Index A | B | C | D | E | F | G | 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) allele (arda.refbuild.imgt.ImgtAllele attribute) ALLELE_MIN_FRAC (in module arda.stats) 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.cluster module arda.dpost module arda.igblast module arda.mmseqs 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.stats module 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) 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) 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) by_gene (arda.dpost.DPosterior attribute) 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 (arda.cdr3fix.Cdr3Markup attribute) cdr3_repaired (arda.cdr3fix.Cdr3Markup attribute) Cdr3Error (class in arda.cdr3fix) Cdr3Markup (class in arda.cdr3fix) check_cigar() (in module arda.annotate.cigar) chunked() (in module arda.annotate.io) cigar_query_length() (in module arda.annotate.cigar) cigar_reference_length() (in module arda.annotate.cigar) 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) confident (arda.dpost.DPosterior property) constant_only_fragments (arda.rnaseq.map.RnaseqReport attribute) Contig (class in arda.annotate.contig) contigs (arda.rnaseq.assemble.AssembleReport attribute) contigs_complete (arda.rnaseq.assemble.AssembleReport 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) (arda.dpost.DPosterior attribute) d_germlines (arda.annotate.reference.Reference attribute) d_sequence_end (arda.annotate.dmap.DCall attribute) d_sequence_start (arda.annotate.dmap.DCall attribute) d_start (arda.dpost.DPosterior attribute) d_start_ci90 (arda.dpost.DPosterior 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) DPosterior (class in arda.dpost) E easy_search() (in module arda.mmseqs) 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) entropy (arda.dpost.DPosterior 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) 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) 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) ImgtAllele (class in arda.refbuild.imgt) implied (arda.annotate.shortlist.Shortlist attribute) input (arda.rnaseq.map.RnaseqReport attribute) input_bytes (arda.rnaseq.map.RnaseqReport attribute) 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_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_sequence_start (arda.annotate.dmap.DCall attribute) (arda.annotate.reference.RefEntry attribute) j_start (arda.cdr3fix.Cdr3Markup attribute) j_targets (arda.refbuild.segments.SegmentStats attribute) jc_combinations() (arda.annotate.reference.Reference method) 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 length (arda.cdr3fix.Cdr3Error attribute) load_anchors() (in module arda.cdr3fix) load_combinations() (in module arda.annotate.shortlist) load_d_prior() (in module arda.dpost) 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_v_fwr3_stops() (in module arda.refbuild.combinations) locus (arda.annotate.dmap.DCall attribute) (arda.annotate.reference.RefEntry attribute) (arda.cdr3fix.Anchor attribute) (arda.cdr3fix.Cdr3Markup attribute) (arda.dpost.DPosterior attribute) (arda.refbuild.combinations.Scaffold attribute) M 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 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.cluster arda.dpost arda.igblast arda.mmseqs 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.stats mutation_quality() (in module arda.rnaseq.map) N n_middle_nt (arda.dpost.DPosterior attribute) n_pad (arda.refbuild.combinations.Scaffold attribute) n_total (arda.annotate.shortlist.Shortlist property) 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 paired (arda.rnaseq.map.RnaseqReport attribute) parse_cigar() (in module arda.annotate.cigar) parse_functionality() (in module arda.refbuild.imgt) 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) pos (arda.cdr3fix.Cdr3Error attribute) posterior (arda.dpost.DPosterior attribute) posterior_d() (in module arda.dpost) prefilter_stats (arda.rnaseq.map.RnaseqReport attribute) project_root() (in module arda.paths) Q qaln (arda.annotate.contig.ReadPlacement attribute) qstart (arda.annotate.contig.ReadPlacement attribute) R 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_pairs() (in module arda.rnaseq.map) read_sequences() (in module arda.annotate.io) ReadPlacement (class in arda.annotate.contig) reads (arda.annotate.contig.Contig attribute) (arda.rnaseq.correct.CorrectReport 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_url() (in module arda._database_fetch) render_rnaseq_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) S 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) seqtype (arda.annotate.reference.Reference attribute) sequence (arda.annotate.contig.Contig attribute) (arda.refbuild.combinations.Scaffold attribute) (arda.refbuild.imgt.ImgtAllele attribute) sequence_id (arda.annotate.contig.Contig attribute) (arda.cdr3fix.Cdr3Markup attribute) setup() (in module arda._log) Shortlist (class in arda.annotate.shortlist) shortlist() (in module arda.annotate.shortlist) side (arda.cdr3fix.Cdr3Error attribute) 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 (class in arda.rnaseq._res) starts (arda.annotate.reference.RefEntry attribute) status (arda.cdr3fix.Anchor attribute) support_aa (arda.dpost.DPosterior 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) Throttle (class in arda._log) 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) tstart (arda.annotate.contig.ReadPlacement attribute) U ungap_gene() (in module arda.refbuild.imgt) V 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_fix (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)