Index A | B | C | D | E | F | G | I | J | L | M | N | O | P | R | S | T | U | V | W A aa_coords_from_nt() (in module arda.refbuild.translate) allele (arda.refbuild.imgt.ImgtAllele attribute) annotate_file() (in module arda.annotate.mapper) annotate_records() (in module arda.annotate.mapper) annotate_sequences() (in module arda.adapter) arda.adapter module arda.annotate.io module arda.annotate.mapper module arda.annotate.reference module arda.annotate.transfer module arda.igblast module arda.mmseqs module arda.refbuild.build module arda.refbuild.combinations module arda.refbuild.imgt module arda.refbuild.translate module B back_translate() (in module arda.refbuild.translate) build() (in module arda.refbuild.build) build_index() (in module arda.annotate.mapper) build_locus_scaffolds() (in module arda.refbuild.combinations) build_species() (in module arda.refbuild.build) C chunked() (in module arda.annotate.io) convertalis() (in module arda.mmseqs) createdb() (in module arda.mmseqs) D d_germlines (arda.annotate.reference.Reference attribute) detect_coding_frame() (in module arda.refbuild.translate) detect_format() (in module arda.annotate.io) download_reference() (in module arda.refbuild.imgt) E easy_search() (in module arda.mmseqs) edit_imgt_file() (in module arda.igblast) ends (arda.annotate.reference.RefEntry attribute) entries (arda.annotate.reference.Reference attribute) F functionality (arda.refbuild.imgt.ImgtAllele attribute) G gene_fasta_path() (in module arda.refbuild.imgt) get() (arda.annotate.reference.Reference method) I IgBlastError igblastn_airr() (in module arda.igblast) igdata_env() (in module arda.igblast) ImgtAllele (class in arda.refbuild.imgt) is_functional (arda.refbuild.imgt.ImgtAllele property) J j_call (arda.annotate.reference.RefEntry attribute) j_calls (arda.refbuild.combinations.Scaffold attribute) j_sequence_start (arda.annotate.reference.RefEntry attribute) L load_j_frames() (in module arda.refbuild.combinations) load_reference() (in module arda.annotate.reference) locus (arda.annotate.reference.RefEntry attribute) (arda.refbuild.combinations.Scaffold attribute) M makeblastdb() (in module arda.igblast) mmseqs_binary() (in module arda.mmseqs) MMseqsError module arda.adapter arda.annotate.io arda.annotate.mapper arda.annotate.reference arda.annotate.transfer arda.igblast arda.mmseqs arda.refbuild.build arda.refbuild.combinations arda.refbuild.imgt arda.refbuild.translate N n_pad (arda.refbuild.combinations.Scaffold attribute) O open_text() (in module arda.annotate.io) organism (arda.annotate.reference.Reference attribute) P parse_functionality() (in module arda.refbuild.imgt) R read_fasta() (in module arda.refbuild.imgt) read_sequences() (in module arda.annotate.io) RefEntry (class in arda.annotate.reference) Reference (class in arda.annotate.reference) reverse_complement() (in module arda.refbuild.translate) run() (in module arda.mmseqs) S Scaffold (class in arda.refbuild.combinations) scaffold_id (arda.refbuild.combinations.Scaffold attribute) search() (in module arda.mmseqs) seqtype (arda.annotate.reference.Reference attribute) sequence (arda.refbuild.combinations.Scaffold attribute) (arda.refbuild.imgt.ImgtAllele attribute) starts (arda.annotate.reference.RefEntry attribute) T target_fasta (arda.annotate.reference.Reference attribute) tool() (in module arda.igblast) transfer_hit() (in module arda.annotate.transfer) translate() (in module arda.refbuild.translate) U ungap_gene() (in module arda.refbuild.imgt) V v_call (arda.annotate.reference.RefEntry attribute) v_calls (arda.refbuild.combinations.Scaffold attribute) v_sequence_end (arda.annotate.reference.RefEntry attribute) version() (in module arda.mmseqs) W write_fasta() (in module arda.annotate.io)