Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W A aa_coords_from_nt() (in module arda.refbuild.translate) AIRR Rearrangement alignment_candidates() (in module arda) allele (arda.refbuild.imgt.ImgtAllele attribute) ALLELE_MIN_FRAC (in module arda.stats) amplicon anchor Anchor (class in arda.cdr3fix) anchor_nt (arda.cdr3fix.Anchor attribute) anchors (arda.annotate.reference.Reference attribute) annotate_file() (in module arda.annotate.mapper) annotate_records() (in module arda.annotate.mapper) annotate_sequences() (in module arda.adapter) applied (arda.cdr3fix.Cdr3Error attribute) arda._database_fetch module arda._log module arda.adapter module arda.annotate.cigar module arda.annotate.contig module arda.annotate.dmap module arda.annotate.io module arda.annotate.mapper module arda.annotate.reference module arda.annotate.shortlist module arda.annotate.transfer module arda.cdr3fix module arda.cell module arda.cluster module arda.igblast module arda.mmseqs module arda.partition module arda.paths module arda.prefilter module arda.refbuild.build module arda.refbuild.combinations module arda.refbuild.imgt module arda.refbuild.segments module arda.refbuild.translate module arda.rnaseq._res module arda.rnaseq.assemble module arda.rnaseq.correct module arda.rnaseq.map module arda.rnaseq.pipeline module arda.scplot module arda.singlecell module arda.stats module arda_binary() (in module arda.cluster) as_dict() (arda.annotate.shortlist.Shortlist method) (arda.refbuild.segments.SegmentStats method) (arda.rnaseq.assemble.AssembleReport method) (arda.rnaseq.correct.CorrectReport method) (arda.rnaseq.map.RnaseqReport method) (arda.singlecell.CellAssemblyReport method) assemble_cell() (in module arda.singlecell) assemble_cells() (in module arda.singlecell) assemble_contigs() (in module arda.rnaseq.assemble) AssembleReport (class in arda.rnaseq.assemble) auxiliary_data() (in module arda.igblast) available() (in module arda.prefilter) B back_translate() (in module arda.refbuild.translate) bin_dir() (in module arda.paths) boundary_nt() (in module arda.cdr3fix) build() (in module arda.prefilter) (in module arda.refbuild.build) build_cigar() (in module arda.annotate.cigar) build_index() (in module arda.annotate.mapper) build_locus_scaffolds() (in module arda.refbuild.combinations) build_segment_reference() (in module arda.refbuild.segments) build_species() (in module arda.refbuild.build) bulk RNA-seq C c_call (arda.annotate.reference.RefEntry attribute) c_targets (arda.refbuild.segments.SegmentStats attribute) cache_root() (in module arda.paths) CALL_LEVELS (in module arda.rnaseq.correct) called (arda.annotate.dmap.DCall property) CDR3 cdr3 (arda.cdr3fix.Cdr3Markup attribute) cdr3_repaired (arda.cdr3fix.Cdr3Markup attribute) Cdr3Error (class in arda.cdr3fix) Cdr3Markup (class in arda.cdr3fix) cell (arda.cell.CellKey attribute) (arda.singlecell.Contig attribute) cell_rank() (in module arda.singlecell) cell_summary() (in module arda.singlecell) CellAssemblyReport (class in arda.singlecell) CellKey (class in arda.cell) cells (arda.singlecell.CellAssemblyReport attribute) check_cigar() (in module arda.annotate.cigar) chimera chunked() (in module arda.annotate.io) cigar_query_length() (in module arda.annotate.cigar) cigar_reference_length() (in module arda.annotate.cigar) clonotype CLONOTYPE_KEYS (in module arda.rnaseq.correct) clonotypes_in (arda.rnaseq.correct.CorrectReport attribute) clonotypes_low_quality (arda.rnaseq.correct.CorrectReport attribute) clonotypes_out (arda.rnaseq.correct.CorrectReport attribute) collapsed (arda.rnaseq.correct.CorrectReport attribute) collect() (in module arda.stats) compare_partitions() (in module arda.partition) consensus_count constant_only_fragments (arda.rnaseq.map.RnaseqReport attribute) contig (arda.cell.CellKey attribute) Contig (class in arda.annotate.contig) (class in arda.singlecell) contig_id (arda.singlecell.Contig property) contig_lengths (arda.singlecell.CellAssemblyReport attribute) contigs (arda.rnaseq.assemble.AssembleReport attribute) (arda.singlecell.CellAssemblyReport attribute) contigs_complete (arda.rnaseq.assemble.AssembleReport attribute) contigs_dropped_small (arda.singlecell.CellAssemblyReport attribute) convertalis() (in module arda.mmseqs) correct_airr() (in module arda.rnaseq.correct) CorrectReport (class in arda.rnaseq.correct) createdb() (in module arda.mmseqs) D d2_call (arda.annotate.dmap.DCall attribute) d2_sequence_end (arda.annotate.dmap.DCall attribute) d2_sequence_start (arda.annotate.dmap.DCall attribute) d2_support (arda.annotate.dmap.DCall attribute) d_call (arda.annotate.dmap.DCall attribute) d_germline_metadata() (in module arda) d_germlines (arda.annotate.reference.Reference attribute) d_sequence_end (arda.annotate.dmap.DCall attribute) d_sequence_start (arda.annotate.dmap.DCall attribute) d_support (arda.annotate.dmap.DCall attribute) data_dir() (in module arda.paths) database_dir() (in module arda.paths) DCall (class in arda.annotate.dmap) detect_coding_frame() (in module arda.refbuild.translate) detect_format() (in module arda.annotate.io) dist (arda.cdr3fix.Cdr3Error attribute) download_reference() (in module arda.refbuild.imgt) draw() (in module arda.scplot) duplicate_count E easy_search() (in module arda.mmseqs) ec-mode edit_imgt_file() (in module arda.igblast) empty_clonotypes (arda.rnaseq.correct.CorrectReport attribute) ends (arda.annotate.reference.RefEntry attribute) entries (arda.annotate.reference.Reference attribute) error_rate (arda.rnaseq.correct.CorrectReport attribute) error_rate_parents (arda.rnaseq.correct.CorrectReport attribute) error_rate_source (arda.rnaseq.correct.CorrectReport attribute) errors (arda.cdr3fix.Cdr3Markup attribute) explain() (arda.cdr3fix.Cdr3Markup method) extra (arda.annotate.dmap.DCall attribute) F fast_fraction (arda.annotate.shortlist.Shortlist property) fetch_database() (in module arda._database_fetch) find_knee() (in module arda.singlecell) finish() (arda.rnaseq._res.Stage method) (in module arda.rnaseq.pipeline) fix_needed (arda.cdr3fix.Cdr3Markup property) format_report() (in module arda.cdr3fix) frm (arda.cdr3fix.Cdr3Error attribute) functionality (arda.cdr3fix.Anchor attribute) (arda.refbuild.imgt.ImgtAllele attribute) G gene_fasta_path() (in module arda.refbuild.imgt) germline_nt (arda.cdr3fix.Anchor attribute) get() (arda.annotate.reference.Reference method) good (arda.cdr3fix.Cdr3Markup property) guess_allele() (in module arda.cdr3fix) guess_alleles() (in module arda.cdr3fix) H HEAVY (in module arda.singlecell) homogeneity_score() (in module arda.partition) I igblast_root() (in module arda.igblast) igblast_version() (in module arda.igblast) IgBlastError igblastn_airr() (in module arda.igblast) igdata_env() (in module arda.igblast) IMGT imgt_completeness (arda.cdr3fix.Anchor attribute) ImgtAllele (class in arda.refbuild.imgt) implied (arda.annotate.shortlist.Shortlist attribute) index (arda.singlecell.Contig attribute) input (arda.rnaseq.map.RnaseqReport attribute) input_bytes (arda.rnaseq.map.RnaseqReport attribute) installed_database() (in module arda._database_fetch) inverse_purity_score() (in module arda.partition) is_dd (arda.annotate.dmap.DCall property) is_functional (arda.refbuild.imgt.ImgtAllele property) is_jc (arda.annotate.reference.RefEntry property) isotype_from_mate (arda.rnaseq.map.RnaseqReport attribute) J J+C scaffold j_alts (arda.cdr3fix.Cdr3Markup attribute) j_call (arda.annotate.reference.RefEntry attribute) (arda.cdr3fix.Cdr3Markup attribute) j_calls (arda.refbuild.combinations.Scaffold attribute) j_canonical (arda.cdr3fix.Cdr3Markup property) j_fix (arda.cdr3fix.Cdr3Markup attribute) j_flags (arda.cdr3fix.Cdr3Markup attribute) j_sequence_start (arda.annotate.dmap.DCall attribute) (arda.annotate.reference.RefEntry attribute) j_start (arda.cdr3fix.Cdr3Markup attribute) j_start_nt (arda.cdr3fix.Cdr3Markup attribute) j_targets (arda.refbuild.segments.SegmentStats attribute) jc_combinations() (arda.annotate.reference.Reference method) junction junction_quality() (in module arda.rnaseq.map) K K (in module arda.prefilter) keep_records() (in module arda.prefilter) kind (arda.cdr3fix.Cdr3Error attribute) L legacy_database() (in module arda._database_fetch) length (arda.cdr3fix.Cdr3Error attribute) load_anchors() (in module arda.cdr3fix) load_combinations() (in module arda.annotate.shortlist) load_j_fr4_offsets() (in module arda.refbuild.combinations) load_j_frames() (in module arda.refbuild.combinations) load_reference() (in module arda.annotate.reference) load_segment_markup() (arda.annotate.reference.Reference method) load_v_fwr3_stops() (in module arda.refbuild.combinations) loci (arda.cdr3fix.Anchor attribute) locus (arda.annotate.dmap.DCall attribute) (arda.annotate.reference.RefEntry attribute) (arda.cdr3fix.Anchor attribute) (arda.cdr3fix.Cdr3Markup attribute) (arda.refbuild.combinations.Scaffold attribute) M major_allele_map() (in module arda) major_alleles (arda.annotate.reference.Reference attribute) major_only (arda.rnaseq.map.RnaseqReport attribute) make_parser() (in module arda.cell) makeblastdb() (in module arda.igblast) map_d_junction() (in module arda.annotate.dmap) map_rnaseq() (in module arda.rnaseq.map) mapped_fraction (arda.rnaseq.map.RnaseqReport property) mapped_reads (arda.rnaseq.map.RnaseqReport attribute) markup() (arda.annotate.dmap.DCall method) markup_batch() (in module arda.cdr3fix) markup_cdr3() (in module arda.cdr3fix) markup_records() (in module arda.cdr3fix) MAX_USEFUL_PASS_RATE (in module arda.prefilter) members_without_junction (arda.rnaseq.assemble.AssembleReport attribute) merge() (in module arda.cluster) merge_contig() (in module arda.annotate.contig) merge_contigs() (in module arda.annotate.contig) merge_pair() (in module arda.rnaseq.map) MIN_HITS (in module arda.prefilter) min_score (arda.rnaseq.map.RnaseqReport attribute) mmseqs_binary() (in module arda.mmseqs) MMseqsError mode module arda._database_fetch arda._log arda.adapter arda.annotate.cigar arda.annotate.contig arda.annotate.dmap arda.annotate.io arda.annotate.mapper arda.annotate.reference arda.annotate.shortlist arda.annotate.transfer arda.cdr3fix arda.cell arda.cluster arda.igblast arda.mmseqs arda.partition arda.paths arda.prefilter arda.refbuild.build arda.refbuild.combinations arda.refbuild.imgt arda.refbuild.segments arda.refbuild.translate arda.rnaseq._res arda.rnaseq.assemble arda.rnaseq.correct arda.rnaseq.map arda.rnaseq.pipeline arda.scplot arda.singlecell arda.stats molecule (arda.cell.CellKey attribute) molecules (arda.singlecell.Contig attribute) molecules_by_cell (arda.singlecell.CellAssemblyReport attribute) molecules_in (arda.singlecell.CellAssemblyReport attribute) molecules_placed (arda.singlecell.CellAssemblyReport attribute) mutation_quality() (in module arda.rnaseq.map) N n_pad (arda.refbuild.combinations.Scaffold attribute) n_total (arda.annotate.shortlist.Shortlist property) normalize_nt() (in module arda.annotate.io) normalize_nt_frame() (in module arda.annotate.io) normalized_inverse_purity_score() (in module arda.partition) normalized_purity_score() (in module arda.partition) np1 (arda.annotate.dmap.DCall attribute) np2 (arda.annotate.dmap.DCall attribute) np3 (arda.annotate.dmap.DCall attribute) O offset (arda.annotate.contig.ReadPlacement attribute) open_text() (in module arda.annotate.io) organism (arda.annotate.reference.Reference attribute) (arda.rnaseq.map.RnaseqReport attribute) orphan_clonotypes (arda.rnaseq.correct.CorrectReport attribute) orphan_reads (arda.rnaseq.correct.CorrectReport attribute) OUTPUTS (in module arda.rnaseq.pipeline) P pair_chains() (in module arda.singlecell) pair_sensitivity_score() (in module arda.partition) pair_specificity_score() (in module arda.partition) paired (arda.rnaseq.map.RnaseqReport attribute) PANELS (in module arda.scplot) parse() (in module arda.cell) parse_cigar() (in module arda.annotate.cigar) parse_functionality() (in module arda.refbuild.imgt) parsimony_score() (in module arda.partition) partial_nt (arda.cdr3fix.Anchor attribute) peak_rss_mb (arda.rnaseq.assemble.AssembleReport attribute) (arda.rnaseq.correct.CorrectReport attribute) (arda.rnaseq.map.RnaseqReport attribute) peak_rss_mb() (in module arda._log) (in module arda.rnaseq._res) per_locus (arda.rnaseq.map.RnaseqReport attribute) plan() (in module arda.cluster) pos (arda.cdr3fix.Cdr3Error attribute) prefilter_stats (arda.rnaseq.map.RnaseqReport attribute) project_root() (in module arda.paths) proposed (arda.cdr3fix.Cdr3Markup attribute) purity_score() (in module arda.partition) Q qaln (arda.annotate.contig.ReadPlacement attribute) qstart (arda.annotate.contig.ReadPlacement attribute) R read group read_called_cells() (in module arda.singlecell) read_fasta() (in module arda.refbuild.imgt) read_length_max (arda.rnaseq.map.RnaseqReport attribute) read_length_mean (arda.rnaseq.map.RnaseqReport attribute) read_length_min (arda.rnaseq.map.RnaseqReport attribute) read_molecules() (in module arda.singlecell) read_pairs() (in module arda.rnaseq.map) read_records() (in module arda.singlecell) read_reference_calls() (in module arda.singlecell) read_sequences() (in module arda.annotate.io) READGROUP_COLUMNS (in module arda.cluster) ReadPlacement (class in arda.annotate.contig) reads (arda.annotate.contig.Contig attribute) (arda.rnaseq.correct.CorrectReport attribute) (arda.singlecell.Contig attribute) reads_assigned (arda.rnaseq.correct.CorrectReport attribute) reads_from_assembly (arda.rnaseq.correct.CorrectReport attribute) reads_in (arda.rnaseq.assemble.AssembleReport attribute) reads_incomplete (arda.rnaseq.correct.CorrectReport attribute) reads_low_quality (arda.rnaseq.correct.CorrectReport attribute) reads_per_second (arda.rnaseq.map.RnaseqReport attribute) reads_rescued (arda.rnaseq.assemble.AssembleReport attribute) reads_with_junction (arda.rnaseq.correct.CorrectReport attribute) ready() (arda._log.Throttle method) reannotate_contigs() (in module arda.annotate.contig) reason_of (arda.annotate.shortlist.Shortlist attribute) reasons (arda.annotate.shortlist.Shortlist attribute) reduce() (in module arda.rnaseq.pipeline) reduction (arda.refbuild.segments.SegmentStats property) RefEntry (class in arda.annotate.reference) Reference (class in arda.annotate.reference) reference_index_identity() (in module arda.annotate.mapper) reference_url() (in module arda._database_fetch) regime regime_flags() (in module arda.cluster) render_rnaseq_submit_script() (in module arda.cluster) render_samples_submit_script() (in module arda.cluster) render_submit_script() (in module arda.cluster) rescue (arda.annotate.shortlist.Shortlist attribute) rescued_clonotypes (arda.rnaseq.correct.CorrectReport attribute) rescued_reads (arda.rnaseq.correct.CorrectReport attribute) reverse_complement() (in module arda.refbuild.translate) RnaseqReport (class in arda.rnaseq.map) rss_gain_mb (arda.rnaseq.assemble.AssembleReport attribute) (arda.rnaseq.correct.CorrectReport attribute) (arda.rnaseq.map.RnaseqReport attribute) run() (in module arda.mmseqs) (in module arda.rnaseq.pipeline) (in module arda.singlecell) S sample (arda.cell.CellKey attribute) SAMPLE_COLUMNS (in module arda.cluster) scaffold Scaffold (class in arda.refbuild.combinations) scaffold_id (arda.refbuild.combinations.Scaffold attribute) search() (in module arda.mmseqs) seeds (arda.rnaseq.assemble.AssembleReport attribute) segment (arda.cdr3fix.Anchor attribute) segment_cigars() (in module arda.annotate.cigar) segment_j_call() (arda.annotate.reference.Reference method) segment_search (arda.rnaseq.map.RnaseqReport attribute) SegmentStats (class in arda.refbuild.segments) select_major_alleles() (in module arda) seqtype (arda.annotate.reference.Reference attribute) sequence (arda.annotate.contig.Contig attribute) (arda.refbuild.combinations.Scaffold attribute) (arda.refbuild.imgt.ImgtAllele attribute) (arda.singlecell.Contig attribute) sequence_id (arda.annotate.contig.Contig attribute) (arda.cdr3fix.Cdr3Markup attribute) setup() (in module arda._log) SHM Shortlist (class in arda.annotate.shortlist) shortlist() (in module arda.annotate.shortlist) side (arda.cdr3fix.Cdr3Error attribute) sniff() (in module arda.cell) source (arda.cdr3fix.Anchor attribute) source_scaffolds (arda.refbuild.segments.SegmentStats attribute) species (arda.cdr3fix.Cdr3Markup attribute) split() (in module arda.cluster) split_pairs() (in module arda.cluster) stage Stage (class in arda.rnaseq._res) starts (arda.annotate.reference.RefEntry attribute) status (arda.cdr3fix.Anchor attribute) T taln (arda.annotate.contig.ReadPlacement attribute) target (arda.annotate.contig.Contig attribute) target_fasta (arda.annotate.reference.Reference attribute) templated_aa (arda.cdr3fix.Anchor attribute) threads (arda.rnaseq.map.RnaseqReport attribute) threshold_sweep() (in module arda.singlecell) Throttle (class in arda._log) tie list to (arda.cdr3fix.Cdr3Error attribute) to_cdr3fix() (arda.cdr3fix.Cdr3Markup method) to_frame() (in module arda.cdr3fix) tool() (in module arda.igblast) top_hit() (in module arda.mmseqs) total (arda.refbuild.segments.SegmentStats property) total_reads (arda.rnaseq.map.RnaseqReport attribute) transfer_hit() (in module arda.annotate.transfer) translate() (in module arda.refbuild.translate) trim() (in module arda.singlecell) tstart (arda.annotate.contig.ReadPlacement attribute) U UMI umi (arda.cell.CellKey attribute) ungap_gene() (in module arda.refbuild.imgt) unmapped (arda.rnaseq.map.RnaseqReport attribute) V v_alts (arda.cdr3fix.Cdr3Markup attribute) v_call (arda.annotate.reference.RefEntry attribute) (arda.cdr3fix.Cdr3Markup attribute) v_calls (arda.refbuild.combinations.Scaffold attribute) v_canonical (arda.cdr3fix.Cdr3Markup property) v_end (arda.cdr3fix.Cdr3Markup attribute) v_end_nt (arda.cdr3fix.Cdr3Markup attribute) v_fix (arda.cdr3fix.Cdr3Markup attribute) v_flags (arda.cdr3fix.Cdr3Markup attribute) v_sequence_end (arda.annotate.dmap.DCall attribute) (arda.annotate.reference.RefEntry attribute) v_targets (arda.refbuild.segments.SegmentStats attribute) vdj_dir() (in module arda.paths) version() (in module arda.mmseqs) version_key() (in module arda.mmseqs) versions_compatible() (in module arda.mmseqs) vj_end (arda.annotate.reference.RefEntry attribute) W wall_seconds (arda.rnaseq._res.Stage property) (arda.rnaseq.assemble.AssembleReport attribute) (arda.rnaseq.correct.CorrectReport attribute) (arda.rnaseq.map.RnaseqReport attribute) write_fasta() (in module arda.annotate.io) write_stats() (in module arda.stats) write_stats_for() (in module arda.rnaseq.pipeline) write_stats_json() (in module arda.stats)