq_id() (minorg.grna.gRNAHits method) assign_seqid() (minorg.grna.gRNAHits method) attr_mod (minorg.reference.AnnotatedFasta attribute) attr_mod_callback() (minorg.MINORgCLI.MINORgCLI method) attr_mods (minorg.MINORg.MINORg property) Attributes (class in minorg.annotation) auto (minorg.MINORg.MINORg attribute) auto_update_files (minorg.MINORg.MINORg attribute)

B

background_check (minorg.MINORgCLI.MINORgCLI attribute) bedtools (minorg.MINORg.MINORg attribute) BhCas12b (in module minorg.pam) bhcas12b (in module minorg.pam) blast() (in module minorg.blast) (minorg.blast.BlastNR method) blast6() (in module minorg.blast) blast6multi() (in module minorg.blast)

blast6threshold() (in module minorg.blast) blast6topn() (in module minorg.blast) blast_mask() (in module minorg.filter_grna) BlastHSP (class in minorg.blast) blastn (minorg.MINORg.MINORg attribute) BlastNR (class in minorg.blast) BlastResult (class in minorg.blast) btop (minorg.blast.BlastHSP property)

C

C (minorg.minweight_sc.e property) Cas12a (in module minorg.pam) cas12a (in module minorg.pam) cat_files() (in module minorg.functions) check() (minorg.grna.CheckObj method) check_exists() (minorg.grna.CheckObj method) check_filter_args() (minorg.MINORgCLI.MINORgCLI method) check_grna_args() (minorg.MINORgCLI.MINORgCLI method) check_id_before_merge (minorg.MINORg.MINORg attribute) check_names (minorg.grna.CheckObj property) (minorg.grna.gRNAHits property) check_names() (minorg.MINORg.MINORg method) check_names_hits (minorg.grna.gRNAHits property) check_names_seqs (minorg.grna.gRNAHits property) check_path_and_return() (in module minorg.dynamic_logger) check_recip (minorg.MINORg.MINORg attribute) (minorg.MINORg.MINORg property) check_reference_args() (minorg.MINORgCLI.MINORgCLI method) check_seq_args() (minorg.MINORgCLI.MINORgCLI method) CheckObj (class in minorg.grna) children (minorg.dynamic_logger.MultiChild property) children_map (minorg.dynamic_logger.MultiChild property) children_names (minorg.dynamic_logger.MultiChild property) CjCas9 (in module minorg.pam) cjcas9 (in module minorg.pam) cleanup() (minorg.MINORgCLI.MINORgCLI method) clear_checks() (minorg.grna.CheckObj method) (minorg.grna.gRNAHits method)

clear_reference() (minorg.MINORg.MINORg method) closer_to_5prime() (minorg.minimum_set.gRNA method) cluster_aliases (minorg.MINORgCLI.MINORgCLI attribute) cluster_set (minorg.MINORgCLI.MINORgCLI attribute) cluster_set_callback() (minorg.MINORgCLI.MINORgCLI method) clusters_callback() (minorg.MINORgCLI.MINORgCLI method) cmd_args (minorg.MINORgCLI.MINORgCLI property) collapse() (minorg.grna.gRNAHits method) collapse_identical_seqs() (in module minorg.fasta) collapse_query() (minorg.blast.BlastNR method) CollapsedgRNA (class in minorg.minimum_set) common_targets() (minorg.minimum_set.gRNA method) config (minorg.MINORgCLI.MINORgCLI attribute) convert_range() (in module minorg.functions) (minorg.reference.AnnotatedFeature method) copy() (minorg.grna.gRNAHits method) (minorg.minimum_set.CollapsedgRNA method) (minorg.minimum_set.SetOfCollapsedgRNA method) (minorg.minweight_sc.e method) (minorg.minweight_sc.Set method) (minorg.minweight_sc.SetOfSets method) copy_annotation() (minorg.reference.AnnotatedFeature method) copy_args() (minorg.MINORgCLI.MINORgCLI method) coverage (minorg.grna.gRNASeq property) (minorg.minimum_set.gRNA property) crosstalk (minorg.dynamic_logger.DynamicMultiFileLogger property) (minorg.dynamic_logger.PublicAwareLogger property) custom_default() (minorg.parse_config.Param method) CustomFormatter (class in minorg.dynamic_logger)

D

db (minorg.MINORg.MINORg attribute) db_callback() (minorg.MINORgCLI.MINORgCLI method) dict_to_fasta() (in module minorg.fasta) dict_to_SeqRecordList() (in module minorg.fasta) directory (minorg.MINORg.MINORg attribute) (minorg.MINORg.PathHandler attribute) domain_callback() (minorg.MINORgCLI.MINORgCLI method) domain_name (minorg.MINORg.MINORg attribute) (minorg.MINORg.MINORg property)

DuplicateName DuplicateObject DuplicateWarning DynamicFileHandler (class in minorg.dynamic_logger) DynamicFileLogger (class in minorg.dynamic_logger) DynamicFileLoggerBase (class in minorg.dynamic_logger) DynamicFileParasiticSingleLogger (class in minorg.dynamic_logger) DynamicMultiFileHandler (class in minorg.dynamic_logger) DynamicMultiFileLogger (class in minorg.dynamic_logger)

E

e (class in minorg.minweight_sc) e1 (class in minorg.minweight_sc) e2 (class in minorg.minweight_sc) elements (minorg.minweight_sc.SetOfSets property) emit() (minorg.dynamic_logger.DynamicMultiFileHandler method) empty_collapsed_grna() (minorg.minimum_set.SetOfCollapsedgRNA method) empty_copy() (minorg.annotation.GFF method) empty_file() (in module minorg.functions) end (minorg.filter_grna.Masked property) (minorg.grna.gRNAHit property) enum_approx_order_SC() (in module minorg.minweight_sc)

exclude (minorg.MINORg.MINORg attribute) expand() (minorg.blast.BlastNR method) expand_ambiguous() (minorg.pam.PAM method) expand_btop_str() (minorg.blast.BlastHSP method) expand_btop_tuple() (minorg.blast.BlastHSP method) extend_reference() (in module minorg.extend_reference) (minorg.MINORg.MINORg method) extend_reference_cli() (in module minorg.extend_reference) extract_annotation() (in module minorg.extend_reference) extract_min() (minorg.minweight_sc.Q method) extract_ranges() (in module minorg.fasta)

F

fasta (minorg.reference.AnnotatedFasta attribute) fasta_to_dict() (in module minorg.fasta) feature (minorg.MINORg.MINORg attribute) (minorg.MINORg.MINORg property) feature_check (minorg.MINORgCLI.MINORgCLI attribute) feature_pos() (minorg.reference.AnnotatedFasta method) feature_range() (minorg.reference.AnnotatedFasta method) (minorg.reference.AnnotatedFeature method) features (minorg.MINORg.MINORg property) file_ends_with_newline() (in module minorg.functions) file_handler_map (minorg.dynamic_logger.MultiHandlerBase property) file_handler_names (minorg.dynamic_logger.GroupLogger property) (minorg.dynamic_logger.MultiHandlerBase property) file_handlers (minorg.dynamic_logger.GroupLogger property) (minorg.dynamic_logger.MultiHandlerBase property) file_in_use() (in module minorg.dynamic_logger) filename (minorg.dynamic_logger.DynamicFileLoggerBase property) fill_template() (in module minorg.functions) filter() (minorg.MINORg.MINORg method) filter_background() (minorg.MINORg.MINORg method) filter_background_imap() (in module minorg.filter_grna) filter_background_multiindv() (in module minorg.filter_grna) filter_blast6_threshold() (in module minorg.blast) filter_blast6_topn() (in module minorg.blast) filter_children() (minorg.dynamic_logger.MultiChild method) filter_children_map() (minorg.dynamic_logger.MultiChild method) filter_children_names() (minorg.dynamic_logger.MultiChild method) filter_exclude() (minorg.MINORg.MINORg method) filter_feature() (minorg.MINORg.MINORg method) filter_gc() (minorg.MINORg.MINORg method)

filter_grna() (in module minorg.console) filter_hits() (minorg.grna.gRNAHits method) filter_hits_all_checks_passed() (minorg.grna.gRNAHits method) filter_hits_some_checks_passed() (minorg.grna.gRNAHits method) filter_min_cds_len() (in module minorg.extract_homologue) filter_rpsblast_for_domain() (in module minorg.blast) filter_seqs() (minorg.grna.gRNAHits method) filter_seqs_all_checks_passed() (minorg.grna.gRNAHits method) filter_seqs_some_checks_passed() (minorg.grna.gRNAHits method) final_fasta (minorg.MINORg.MINORg attribute) final_map (minorg.MINORg.MINORg attribute) find_executable() (in module minorg.parse_config) find_homologue_imap() (in module minorg.extract_homologue) find_identical_in_fasta() (in module minorg.fasta) find_multi_gRNA() (in module minorg.generate_grna) five_prime() (minorg.pam.PAM method) five_prime_maxlen() (minorg.pam.PAM method) flank() (minorg.grna.gRNAHit method) flatten_gRNAseqs() (minorg.grna.gRNAHits method) flatten_hits() (minorg.grna.gRNAHits method) fname() (minorg.parse_config.Lookup method) format (minorg.dynamic_logger.GroupLogger property) format() (minorg.dynamic_logger.CustomFormatter method) format_children (minorg.dynamic_logger.GroupLogger property) format_log() (minorg.parse_config.Param method) format_map (minorg.dynamic_logger.GroupLogger property) format_names (minorg.dynamic_logger.GroupLogger property) formats (minorg.dynamic_logger.GroupLogger property) full() (in module minorg.console) (minorg.MINORg.MINORg method)

G

gc_check (minorg.MINORgCLI.MINORgCLI attribute) gc_content() (in module minorg.functions) gc_max (minorg.MINORg.MINORg attribute) gc_min (minorg.MINORg.MINORg attribute) gene_sets (minorg.MINORgCLI.MINORgCLI attribute) generate_attr() (minorg.annotation.Annotation method) (minorg.extend_reference.UserAnnotation method) generate_bed() (minorg.annotation.Annotation method) (minorg.extend_reference.UserAnnotation method) generate_gff() (minorg.annotation.Annotation method) (minorg.extend_reference.UserAnnotation method) generate_grna() (in module minorg.console) generate_grna_set() (minorg.minimum_set.SetOfCollapsedgRNA method) generate_grna_sets() (minorg.minimum_set.SetOfCollapsedgRNA method) generate_ref_gene_cds() (minorg.MINORg.MINORg method) generate_str() (minorg.annotation.Annotation method) (minorg.extend_reference.UserAnnotation method) genes (minorg.MINORg.MINORg attribute) (minorg.MINORg.MINORg property) genetic_code (minorg.reference.AnnotatedFasta attribute) genetic_code_callback() (minorg.MINORgCLI.MINORgCLI method) genome_aliases (minorg.MINORgCLI.MINORgCLI attribute) genome_set (minorg.MINORgCLI.MINORgCLI attribute) genome_set_callback() (minorg.MINORgCLI.MINORgCLI method) get() (minorg.annotation.Annotation method) (minorg.annotation.Attributes method) (minorg.minweight_sc.SetOfSets method) get_attr() (minorg.annotation.Annotation method) get_child() (minorg.dynamic_logger.MultiChild method) get_child_name() (minorg.dynamic_logger.MultiChild method) get_cluster_genes() (minorg.MINORgCLI.MINORgCLI method) get_count_dict() (in module minorg.functions) get_dat() (in module minorg.functions) get_feature_seq() (minorg.reference.AnnotatedFasta method) get_features() (minorg.annotation.GFF method) get_features_and_subfeatures() (minorg.annotation.GFF method) get_gRNAseq_by_id() (minorg.grna.gRNAHits method) get_gRNAseq_by_seq() (minorg.grna.gRNAHits method)

get_gRNAseqs_by_id() (minorg.grna.gRNAHits method) get_gRNAseqs_by_seq() (minorg.grna.gRNAHits method) get_handler() (minorg.dynamic_logger.GroupLogger method) get_hits() (minorg.grna.gRNAHits method) get_i() (minorg.annotation.GFF method) get_i_raw() (minorg.annotation.GFF method) get_id() (minorg.annotation.GFF method) get_line() (minorg.index.IndexedFile method) get_logger() (minorg.dynamic_logger.MultiLogger method) get_merged_seqs() (in module minorg.extract_homologue) get_param() (minorg.parse_config.Params method) get_recursively() (in module minorg.annotation) (in module minorg.extend_reference) get_ref_seqid() (minorg.MINORg.MINORg method) get_reference_seq() (minorg.MINORg.MINORg method) get_seq() (minorg.index.IndexedFasta method) (minorg.reference.AnnotatedFeature method) get_spliced_seq() (minorg.index.IndexedFasta method) get_subfeatures() (minorg.annotation.GFF method) get_subfeatures_full() (minorg.annotation.GFF method) get_val_default() (in module minorg.parse_config) get_val_none() (in module minorg.parse_config) GFF (class in minorg.annotation) gff (minorg.reference.AnnotatedFasta attribute) greedy (minorg.parse_config.SetCoverAlgo attribute) gRNA (class in minorg.minimum_set) grna() (minorg.MINORg.MINORg method) gRNA_length (minorg.pam.PAM attribute) gRNAHit (class in minorg.grna) gRNAHits (class in minorg.grna) grnahits (minorg.grna.gRNASeq property) gRNASeq (class in minorg.grna) gRNAseqs (minorg.grna.gRNAHits property) group_by_gene() (in module minorg.extend_reference) group_names (minorg.dynamic_logger.DynamicFileParasiticSingleLogger property) (minorg.dynamic_logger.GroupLogger property) GroupLogger (class in minorg.dynamic_logger) groups (minorg.dynamic_logger.DynamicFileParasiticSingleLogger property) groups() (minorg.dynamic_logger.GroupLogger method)

H

handler (minorg.dynamic_logger.GroupLogger property) handler_children (minorg.dynamic_logger.GroupLogger property) handler_group_names (minorg.dynamic_logger.DynamicFileParasiticSingleLogger property) handler_groups (minorg.dynamic_logger.DynamicFileParasiticSingleLogger property) handler_map (minorg.dynamic_logger.GroupLogger property) (minorg.dynamic_logger.MultiHandlerBase property) handler_names (minorg.dynamic_logger.GroupLogger property) (minorg.dynamic_logger.MultiHandlerBase property) handlers (minorg.dynamic_logger.DynamicFileLogger property) (minorg.dynamic_logger.DynamicMultiFileLogger property) (minorg.dynamic_logger.MultiHandler property)

has_attr() (minorg.annotation.Annotation method) (minorg.annotation.Attributes method) has_file() (minorg.annotation.GFF method) help() (minorg.parse_config.Param method) HiddenAttribute HiddenMethod HiddenProperty hit_check_exists() (minorg.grna.gRNAHits method) hit_id (minorg.grna.gRNAHit property) hits (minorg.grna.gRNAHits property) (minorg.grna.gRNASeq property) (minorg.minimum_set.gRNA property)

I

id (minorg.grna.gRNASeq property) (minorg.grna.Target property) (minorg.minimum_set.gRNA property) imap_progress() (in module minorg.functions) index() (minorg.annotation.GFF method) (minorg.index.IndexedFile method) index_seqids() (minorg.annotation.GFF method) IndexedFasta (class in minorg.index) IndexedFile (class in minorg.index) indexname (minorg.index.rFaidx property) infer_full() (minorg.pam.PAM method) InputFormatError intersection() (minorg.minweight_sc.SetOfSets method) InvalidArgs InvalidFeatureID InvalidFile InvalidName InvalidPath InvalidType inverse_dict() (in module minorg.parse_config) invert_attr_fields() (minorg.annotation.GFF method)

is_attr() (minorg.annotation.Annotation method) (minorg.annotation.Attributes method) is_bed() (minorg.annotation.GFF method) is_child() (minorg.dynamic_logger.MultiChild method) is_child_class() (minorg.dynamic_logger.MultiChild method) is_empty() (minorg.minimum_set.CollapsedgRNA method) (minorg.minweight_sc.Q method) is_empty_file() (in module minorg.functions) is_enabled_for() (minorg.dynamic_logger.DynamicFileLoggerBase method) (minorg.dynamic_logger.DynamicFileParasiticSingleLogger method) is_gff() (minorg.annotation.GFF method) is_indexed() (minorg.annotation.GFF method) is_logger() (minorg.dynamic_logger.MultiLogger method) is_offtarget_aln() (minorg.MINORg.MINORg method) is_offtarget_hit() (minorg.MINORg.MINORg method) is_offtarget_pam() (minorg.MINORg.MINORg method) is_offtarget_pos() (minorg.MINORg.MINORg method) is_range() (in module minorg.functions) is_user_set() (minorg.MINORgCLI.MINORgCLI method) iter_fasta_raw() (minorg.annotation.GFF method) iter_raw() (minorg.annotation.GFF method)

K

keep_on_crash (minorg.MINORgCLI.MINORgCLI attribute)

keep_tmp (minorg.MINORg.PathHandler attribute)

L

lar (minorg.parse_config.SetCoverAlgo attribute) last_line() (in module minorg.functions) least_5prime() (minorg.minimum_set.CollapsedgRNA method) length (minorg.MINORg.MINORg attribute) (minorg.MINORg.MINORg property) (minorg.reference.AnnotatedFeature property) level (minorg.dynamic_logger.DynamicFileLoggerBase property) (minorg.dynamic_logger.DynamicFileParasiticSingleLogger property)

limited_minweight_SC() (in module minorg.minimum_set) limited_optimal_SC() (in module minorg.minimum_set) logger_map (minorg.dynamic_logger.MultiLogger property) logger_names (minorg.dynamic_logger.MultiLogger property) loggers (minorg.dynamic_logger.MultiLogger property) long (minorg.parse_config.Param property) Lookup (class in minorg.parse_config) lookup() (minorg.parse_config.Lookup method) lookup_inv() (minorg.parse_config.Lookup method)

M

mafft (minorg.MINORg.MINORg attribute) MafftCommandline (class in minorg.mafftcommandline_add) main() (in module minorg.console) make_annotation_from_str_gen() (minorg.annotation.GFF method) make_custom_get() (in module minorg.functions) make_examples() (in module minorg.minweight_sc) make_examples_2() (in module minorg.minweight_sc) make_genomes_callback() (minorg.MINORgCLI.MINORgCLI method) make_get_minimum_set() (in module minorg.minimum_set) make_local_print() (in module minorg.functions) make_print_overwrite_multi_preindent() (in module minorg.display) make_print_preindent() (in module minorg.display) make_set_cover_nr() (in module minorg.minimum_set) make_set_cover_pos() (in module minorg.minimum_set) make_target_feature_ranges_function() (in module minorg.filter_grna) manual_check_prompt() (in module minorg.minimum_set) map_field_name() (minorg.annotation.Attributes method) mask (minorg.MINORg.MINORg attribute) mask_and_generate_outside() (in module minorg.filter_grna) mask_gene_sets (minorg.MINORgCLI.MINORgCLI attribute) mask_identical() (in module minorg.filter_grna) Masked (class in minorg.filter_grna) masked (minorg.filter_grna.Masked property) master_prefix (minorg.MINORgCLI.MINORgCLI attribute) max_coverage (minorg.minimum_set.SetOfCollapsedgRNA property) max_insertion (minorg.MINORg.MINORg attribute) members_callback() (minorg.MINORgCLI.MINORgCLI method) memsave (minorg.reference.AnnotatedFasta attribute) merge_hits() (in module minorg.extract_homologue) merge_hits_and_filter() (in module minorg.extract_homologue) merge_within (minorg.MINORg.MINORg attribute) min_coverage (minorg.minimum_set.SetOfCollapsedgRNA property) min_within_fraction (minorg.MINORg.MINORg attribute) min_within_n (minorg.MINORg.MINORg attribute) mincdslen (minorg.MINORg.MINORg attribute) minid (minorg.MINORg.MINORg attribute) minimumset() (in module minorg.console) (minorg.MINORg.MINORg method) (minorg.MINORgCLI.MINORgCLI method) minlen (minorg.MINORg.MINORg attribute) minorg module MINORg (class in minorg.MINORg) minorg.annotation module minorg.blast module minorg.console module minorg.constants module minorg.display module minorg.dynamic_logger module minorg.extend_reference module minorg.extract_homologue module minorg.fasta module minorg.filter_grna module minorg.functions module minorg.generate_grna module

minorg.grna module minorg.index module minorg.log module minorg.mafftcommandline_add module minorg.main module minorg.minimum_set module minorg.MINORg module minorg.MINORgCLI module minorg.minweight_sc module minorg.pam module minorg.parse_config module minorg.reference module MINORgCLI (class in minorg.MINORgCLI) MINORgError MINORgLogger (class in minorg.log) MINORgWarning mkdir() (minorg.MINORg.PathHandler method) mkfname() (minorg.MINORg.MINORg method) (minorg.MINORg.PathHandler method) module minorg minorg.annotation minorg.blast minorg.console minorg.constants minorg.display minorg.dynamic_logger minorg.extend_reference minorg.extract_homologue minorg.fasta minorg.filter_grna minorg.functions minorg.generate_grna minorg.grna minorg.index minorg.log minorg.mafftcommandline_add minorg.main minorg.minimum_set minorg.MINORg minorg.MINORgCLI minorg.minweight_sc minorg.pam minorg.parse_config minorg.reference molecule (minorg.filter_grna.Masked property) most_5prime() (minorg.minimum_set.CollapsedgRNA method) move() (minorg.log.MINORgLogger method) MultiChild (class in minorg.dynamic_logger) MultiHandler (class in minorg.dynamic_logger) MultiHandlerBase (class in minorg.dynamic_logger) MultiLogger (class in minorg.dynamic_logger) mv_dir_overwrite() (in module minorg.parse_config)

N

N_trailing_newlines() (in module minorg.functions) name (minorg.reference.AnnotatedFasta attribute) name_available() (minorg.dynamic_logger.MultiChild method) new_dirs (minorg.MINORg.PathHandler attribute) NmeCas9 (in module minorg.pam) nmecas9 (in module minorg.pam) non_negative_callback() (in module minorg.console)

non_string_iter() (in module minorg.functions) num_deletion() (minorg.blast.BlastHSP method) num_gap() (minorg.blast.BlastHSP method) num_grna() (minorg.minimum_set.CollapsedgRNA method) num_insertion() (minorg.blast.BlastHSP method) num_lines() (in module minorg.functions) num_mismatch() (minorg.blast.BlastHSP method)

O

offtarget (minorg.MINORg.MINORg attribute) (minorg.MINORg.MINORg property) OptionParams (class in minorg.parse_config) orphan_handler_names (minorg.dynamic_logger.GroupLogger property) orphan_handlers (minorg.dynamic_logger.GroupLogger property) ot_gap (minorg.MINORg.MINORg attribute) ot_mismatch (minorg.MINORg.MINORg attribute) ot_pam (minorg.MINORg.MINORg property)

ot_pamless (minorg.MINORg.MINORg attribute) ot_pattern (minorg.MINORg.MINORg attribute) (minorg.MINORg.MINORg property) ot_unaligned_as_gap (minorg.MINORg.MINORg attribute) (minorg.MINORg.MINORg property) ot_unaligned_as_mismatch (minorg.MINORg.MINORg attribute) (minorg.MINORg.MINORg property) out_dir (minorg.MINORg.PathHandler attribute)

P

PAM (class in minorg.pam) pam (minorg.MINORg.MINORg attribute) (minorg.MINORg.MINORg property) (minorg.pam.PAM attribute) Param (class in minorg.parse_config) Params (class in minorg.parse_config) parent_sense() (minorg.grna.gRNAHit method) (minorg.grna.Target method) parse() (minorg.annotation.GFF method) (minorg.pam.PAM method) parse_args() (minorg.MINORgCLI.MINORgCLI method) parse_attr_mod() (minorg.parse_config.Params method) parse_attr_mod_sdict() (in module minorg.parse_config) parse_btop() (minorg.blast.BlastHSP method) parse_cluster() (minorg.MINORgCLI.MINORgCLI method) parse_domain() (minorg.parse_config.Params method) parse_fasta() (minorg.annotation.GFF method) parse_filter_args() (minorg.MINORgCLI.MINORgCLI method) parse_from_dict() (minorg.grna.gRNAHits method) parse_from_file() (minorg.parse_config.Lookup method) parse_from_mapping() (minorg.grna.gRNAHits method) parse_from_string() (minorg.parse_config.Lookup method) parse_full_args() (minorg.MINORgCLI.MINORgCLI method) parse_genes() (minorg.MINORgCLI.MINORgCLI method) parse_genes_for_filter() (minorg.MINORgCLI.MINORgCLI method) parse_get_data() (in module minorg.functions) parse_gff() (minorg.reference.AnnotatedFasta method) parse_grna_args() (minorg.MINORgCLI.MINORgCLI method) parse_grna_map_from_file() (minorg.MINORg.MINORg method)

parse_lookup() (in module minorg.MINORg) parse_minimumset_args() (minorg.MINORgCLI.MINORgCLI method) parse_multiline_inv_sdict() (in module minorg.parse_config) parse_multiline_multikey_sdict() (in module minorg.parse_config) parse_multiline_sdict() (in module minorg.parse_config) parse_ot_pattern() (minorg.MINORgCLI.MINORgCLI method) parse_PAM() (minorg.MINORgCLI.MINORgCLI method) parse_sep_sdict() (in module minorg.parse_config) parse_seq_args() (minorg.MINORgCLI.MINORgCLI method) pass_fasta (minorg.MINORg.MINORg attribute) pass_map (minorg.MINORg.MINORg attribute) passed_grna (minorg.MINORg.MINORg property) PathHandler (class in minorg.MINORg) plus (minorg.annotation.Annotation property) pos_to_ranges() (in module minorg.functions) positive_callback() (in module minorg.console) prefix (minorg.MINORg.MINORg attribute) prepend() (in module minorg.functions) prepend_line() (in module minorg.functions) print() (minorg.parse_config.Lookup method) print_indent() (in module minorg.display) print_message() (minorg.MINORgError method) print_overwrite_multi() (in module minorg.display) prioritise_nr (minorg.MINORg.MINORg property) prioritise_pos (minorg.MINORg.MINORg property) prioritize_nr (minorg.MINORg.MINORg property) prioritize_pos (minorg.MINORg.MINORg property) pssm_ids (minorg.MINORg.MINORg attribute) PublicAwareLogger (class in minorg.dynamic_logger) PublicLogger (class in minorg.dynamic_logger)

Q

Q (class in minorg.minweight_sc)

query_map (minorg.MINORg.MINORg property) query_reference (minorg.MINORg.MINORg attribute)

R

range (minorg.grna.gRNAHit property) range_from_genomic() (minorg.reference.AnnotatedFeature method) range_in_genomic_coords() (minorg.reference.AnnotatedFeature method) range_to_genomic() (minorg.reference.AnnotatedFeature method) ranges_intersect() (in module minorg.functions) ranges_subtract() (in module minorg.functions) ranges_to_pos() (in module minorg.functions) ranges_union() (in module minorg.functions) raw_pam (minorg.pam.PAM attribute) read_file() (minorg.annotation.GFF method) recip_blast() (in module minorg.extract_homologue) recip_blast_multiref() (in module minorg.extract_homologue) reduce_annotation() (minorg.reference.AnnotatedFasta method) redundancy (minorg.minweight_sc.SetOfSets property) reference (minorg.MINORg.MINORg property) reference_aliases (minorg.MINORgCLI.MINORgCLI attribute) reference_required() (minorg.MINORgCLI.MINORgCLI method) reference_set (minorg.MINORgCLI.MINORgCLI attribute) reference_set_callback() (minorg.MINORgCLI.MINORgCLI method) references_callback() (minorg.MINORgCLI.MINORgCLI method) regex() (minorg.pam.PAM method) relative_5prime_pos (minorg.minimum_set.gRNA property) relative_distance_to_5prime() (minorg.minimum_set.gRNA method) relax_recip (minorg.MINORg.MINORg attribute) remote_rps (minorg.MINORg.MINORg attribute) remove() (minorg.minimum_set.CollapsedgRNA method) (minorg.minweight_sc.e method) (minorg.minweight_sc.SetOfSets method) remove_background() (minorg.MINORg.MINORg method)

remove_child() (minorg.dynamic_logger.MultiChild method) remove_empty() (minorg.minimum_set.SetOfCollapsedgRNA method) remove_file() (minorg.dynamic_logger.DynamicMultiFileHandler method) remove_grna() (minorg.minimum_set.SetOfCollapsedgRNA method) remove_group() (minorg.dynamic_logger.DynamicFileParasiticSingleLogger method) (minorg.dynamic_logger.GroupLogger method) remove_handler() (minorg.dynamic_logger.DynamicFileParasiticSingleLogger method) (minorg.dynamic_logger.MultiHandlerBase method) remove_logger (minorg.dynamic_logger.DynamicFileParasiticSingleLogger property) remove_logger() (minorg.dynamic_logger.MultiLogger method) remove_non_max_bitscore() (in module minorg.extract_homologue) remove_query() (minorg.MINORg.MINORg method) remove_reference() (minorg.MINORg.MINORg method) remove_seqs() (minorg.grna.gRNAHits method) remove_tmp() (minorg.annotation.GFF method) removeHandler() (minorg.dynamic_logger.DynamicFileParasiticSingleLogger method) (minorg.dynamic_logger.PublicLogger method) rename_grna() (minorg.MINORg.MINORg method) rename_seqs() (minorg.grna.gRNAHits method) reserve_fname() (minorg.MINORg.PathHandler method) ReservedName reset_prefix() (minorg.MINORgCLI.MINORgCLI method) resolve() (minorg.MINORg.MINORg method) (minorg.MINORg.PathHandler method) results_fname() (minorg.MINORg.MINORg method) reverse_range (minorg.grna.gRNAHit property) rFaidx (class in minorg.index) rm_tmpfiles() (minorg.MINORg.PathHandler method) rpsblast (minorg.MINORg.MINORg attribute)

S

SaCas9N (in module minorg.pam) sacas9n (in module minorg.pam) SaCas9T (in module minorg.pam) sacas9t (in module minorg.pam) Sc (minorg.minweight_sc.e2 property) screen_reference (minorg.MINORg.MINORg attribute) sense (minorg.grna.Target property) seq (minorg.grna.gRNASeq property) (minorg.grna.Target property) (minorg.minimum_set.gRNA property) seq() (in module minorg.console) (minorg.MINORg.MINORg method) seq_check_exists() (minorg.grna.gRNAHits method) seqs (minorg.grna.gRNAHits property) Set (class in minorg.minweight_sc) set_all_seqs_check_by_function() (minorg.grna.gRNAHits method) set_bg_check() (minorg.grna.gRNAHit method) (minorg.grna.gRNASeq method) set_check() (minorg.grna.CheckObj method) set_cover_greedy() (in module minorg.minimum_set) set_cover_LAR() (in module minorg.minimum_set) set_exclude_check() (minorg.grna.gRNAHit method) (minorg.grna.gRNASeq method) set_feature_check() (minorg.grna.gRNAHit method) set_gc_check() (minorg.grna.gRNAHit method) (minorg.grna.gRNASeq method) set_genes() (minorg.MINORgCLI.MINORgCLI method) set_level() (minorg.dynamic_logger.DynamicFileLoggerBase method) (minorg.dynamic_logger.DynamicFileParasiticSingleLogger method) set_names (minorg.minweight_sc.SetOfSets property) set_overlap() (in module minorg.functions) set_parent_sense() (minorg.grna.gRNAHit method) set_phase() (minorg.extend_reference.UserAnnotation method) set_range() (minorg.extend_reference.UserAnnotation method) set_sense() (minorg.grna.Target method) set_sense_by_parent() (minorg.grna.Target method) set_seqs_check() (minorg.grna.gRNAHits method) set_seqs_check_by_function() (minorg.grna.gRNAHits method) SetCoverAlgo (class in minorg.parse_config) SetOfCollapsedgRNA (class in minorg.minimum_set) SetOfSets (class in minorg.minweight_sc) sets (minorg.MINORg.MINORg attribute) (minorg.minweight_sc.SetOfSets property)

Sf (minorg.minweight_sc.e1 property) Sfc (minorg.minweight_sc.e property) short (minorg.parse_config.Param property) So (minorg.minweight_sc.e property) So_min() (minorg.minweight_sc.e method) some_checks_passed() (minorg.grna.CheckObj method) some_valid_checks_passed() (minorg.grna.CheckObj method) sort() (minorg.annotation.GFF method) sorted_coverage (minorg.grna.gRNASeq property) SpCas9 (in module minorg.pam) spcas9 (in module minorg.pam) splice_expanded_btop() (minorg.blast.BlastHSP method) split_list() (in module minorg.functions) split_none() (in module minorg.functions) split_str() (in module minorg.functions) splitlines() (in module minorg.functions) standardise_fields() (minorg.annotation.Attributes method) start (minorg.filter_grna.Masked property) (minorg.grna.gRNAHit property) StCas9 (in module minorg.pam) stcas9 (in module minorg.pam) strand (minorg.grna.gRNAHit property) (minorg.grna.Target property) stream_handler_map (minorg.dynamic_logger.MultiHandlerBase property) stream_handler_names (minorg.dynamic_logger.GroupLogger property) (minorg.dynamic_logger.MultiHandlerBase property) stream_handlers (minorg.dynamic_logger.GroupLogger property) (minorg.dynamic_logger.MultiHandlerBase property) sub_main() (in module minorg.console) subcmd_filter() (minorg.MINORgCLI.MINORgCLI method) subcmd_full() (minorg.MINORgCLI.MINORgCLI method) subcmd_grna() (minorg.MINORgCLI.MINORgCLI method) subcmd_minimumset() (minorg.MINORgCLI.MINORgCLI method) subcmd_seq() (minorg.MINORgCLI.MINORgCLI method) subfeature_range() (minorg.reference.AnnotatedFeature method) subset() (minorg.annotation.GFF method) (minorg.reference.AnnotatedFeature method) subset_annotation() (minorg.MINORg.MINORg method) (minorg.MINORgCLI.MINORgCLI method) (minorg.reference.AnnotatedFasta method) subset_hits_by_target() (minorg.minimum_set.gRNA method) symmetric_difference() (minorg.minweight_sc.SetOfSets method)

T

Target (class in minorg.grna) target (minorg.grna.gRNAHit property) target_id (minorg.grna.gRNAHit property) target_len (minorg.grna.gRNAHit property) target_strand (minorg.grna.gRNAHit property) targets (minorg.grna.gRNASeq property) (minorg.minimum_set.gRNA property) test_logger() (in module minorg.dynamic_logger) thread (minorg.MINORg.MINORg attribute)

three_prime() (minorg.pam.PAM method) three_prime_maxlen() (minorg.pam.PAM method) tie_break_first() (in module minorg.minimum_set) tmp (minorg.MINORg.PathHandler attribute) tmp_dir (minorg.MINORg.PathHandler attribute) tmp_files (minorg.MINORg.PathHandler attribute) top (minorg.minweight_sc.Q property) tracebacklimit (minorg.MINORg.PathHandler property) tsv_entries_as_dict() (in module minorg.functions)

U

union() (minorg.minweight_sc.SetOfSets method) UnknownChild UnknownInitialiser UnknownReferenceWarning UnreadableFile unused_hit_check() (minorg.grna.gRNAHits method) unused_seq_check() (minorg.grna.gRNAHits method) update() (minorg.dynamic_logger.DynamicFileParasiticSingleLogger method) update_attr_fields() (minorg.annotation.GFF method) update_file() (minorg.dynamic_logger.DynamicMultiFileLogger method) update_filename() (minorg.dynamic_logger.DynamicFileHandler method) (minorg.dynamic_logger.DynamicFileLoggerBase method) (minorg.dynamic_logger.DynamicFileParasiticSingleLogger method) (minorg.dynamic_logger.DynamicMultiFileHandler method) (minorg.dynamic_logger.DynamicMultiFileLogger method)

update_group (minorg.dynamic_logger.DynamicFileParasiticSingleLogger property) update_group() (minorg.dynamic_logger.DynamicMultiFileLogger method) (minorg.dynamic_logger.GroupLogger method) update_handlers() (minorg.dynamic_logger.DynamicFileParasiticSingleLogger method) update_level() (minorg.dynamic_logger.DynamicFileParasiticSingleLogger method) update_records() (minorg.grna.gRNAHits method) UserAnnotation (class in minorg.extend_reference)

V

valid_aliases() (in module minorg.MINORg) (in module minorg.MINORgCLI) valid_grna() (minorg.MINORg.MINORg method) valid_hit_check() (minorg.grna.gRNAHits method)

valid_len() (minorg.grna.Target method) valid_readable_file() (in module minorg.MINORg) (in module minorg.MINORgCLI) valid_seq_check() (minorg.grna.gRNAHits method) version_callback() (minorg.MINORgCLI.MINORgCLI method)

W

w (minorg.minweight_sc.e property) (minorg.minweight_sc.Set property) (minorg.minweight_sc.SetOfSets property) wc_ratio() (in module minorg.minweight_sc) weight (minorg.minweight_sc.SetOfSets property) within() (in module minorg.functions) (minorg.filter_grna.Masked method) within_any() (in module minorg.functions) within_feature() (in module minorg.filter_grna) write() (minorg.annotation.GFF method) (minorg.minimum_set.SetOfCollapsedgRNA method) write_all_grna_eqv() (minorg.MINORg.MINORg method) write_all_grna_fasta() (minorg.MINORg.MINORg method)

write_all_grna_map() (minorg.MINORg.MINORg method) write_equivalents() (minorg.grna.gRNAHits method) write_fasta() (minorg.grna.gRNAHits method) write_i() (minorg.annotation.GFF method) write_id() (minorg.annotation.GFF method) write_mapping() (minorg.grna.gRNAHits method) write_mask_report() (minorg.MINORg.MINORg method) write_pass_grna_eqv() (minorg.MINORg.MINORg method) write_pass_grna_fasta() (minorg.MINORg.MINORg method) write_pass_grna_files() (minorg.MINORg.MINORg method) write_pass_grna_map() (minorg.MINORg.MINORg method) write_table() (in module minorg.functions) write_tsv() (in module minorg.functions)

Z

zero_to_one_callback() (in module minorg.console)