Index

Symbols

--acc2taxid-dir command line option --add-taxonomy command line option --alignment-tolerance command line option --blastdb-path command line option, [1], [2] --combined-tree-label-rank command line option --database command line option, [1] --force command line option --group-rank command line option --min-coverage command line option, [1] --min-identity command line option, [1] --mmseqs-database command line option, [1] --mmseqs-db-dir command line option --mmseqs-db-path command line option, [1] --mmseqs-db-source command line option, [1]

--mmseqs-memory-limit command line option, [1] --mmseqs-search-type command line option, [1] --mmseqs-sensitivity command line option, [1] --mmseqs-threads command line option --ncbi-taxonomy command line option --num-threads command line option, [1] --output-classification command line option, [1] --overwrite-existing-blast command line option, [1] --rank command line option, [1], [2] --skip-alignment command line option, [1] --skip-memory-check command line option --target command line option --taxonomy-workdir command line option --tree-label-rank command line option, [1]

_

__init__() (eplace_lib.blast_analysis.BlastRunner method) (eplace_lib.blast_analysis.MMseqs2Runner method) (eplace_lib.ncbi_download.MMseqsDownloader method) (eplace_lib.ncbi_download.NCBIDownloader method) (eplace_lib.taxonomy.SequenceExtractor method)

A

ACC2TAXID_BASE (eplace_lib.ncbi_download.MMseqsDownloader attribute) add_taxonomy_to_database() (eplace_lib.ncbi_download.MMseqsDownloader method)

align_sequences() (eplace_lib.alignment.MAFFTAligner static method) alignment_length (eplace_lib.blast_analysis.BlastHit attribute), [1]

B

bit_score (eplace_lib.blast_analysis.BlastHit attribute), [1] blast_command() (in module eplace_lib.cli) BLAST_OUTPUT command line option

BlastHit (class in eplace_lib.blast_analysis) BlastRunner (class in eplace_lib.blast_analysis) build_tree() (eplace_lib.alignment.IQTreeBuilder static method) build_tree_background() (eplace_lib.alignment.IQTreeBuilder static method)

C

calculate_gc_content() (eplace_lib.sequences.SequenceAnalyzer method) check_alignment_consistency() (in module eplace_lib.alignment) check_available_memory_gb() (in module eplace_lib.ncbi_download) check_blastdbcmd_available() (eplace_lib.taxonomy.SequenceExtractor method) check_blastn_available() (eplace_lib.blast_analysis.BlastRunner method) check_database_exists() (eplace_lib.ncbi_download.NCBIDownloader method) check_iqtree_available() (eplace_lib.alignment.IQTreeBuilder static method) check_mafft_available() (eplace_lib.alignment.MAFFTAligner static method) check_mmseqs_available() (eplace_lib.blast_analysis.MMseqs2Runner method) command line option --acc2taxid-dir --add-taxonomy --alignment-tolerance --blastdb-path, [1], [2] --combined-tree-label-rank --database, [1] --force --group-rank --min-coverage, [1] --min-identity, [1] --mmseqs-database, [1] --mmseqs-db-dir --mmseqs-db-path, [1] --mmseqs-db-source, [1] --mmseqs-memory-limit, [1] --mmseqs-search-type, [1] --mmseqs-sensitivity, [1] --mmseqs-threads --ncbi-taxonomy --num-threads, [1] --output-classification, [1] --overwrite-existing-blast, [1] --rank, [1], [2] --skip-alignment, [1] --skip-memory-check --target --taxonomy-workdir --tree-label-rank, [1] BLAST_OUTPUT OUTPUT_DIR, [1] OUTPUT_TREE QUERY_FASTA, [1] TREE_FILE

concatenate_all_groups_and_build_tree() (in module eplace_lib.alignment) CORE_NT_PREFIX (eplace_lib.ncbi_download.NCBIDownloader attribute) count_bases() (eplace_lib.sequences.SequenceAnalyzer method) create_grouped_fasta_with_queries() (in module eplace_lib.alignment)

D

download_and_setup_database() (eplace_lib.ncbi_download.NCBIDownloader method) download_command() (in module eplace_lib.cli)

download_file() (eplace_lib.ncbi_download.NCBIDownloader method) download_nt_database() (eplace_lib.ncbi_download.MMseqsDownloader method)

E

eplace_lib.alignment module eplace_lib.blast_analysis module eplace_lib.cli module eplace_lib.ncbi_download module

eplace_lib.sequences module eplace_lib.taxonomy module evalue (eplace_lib.blast_analysis.BlastHit attribute), [1] extract_representatives_for_query() (eplace_lib.taxonomy.SequenceExtractor method) extract_sequences() (eplace_lib.taxonomy.SequenceExtractor method) extract_tarball() (eplace_lib.ncbi_download.NCBIDownloader method)

F

FastaReader (class in eplace_lib.blast_analysis) filter_blast_hits() (eplace_lib.blast_analysis.BlastRunner method)

filter_hits() (eplace_lib.blast_analysis.MMseqs2Runner method) find_nearest_neighbor_in_tree() (in module eplace_lib.alignment)

G

generate_classification_summary() (in module eplace_lib.taxonomy) get_accession() (eplace_lib.blast_analysis.BlastHit method) get_available_files() (eplace_lib.ncbi_download.NCBIDownloader method) get_blastdb_directory() (eplace_lib.ncbi_download.NCBIDownloader method) get_leaves() (eplace_lib.alignment.SimpleNewickNode method) get_mmseqsdb_directory() (eplace_lib.ncbi_download.MMseqsDownloader method)

get_sequence_lengths() (eplace_lib.blast_analysis.FastaReader static method) get_subject_taxonomy() (eplace_lib.blast_analysis.BlastHit method) get_total_memory_gb() (in module eplace_lib.ncbi_download) group_hits_by_group_rank() (in module eplace_lib.alignment) group_hits_by_query() (eplace_lib.taxonomy.TaxonomyExtractor method) grouped_command() (in module eplace_lib.cli)

I

IQTreeBuilder (class in eplace_lib.alignment)

is_leaf() (eplace_lib.alignment.SimpleNewickNode method)

L

LEGACY_MMSEQS_DB_DIR_ENV (eplace_lib.ncbi_download.MMseqsDownloader attribute)

M

MAFFTAligner (class in eplace_lib.alignment) main() (in module eplace_lib.cli) MMseqs2Runner (class in eplace_lib.blast_analysis) MMSEQS_DB_DIR_ENV (eplace_lib.ncbi_download.MMseqsDownloader attribute) MMseqsDownloader (class in eplace_lib.ncbi_download) module eplace_lib.alignment eplace_lib.blast_analysis eplace_lib.cli eplace_lib.ncbi_download eplace_lib.sequences eplace_lib.taxonomy

N

NCBI_FTP_BASE (eplace_lib.ncbi_download.NCBIDownloader attribute) NCBIDownloader (class in eplace_lib.ncbi_download)

normalize_sequence_id() (in module eplace_lib.blast_analysis) NUCLEOTIDE_DB_NAME (eplace_lib.ncbi_download.MMseqsDownloader attribute)

O

OUTPUT_DIR command line option, [1]

OUTPUT_TREE command line option

P

parse_blast_results() (eplace_lib.blast_analysis.BlastRunner method) parse_mmseqs_results() (eplace_lib.blast_analysis.MMseqs2Runner method) parse_simple_newick() (in module eplace_lib.alignment) parse_taxids() (eplace_lib.taxonomy.TaxonomyExtractor method) percent_identity (eplace_lib.blast_analysis.BlastHit attribute), [1]

process_blast_results_for_taxonomy() (in module eplace_lib.taxonomy) process_grouped_alignment_and_tree() (in module eplace_lib.alignment) process_grouped_alignment_and_tree_parallel() (in module eplace_lib.alignment) process_query_alignment_and_tree() (in module eplace_lib.alignment) process_query_alignment_and_tree_parallel() (in module eplace_lib.alignment)

Q

query_coverage (eplace_lib.blast_analysis.BlastHit attribute), [1] query_end (eplace_lib.blast_analysis.BlastHit attribute), [1] QUERY_FASTA command line option, [1]

query_id (eplace_lib.blast_analysis.BlastHit attribute), [1] query_length (eplace_lib.blast_analysis.BlastHit attribute), [1] query_start (eplace_lib.blast_analysis.BlastHit attribute), [1]

R

read_fasta() (eplace_lib.blast_analysis.FastaReader static method) relabel_command() (in module eplace_lib.cli) relabel_tree_with_taxonomy() (eplace_lib.alignment.IQTreeBuilder static method) reverse_complement() (eplace_lib.sequences.SequenceAnalyzer method)

rewrite_blast_hits() (in module eplace_lib.taxonomy) run_blast_search() (in module eplace_lib.blast_analysis) run_blastn() (eplace_lib.blast_analysis.BlastRunner method) run_easy_search() (eplace_lib.blast_analysis.MMseqs2Runner method) run_mmseqs_search() (in module eplace_lib.blast_analysis)

S

select_representatives_by_rank() (eplace_lib.taxonomy.TaxonomyExtractor method) SequenceAnalyzer (class in eplace_lib.sequences) SequenceExtractor (class in eplace_lib.taxonomy) SequenceTrimmer (class in eplace_lib.alignment) setup_mmseqs_database() (in module eplace_lib.ncbi_download) setup_mmseqs_taxonomy() (in module eplace_lib.ncbi_download) setup_ncbi_database() (in module eplace_lib.ncbi_download) SimpleNewickNode (class in eplace_lib.alignment)

sort_strings_and_numbers() (in module eplace_lib.taxonomy) subject_end (eplace_lib.blast_analysis.BlastHit attribute), [1] subject_id (eplace_lib.blast_analysis.BlastHit attribute), [1] subject_length (eplace_lib.blast_analysis.BlastHit attribute), [1] subject_start (eplace_lib.blast_analysis.BlastHit attribute), [1] subject_taxid (eplace_lib.blast_analysis.BlastHit attribute) subject_taxids (eplace_lib.blast_analysis.BlastHit attribute) subject_taxonomy (eplace_lib.blast_analysis.BlastHit attribute), [1]

T

TaxonomyExtractor (class in eplace_lib.taxonomy) TREE_FILE command line option

trim_grouped_sequences() (in module eplace_lib.alignment) trim_sequence_by_coordinates() (eplace_lib.alignment.SequenceTrimmer static method) trim_sequences_from_blast_hits() (eplace_lib.alignment.SequenceTrimmer static method)

V

validate_mmseqs_memory_limit() (in module eplace_lib.blast_analysis)

verify_md5() (eplace_lib.ncbi_download.NCBIDownloader method)

W

wait_for_tree_jobs() (eplace_lib.alignment.IQTreeBuilder static method)