Table of Contents - bacterial-annotator-1.0.1 Documentation
Classes and Modules
- BacterialAnnotator
- BacterialComparator
- BacterialIdentificator
- Helper
- SequenceAnnotation
- SequenceFasta
- SequenceSynteny
Methods
- ::new — BacterialAnnotator
- ::new — SequenceAnnotation
- ::new — SequenceFasta
- ::new — SequenceSynteny
- ::new — BacterialComparator
- ::new — BacterialIdentificator
- ::sec2str — Helper
- #add_annotation_ref_synteny_prot — SequenceAnnotation
- #add_annotations — SequenceAnnotation
- #build_multifasta — BacterialComparator
- #choose_best_hit — SequenceSynteny
- #concat_alignments — BacterialComparator
- #consensus_reference — BacterialIdentificator
- #cumulate_annotation_stats_reference — BacterialAnnotator
- #dump_cds — BacterialAnnotator
- #dump_ref_synteny_to_file — BacterialAnnotator
- #extract_cds_names — SequenceFasta
- #extract_externaldb_prot_info — BacterialAnnotator
- #extract_hits — SequenceSynteny
- #extract_hits_dna — SequenceSynteny
- #extract_syntenic_fasta — BacterialComparator
- #fasttree_tree_dna — BacterialComparator
- #fasttree_tree_pep — BacterialComparator
- #fetch_ncbi_genome — SequenceAnnotation
- #finish_annotation — BacterialAnnotator
- #get_DNA — SequenceAnnotation
- #get_annotation_for_contig — SequenceSynteny
- #get_cds — SequenceAnnotation
- #get_fasta_length — BacterialComparator
- #get_ref_prot — BacterialComparator
- #get_rna — SequenceAnnotation
- #get_sequences — SequenceSynteny
- #load_genome_cds — BacterialComparator
- #mafft_align — BacterialComparator
- #mafft_align_all_dna — BacterialComparator
- #mafft_align_all_pep — BacterialComparator
- #mash_genome — BacterialIdentificator
- #new_gbk — SequenceAnnotation
- #parse_genbank_files — BacterialAnnotator
- #prepare_files_for_annotation — BacterialAnnotator
- #print_output — BacterialIdentificator
- #print_sequence_for_gbk — SequenceFasta
- #print_stats — BacterialAnnotator
- #prune_aln_hits — SequenceSynteny
- #raxml_tree_dna — BacterialComparator
- #raxml_tree_pep — BacterialComparator
- #read_prot_synteny — BacterialComparator
- #reference_db — SequenceAnnotation
- #reference_gbk — SequenceAnnotation
- #run_annotation — BacterialAnnotator
- #run_blat — SequenceSynteny
- #run_comparison — BacterialComparator
- #run_diamond — SequenceSynteny
- #run_fasta36 — SequenceSynteny
- #run_identification — BacterialIdentificator
- #run_mafft_aln — BacterialComparator
- #run_mergem_synteny_prot — BacterialAnnotator
- #run_phylo — BacterialComparator
- #run_prodigal — SequenceFasta
- #run_reference_synteny_prot — BacterialAnnotator
- #run_synteny_prot — BacterialComparator
- #save_genbank_to_file — SequenceAnnotation
- #single_fasta — SequenceAnnotation
- #split_fasta — SequenceFasta
- #split_genbank — SequenceFasta
- #split_remaining_cds_file — BacterialAnnotator
- #summary — BacterialIdentificator
- #write_cds_to_file — SequenceAnnotation
- #write_rna_to_file — SequenceAnnotation