Index

Symbols

--attr-index <attr_index> edit-gff-table command line option --attr-value <attr_value> blast2gff-blastdb command line option blast2gff-uniprot command line option --attribute <attribute> edit-gff-table command line option filter-gff-sequence command line option --attributes <attributes> edit-gff-add command line option edit-gff-remove command line option edit-gff-rename command line option edit-gff-view command line option --average add-gff-info-cov_samtools command line option --bin-attribute <bin_attribute> add-gff-info-bins command line option --bin-id <bin_id> add-gff-info-bins command line option --bins-results <bins_results> add-gff-info-bins command line option --bitscore <bitscore> blast2gff-blastdb command line option blast2gff-uniprot command line option taxon-utils-lca command line option --buffer <buffer> add-gff-info-uniprot command line option --cache-table add-gff-info-addtaxa command line option --choose-func <choose_func> filter-gff-overlap command line option --chunk-size <chunk_size> taxon-utils-to_hdf command line option --cite add-gff-info command line option blast2gff command line option edit-gff command line option fasta-utils command line option fastq-utils command line option filter-gff command line option get-gff-info command line option json2gff command line option pnps-gen command line option sampling-utils command line option taxon-utils command line option --coding-prop <coding_prop> sampling-utils-rand_seq command line option --comment <comment> edit-gff-table command line option --comparison <comparison> filter-gff-sequence command line option --const-model sampling-utils-rand_seq command line option --count-files <count_files> add-gff-info-counts command line option --db-quality <db_quality> blast2gff-blastdb command line option blast2gff-uniprot command line option --db-used <db_used> blast2gff-blastdb command line option blast2gff-uniprot command line option --default-value <default_value> edit-gff-table command line option --depths <depths> add-gff-info-cov_samtools command line option --description add-gff-info-kegg command line option --dictionary <dictionary> add-gff-info-addtaxa command line option --dist-loc <dist_loc> sampling-utils-rand_seq command line option --eggnog add-gff-info-uniprot command line option --email <email> add-gff-info-kegg command line option add-gff-info-uniprot command line option --enzymes add-gff-info-uniprot command line option --exclude-taxon-id <exclude_taxon_id> taxon-utils-filter command line option --exclude-taxon-name <exclude_taxon_name> taxon-utils-filter command line option --fasta-file <fasta_file> blast2gff-blastdb command line option blast2gff-uniprot command line option pnps-gen-vcf command line option pnps-gen-vcf_alt command line option --fastq sampling-utils-rand_seq command line option sampling-utils-sample command line option sampling-utils-sample_stream command line option --feat-type <feat_type> blast2gff-blastdb command line option blast2gff-uniprot command line option taxon-utils-lca command line option --feature <feature> pnps-gen-vcf command line option pnps-gen-vcf_alt command line option --featureCounts add-gff-info-counts command line option --file-list <file_list> pnps-gen-vcf_alt command line option --file-name fasta-utils-rename command line option --force-taxon-id add-gff-info-unipfile command line option add-gff-info-uniprot command line option --fpkms add-gff-info-counts command line option --function <function> filter-gff-sequence command line option --gc-content fasta-utils-info command line option --gc-content <gc_content> sampling-utils-rand_seq command line option --gene-attr <gene_attr> add-gff-info-addtaxa command line option --gene-id <gene_id> get-gff-info-gtf command line option --gene-index <gene_index> blast2gff-blastdb command line option --gene-map <gene_map> pnps-gen-full command line option --gene-taxon-table <gene_taxon_table> add-gff-info-addtaxa command line option --gff-file <gff_file> pnps-gen-vcf command line option pnps-gen-vcf_alt command line option --group-by-attr <group_by_attr> taxon-utils-lca command line option --gzip fasta-utils-split command line option get-gff-info-split command line option sampling-utils-sample command line option --hash-type <hash_type> fasta-utils-info command line option --hdf-table <hdf_table> add-gff-info-addtaxa command line option --header edit-gff-view command line option fasta-utils-info command line option taxon-utils-get command line option --header-bin add-gff-info-bins command line option --header-contains <header_contains> fasta-utils-filter command line option --header-file <header_file> fasta-utils-filter command line option --header-index <header_index> add-gff-info-bins command line option --header-replace <header_replace> add-gff-info-bins command line option --header-sep <header_sep> blast2gff-blastdb command line option --header-separator <header_separator> add-gff-info-bins command line option --id-attr <id_attr> add-gff-info-pfam command line option --id-file <id_file> taxon-utils-get command line option --ignore-missing-bin add-gff-info-bins command line option --include-children taxon-utils-get command line option --include-seq fasta-utils-info command line option --include-taxon-id <include_taxon_id> taxon-utils-filter command line option --include-taxon-name <include_taxon_name> taxon-utils-filter command line option --indent <indent> get-gff-info-mongodb command line option --index-size <index_size> taxon-utils-to_hdf command line option --infer-params <infer_params> sampling-utils-rand_seq command line option --iterations <iterations> filter-gff-overlap command line option --json-out get-gff-info-cov command line option --keep-empty edit-gff-view command line option --kegg-id <kegg_id> add-gff-info-kegg command line option --kegg_orthologs add-gff-info-uniprot command line option --key <key> edit-gff-table command line option --key-index <key_index> edit-gff-table command line option --krona-total <krona_total> taxon-utils-lca command line option --len-gt <len_gt> fasta-utils-filter command line option --len-lt <len_lt> fasta-utils-filter command line option --length <length> sampling-utils-rand_seq command line option --lineage add-gff-info-uniprot command line option pnps-gen-full command line option pnps-gen-rank command line option --manual add-gff-info command line option --mapping <mapping> add-gff-info-unipfile command line option add-gff-info-uniprot command line option --mapping-file <mapping_file> add-gff-info-unipfile command line option --master-file <master_file> sampling-utils-sync command line option --max-seq <max_seq> sampling-utils-sample command line option sampling-utils-sample_stream command line option --min-cov <min_cov> pnps-gen-full command line option pnps-gen-rank command line option --min-coverage <min_coverage> filter-gff-cov command line option --min-freq <min_freq> pnps-gen-vcf command line option pnps-gen-vcf_alt command line option --min-num <min_num> pnps-gen-full command line option pnps-gen-rank command line option --min-qual <min_qual> pnps-gen-vcf command line option pnps-gen-vcf_alt command line option --min-reads <min_reads> pnps-gen-vcf command line option pnps-gen-vcf_alt command line option --name-file <name_file> taxon-utils-get command line option --no-cache get-gff-info-mongodb command line option --no-fuzzy taxon-utils-get command line option --no-lca <no_lca> taxon-utils-lca command line option taxon-utils-lca_line command line option --no-rename fasta-utils-info command line option --no-split blast2gff-blastdb command line option blast2gff-uniprot command line option --no-strand filter-gff-overlap command line option --no-wrap fasta-utils-translate command line option get-gff-info-sequence command line option --num-ann <num_ann> edit-gff-fields command line option --num-eq <num_eq> filter-gff-values command line option --num-ge <num_ge> filter-gff-values command line option --num-gt <num_gt> filter-gff-values command line option --num-le <num_le> filter-gff-values command line option --num-lines <num_lines> pnps-gen-vcf command line option pnps-gen-vcf_alt command line option --num-lt <num_lt> filter-gff-values command line option --num-seqs <num_seqs> add-gff-info-cov_samtools command line option sampling-utils-rand_seq command line option --number <number> fasta-utils-split command line option get-gff-info-split command line option sampling-utils-sample command line option --one-seq fasta-utils-translate command line option --only-edited edit-gff-add command line option edit-gff-table command line option --only-ids <only_ids> taxon-utils-get command line option --only-names <only_names> taxon-utils-get command line option --only-pn pnps-gen-full command line option pnps-gen-rank command line option --only-ps pnps-gen-full command line option pnps-gen-rank command line option --only-ranked taxon-utils-lca command line option taxon-utils-lca_line command line option --out-format <out_format> taxon-utils-lca command line option --out-gff fasta-utils-info command line option --output-dir <output_dir> get-gff-info-dbm command line option --overwrite edit-gff-add command line option taxon-utils-to_hdf command line option --parquet pnps-gen-full command line option --partial taxon-utils-get command line option --pathways add-gff-info-kegg command line option --prefix <prefix> fasta-utils-rename command line option fasta-utils-split command line option get-gff-info-split command line option sampling-utils-sample command line option --prob <prob> sampling-utils-sample command line option sampling-utils-sample_stream command line option --prodigal-gene edit-gff-table command line option --progress add-gff-info-addtaxa command line option add-gff-info-counts command line option add-gff-info-cov_samtools command line option add-gff-info-exp_syn command line option add-gff-info-unipfile command line option blast2gff-blastdb command line option blast2gff-uniprot command line option fasta-utils-translate command line option filter-gff-cov command line option filter-gff-overlap command line option filter-gff-sequence command line option filter-gff-values command line option get-gff-info-cov command line option get-gff-info-mongodb command line option get-gff-info-sequence command line option sampling-utils-rand_seq command line option taxon-utils-filter command line option taxon-utils-lca command line option taxon-utils-to_hdf command line option --protein-names add-gff-info-uniprot command line option --rank <rank> pnps-gen-full command line option pnps-gen-rank command line option --read-model <read_model> sampling-utils-rand_seq command line option --reference <reference> add-gff-info-exp_syn command line option filter-gff-cov command line option get-gff-info-cov command line option get-gff-info-sequence command line option taxon-utils-lca command line option --remove-version blast2gff-blastdb command line option --rename filter-gff-cov command line option get-gff-info-cov command line option taxon-utils-lca command line option --results-type <results_type> add-gff-info-bins command line option --reverse get-gff-info-sequence command line option --sample-alignment <sample_alignment> add-gff-info-coverage command line option --sample-file <sample_file> pnps-gen-vcf_alt command line option --sample-ids <sample_ids> pnps-gen-vcf command line option --samples <samples> add-gff-info-counts command line option add-gff-info-cov_samtools command line option --save-model <save_model> sampling-utils-rand_seq command line option --separator <separator> edit-gff-table command line option edit-gff-view command line option fasta-utils-rename command line option pnps-gen-full command line option taxon-utils-get command line option taxon-utils-lca_line command line option --seq-pattern <seq_pattern> fasta-utils-filter command line option --simple-table taxon-utils-lca command line option --size <size> filter-gff-overlap command line option --skip-no-taxon add-gff-info-addtaxa command line option --skip-rows <skip_rows> edit-gff-table command line option --snp-data <snp_data> pnps-gen-full command line option pnps-gen-rank command line option --sort-attr <sort_attr> filter-gff-overlap command line option --sorted filter-gff-cov command line option filter-gff-overlap command line option filter-gff-sequence command line option taxon-utils-lca command line option --split add-gff-info-exp_syn command line option get-gff-info-sequence command line option --str-eq <str_eq> filter-gff-values command line option --str-in <str_in> filter-gff-values command line option --strand-specific filter-gff-cov command line option get-gff-info-cov command line option --strict edit-gff-rename command line option --strip fastq-utils-di command line option --strip-kegg edit-gff-table command line option --suffix-len <suffix_len> fasta-utils-rename command line option --table taxon-utils-filter command line option --table <table> fasta-utils-uid command line option --table-file <table_file> edit-gff-table command line option --table-name <table_name> taxon-utils-to_hdf command line option --tax-sep <tax_sep> taxon-utils-get command line option --tax-type <tax_type> taxon-utils-import command line option --taxon-db <taxon_db> add-gff-info-addtaxa command line option --taxon-id add-gff-info-uniprot command line option --taxon-ids <taxon_ids> pnps-gen-full command line option

--taxon_ids <taxon_ids> pnps-gen-rank command line option --taxonomy <taxonomy> add-gff-info-addtaxa command line option add-gff-info-bins command line option get-gff-info-mongodb command line option pnps-gen-full command line option pnps-gen-rank command line option taxon-utils-filter command line option taxon-utils-lca command line option taxon-utils-lca_line command line option --trans-table <trans_table> fasta-utils-translate command line option --trim-tail fasta-utils-filter command line option --two-columns pnps-gen-full command line option --uid-map <uid_map> pnps-gen-vcf_alt command line option --uids <uids> edit-gff-add command line option edit-gff-remove command line option --unstack pnps-gen-rank command line option --use-accession add-gff-info-pfam command line option --use-cname taxon-utils-get command line option --use-uid pnps-gen-full command line option --value <value> filter-gff-sequence command line option --verbose add-gff-info-addtaxa command line option add-gff-info-bins command line option add-gff-info-counts command line option add-gff-info-cov_samtools command line option add-gff-info-coverage command line option add-gff-info-exp_syn command line option add-gff-info-kegg command line option add-gff-info-pfam command line option add-gff-info-unipfile command line option add-gff-info-uniprot command line option blast2gff-blastdb command line option blast2gff-uniprot command line option edit-gff-add command line option edit-gff-fields command line option edit-gff-remove command line option edit-gff-rename command line option edit-gff-table command line option edit-gff-view command line option fasta-utils-filter command line option fasta-utils-info command line option fasta-utils-rename command line option fasta-utils-split command line option fasta-utils-translate command line option fasta-utils-uid command line option fastq-utils-convert command line option fastq-utils-di command line option fastq-utils-il command line option fastq-utils-sort command line option filter-gff-cov command line option filter-gff-overlap command line option filter-gff-sequence command line option filter-gff-values command line option get-gff-info-cov command line option get-gff-info-dbm command line option get-gff-info-gtf command line option get-gff-info-mongodb command line option get-gff-info-sequence command line option get-gff-info-split command line option json2gff-mongodb command line option pnps-gen-full command line option pnps-gen-rank command line option pnps-gen-vcf command line option pnps-gen-vcf_alt command line option sampling-utils-rand_seq command line option sampling-utils-sample command line option sampling-utils-sample_stream command line option sampling-utils-sync command line option taxon-utils-filter command line option taxon-utils-get command line option taxon-utils-import command line option taxon-utils-lca command line option taxon-utils-lca_line command line option taxon-utils-to_hdf command line option --version add-gff-info command line option blast2gff command line option edit-gff command line option fasta-utils command line option fastq-utils command line option filter-gff command line option get-gff-info command line option json2gff command line option pnps-gen command line option sampling-utils command line option taxon-utils command line option --wrap fasta-utils-filter command line option -1 fasta-utils-translate command line option -2 pnps-gen-full command line option -a add-gff-info-addtaxa command line option add-gff-info-bins command line option add-gff-info-coverage command line option add-gff-info-pfam command line option blast2gff-blastdb command line option blast2gff-uniprot command line option edit-gff-add command line option edit-gff-remove command line option edit-gff-rename command line option edit-gff-table command line option edit-gff-view command line option fasta-utils-info command line option filter-gff-overlap command line option filter-gff-sequence command line option pnps-gen-vcf command line option pnps-gen-vcf_alt command line option sampling-utils-rand_seq command line option taxon-utils-get command line option taxon-utils-lca command line option taxon-utils-lca_line command line option -ai edit-gff-table command line option -b blast2gff-blastdb command line option blast2gff-uniprot command line option taxon-utils-lca command line option -c add-gff-info-addtaxa command line option add-gff-info-counts command line option add-gff-info-kegg command line option add-gff-info-uniprot command line option edit-gff-table command line option filter-gff-cov command line option filter-gff-overlap command line option filter-gff-sequence command line option get-gff-info-mongodb command line option pnps-gen-full command line option pnps-gen-rank command line option taxon-utils-get command line option taxon-utils-to_hdf command line option -d add-gff-info-addtaxa command line option add-gff-info-cov_samtools command line option add-gff-info-kegg command line option add-gff-info-uniprot command line option edit-gff-table command line option filter-gff-overlap command line option get-gff-info-dbm command line option sampling-utils-rand_seq command line option taxon-utils-get command line option -db add-gff-info-addtaxa command line option blast2gff-blastdb command line option blast2gff-uniprot command line option -dbq blast2gff-blastdb command line option blast2gff-uniprot command line option -e add-gff-info-addtaxa command line option add-gff-info-bins command line option add-gff-info-counts command line option add-gff-info-uniprot command line option pnps-gen-full command line option taxon-utils-filter command line option -ec add-gff-info-uniprot command line option -en taxon-utils-filter command line option -f add-gff-info-addtaxa command line option add-gff-info-counts command line option add-gff-info-unipfile command line option add-gff-info-uniprot command line option edit-gff-add command line option edit-gff-remove command line option fasta-utils-filter command line option fasta-utils-rename command line option filter-gff-cov command line option filter-gff-sequence command line option get-gff-info-cov command line option get-gff-info-sequence command line option pnps-gen-vcf command line option pnps-gen-vcf_alt command line option taxon-utils-lca command line option -ft blast2gff-blastdb command line option blast2gff-uniprot command line option pnps-gen-vcf command line option pnps-gen-vcf_alt command line option taxon-utils-lca command line option -g fasta-utils-info command line option get-gff-info-gtf command line option pnps-gen-full command line option pnps-gen-vcf command line option pnps-gen-vcf_alt command line option taxon-utils-lca command line option -gc fasta-utils-info command line option sampling-utils-rand_seq command line option -h add-gff-info-bins command line option edit-gff-view command line option fasta-utils-info command line option -i add-gff-info-bins command line option add-gff-info-pfam command line option add-gff-info-unipfile command line option blast2gff-blastdb command line option get-gff-info-mongodb command line option pnps-gen-full command line option pnps-gen-rank command line option sampling-utils-rand_seq command line option taxon-utils-filter command line option taxon-utils-get command line option -in taxon-utils-filter command line option -j get-gff-info-cov command line option -k blast2gff-blastdb command line option blast2gff-uniprot command line option edit-gff-table command line option edit-gff-view command line option -ki edit-gff-table command line option -ko add-gff-info-uniprot command line option -kt taxon-utils-lca command line option -l add-gff-info-uniprot command line option fasta-utils-rename command line option filter-gff-sequence command line option pnps-gen-full command line option pnps-gen-rank command line option pnps-gen-vcf_alt command line option sampling-utils-rand_seq command line option -m add-gff-info-cov_samtools command line option add-gff-info-kegg command line option add-gff-info-unipfile command line option add-gff-info-uniprot command line option pnps-gen-full command line option pnps-gen-rank command line option pnps-gen-vcf command line option sampling-utils-rand_seq command line option sampling-utils-sync command line option taxon-utils-lca command line option -n add-gff-info-cov_samtools command line option blast2gff-blastdb command line option blast2gff-uniprot command line option edit-gff-fields command line option fasta-utils-split command line option filter-gff-overlap command line option get-gff-info-split command line option pnps-gen-vcf command line option pnps-gen-vcf_alt command line option sampling-utils-rand_seq command line option sampling-utils-sample command line option taxon-utils-lca command line option taxon-utils-lca_line command line option taxon-utils-to_hdf command line option -o edit-gff-add command line option edit-gff-table command line option taxon-utils-get command line option -p add-gff-info-kegg command line option edit-gff-table command line option fasta-utils-rename command line option fasta-utils-split command line option get-gff-info-split command line option pnps-gen-full command line option sampling-utils-sample command line option taxon-utils-filter command line option taxon-utils-get command line option taxon-utils-lca command line option -pn pnps-gen-full command line option pnps-gen-rank command line option -ps pnps-gen-full command line option pnps-gen-rank command line option -q pnps-gen-vcf command line option pnps-gen-vcf_alt command line option sampling-utils-rand_seq command line option sampling-utils-sample command line option sampling-utils-sample_stream command line option -r add-gff-info-bins command line option add-gff-info-exp_syn command line option blast2gff-blastdb command line option edit-gff-table command line option fasta-utils-info command line option filter-gff-cov command line option get-gff-info-cov command line option get-gff-info-sequence command line option pnps-gen-full command line option pnps-gen-rank command line option pnps-gen-vcf command line option pnps-gen-vcf_alt command line option sampling-utils-rand_seq command line option sampling-utils-sample command line option sampling-utils-sample_stream command line option taxon-utils-lca command line option -s add-gff-info-bins command line option, [1] add-gff-info-counts command line option add-gff-info-cov_samtools command line option add-gff-info-exp_syn command line option blast2gff-blastdb command line option edit-gff-rename command line option edit-gff-table command line option edit-gff-view command line option fasta-utils-filter command line option fasta-utils-info command line option fasta-utils-rename command line option fastq-utils-di command line option filter-gff-cov command line option filter-gff-overlap command line option get-gff-info-cov command line option get-gff-info-sequence command line option pnps-gen-full command line option pnps-gen-rank command line option pnps-gen-vcf_alt command line option taxon-utils-get command line option taxon-utils-lca command line option taxon-utils-lca_line command line option taxon-utils-to_hdf command line option -t add-gff-info-addtaxa command line option add-gff-info-bins command line option add-gff-info-uniprot command line option edit-gff-table command line option fasta-utils-translate command line option fasta-utils-uid command line option filter-gff-cov command line option filter-gff-overlap command line option filter-gff-sequence command line option get-gff-info-mongodb command line option pnps-gen-full command line option pnps-gen-rank command line option taxon-utils-filter command line option taxon-utils-import command line option taxon-utils-lca command line option taxon-utils-lca_line command line option -u pnps-gen-full command line option pnps-gen-rank command line option pnps-gen-vcf_alt command line option -v add-gff-info-addtaxa command line option add-gff-info-bins command line option add-gff-info-counts command line option add-gff-info-cov_samtools command line option add-gff-info-coverage command line option add-gff-info-exp_syn command line option add-gff-info-kegg command line option add-gff-info-pfam command line option add-gff-info-unipfile command line option add-gff-info-uniprot command line option blast2gff-blastdb command line option blast2gff-uniprot command line option edit-gff-add command line option edit-gff-fields command line option edit-gff-remove command line option edit-gff-rename command line option edit-gff-table command line option edit-gff-view command line option fasta-utils-filter command line option fasta-utils-info command line option fasta-utils-rename command line option fasta-utils-split command line option fasta-utils-translate command line option fasta-utils-uid command line option fastq-utils-convert command line option fastq-utils-di command line option fastq-utils-il command line option fastq-utils-sort command line option filter-gff-cov command line option filter-gff-overlap command line option filter-gff-sequence command line option filter-gff-values command line option get-gff-info-cov command line option get-gff-info-dbm command line option get-gff-info-gtf command line option get-gff-info-mongodb command line option get-gff-info-sequence command line option get-gff-info-split command line option json2gff-mongodb command line option pnps-gen-full command line option pnps-gen-rank command line option pnps-gen-vcf command line option pnps-gen-vcf_alt command line option sampling-utils-rand_seq command line option sampling-utils-sample command line option sampling-utils-sample_stream command line option sampling-utils-sync command line option taxon-utils-filter command line option taxon-utils-get command line option taxon-utils-import command line option taxon-utils-lca command line option taxon-utils-lca_line command line option taxon-utils-to_hdf command line option -w edit-gff-add command line option fasta-utils-filter command line option fasta-utils-translate command line option get-gff-info-sequence command line option taxon-utils-to_hdf command line option -x add-gff-info-addtaxa command line option add-gff-info-bins command line option sampling-utils-rand_seq command line option sampling-utils-sample command line option sampling-utils-sample_stream command line option taxon-utils-get command line option -y add-gff-info-bins command line option -z fasta-utils-split command line option get-gff-info-split command line option sampling-utils-sample command line option taxon-utils-get command line option

_

__contains__() (mgkit.io.gff.GenomicRange method) (mgkit.taxon.Taxonomy method) __eq__() (mgkit.graphs.Reaction method) __getitem__() (mgkit.db.mongo.GFFDB method) (mgkit.taxon.Taxonomy method) __iter__() (mgkit.db.mongo.GFFDB method) (mgkit.taxon.Taxonomy method)

__len__() (mgkit.taxon.Taxonomy method) __repr__() (mgkit.taxon.Taxonomy method) _get_kmers() (in module mgkit.utils.sequence) _sequence_signature() (in module mgkit.utils.sequence) _signatures_matrix() (in module mgkit.utils.sequence) _sliding_window() (in module mgkit.utils.sequence)

A

aa_change (mgkit.io.snpdat.SNPDatRow attribute), [1] add() (mgkit.snps.classes.GeneSNP method) add-gff-info command line option --cite --manual --version add-gff-info-addtaxa command line option --cache-table --dictionary <dictionary> --gene-attr <gene_attr> --gene-taxon-table <gene_taxon_table> --hdf-table <hdf_table> --progress --skip-no-taxon --taxon-db <taxon_db> --taxonomy <taxonomy> --verbose -a -c -d -db -e -f -t -v -x INPUT_FILE OUTPUT_FILE add-gff-info-bins command line option --bin-attribute <bin_attribute> --bin-id <bin_id> --bins-results <bins_results> --header-bin --header-index <header_index> --header-replace <header_replace> --header-separator <header_separator> --ignore-missing-bin --results-type <results_type> --taxonomy <taxonomy> --verbose -a -e -h -i -r -s, [1] -t -v -x -y INPUT_FILE OUTPUT_FILE add-gff-info-counts command line option --count-files <count_files> --featureCounts --fpkms --progress --samples <samples> --verbose -c -e -f -s -v INPUT_FILE OUTPUT_FILE add-gff-info-cov_samtools command line option --average --depths <depths> --num-seqs <num_seqs> --progress --samples <samples> --verbose -d -m -n -s -v INPUT_FILE OUTPUT_FILE add-gff-info-coverage command line option --sample-alignment <sample_alignment> --verbose -a -v INPUT_FILE OUTPUT_FILE add-gff-info-exp_syn command line option --progress --reference <reference> --split --verbose -r -s -v INPUT_FILE OUTPUT_FILE

add-gff-info-kegg command line option --description --email <email> --kegg-id <kegg_id> --pathways --verbose -c -d -m -p -v INPUT_FILE OUTPUT_FILE add-gff-info-pfam command line option --id-attr <id_attr> --use-accession --verbose -a -i -v INPUT_FILE OUTPUT_FILE add-gff-info-unipfile command line option --force-taxon-id --mapping <mapping> --mapping-file <mapping_file> --progress --verbose -f -i -m -v INPUT_FILE OUTPUT_FILE add-gff-info-uniprot command line option --buffer <buffer> --eggnog --email <email> --enzymes --force-taxon-id --kegg_orthologs --lineage --mapping <mapping> --protein-names --taxon-id --verbose -c -d -e -ec -f -ko -l -m -t -v INPUT_FILE OUTPUT_FILE add_basic_options() (in module mgkit.workflow.utils) add_bin_information() (in module mgkit.workflow.add_gff_info) add_blast_result_to_annotation() (in module mgkit.io.blast) add_coverage_info() (in module mgkit.align) add_exp_syn_count() (mgkit.io.gff.Annotation method) add_gc_content() (mgkit.io.gff.Annotation method) add_gc_ratio() (mgkit.io.gff.Annotation method) add_lineage() (mgkit.taxon.Taxonomy method) add_module_compounds() (in module mgkit.graphs) add_seq() (mgkit.utils.sequence.Alignment method) add_seqs() (mgkit.utils.sequence.Alignment method) add_significance_to_boxplot() (in module mgkit.plots.boxplot) add_snp() (mgkit.snps.classes.GeneSNP method) add_taxon() (mgkit.taxon.Taxonomy method) add_uniprot_info() (in module mgkit.workflow.add_gff_info) add_values_to_boxplot() (in module mgkit.plots.boxplot) advance_file() (mgkit.align.SamtoolsDepth method) aggr_filtered_list() (in module mgkit.filter.lists) Alignment (class in mgkit.utils.sequence) ann_frame (mgkit.io.snpdat.SNPDatRow attribute), [1] annotate_graph_nodes() (in module mgkit.graphs) annotate_sequence() (in module mgkit.io.gff) Annotation (class in mgkit.io.gff) annotation_coverage() (in module mgkit.io.gff) annotation_coverage_sorted() (in module mgkit.io.gff) annotation_elongation() (in module mgkit.io.gff) api_url (mgkit.kegg.KeggClientRest attribute) apply_func_to_values() (in module mgkit.utils.dictionary) apply_func_window() (in module mgkit.utils.common) attr (mgkit.io.gff.Annotation attribute) AttributeNotFound average_length() (in module mgkit.utils.common)

B

BAC_PLT (in module mgkit.utils.trans_tables) barchart_categories() (in module mgkit.plots.unused) baseheatmap() (in module mgkit.plots.heatmap) batch_load_htseq_counts() (in module mgkit.counts.func) between() (in module mgkit.utils.common) bitscore() (mgkit.io.gff.Annotation property) BLACK_LIST (in module mgkit.consts) blast2gff command line option --cite --version blast2gff-blastdb command line option --attr-value <attr_value> --bitscore <bitscore> --db-quality <db_quality> --db-used <db_used> --fasta-file <fasta_file> --feat-type <feat_type> --gene-index <gene_index> --header-sep <header_sep> --no-split --progress --remove-version --verbose -a -b -db -dbq -ft -i -k -n -r -s -v BLAST_FILE GFF_FILE

blast2gff-uniprot command line option --attr-value <attr_value> --bitscore <bitscore> --db-quality <db_quality> --db-used <db_used> --fasta-file <fasta_file> --feat-type <feat_type> --no-split --progress --verbose -a -b -db -dbq -ft -k -n -v BLAST_FILE GFF_FILE BLAST_FILE blast2gff-blastdb command line option blast2gff-uniprot command line option boxplot_dataframe() (in module mgkit.plots.boxplot) boxplot_dataframe_multindex() (in module mgkit.plots.boxplot) build_graph() (in module mgkit.graphs) build_rank_matrix() (in module mgkit.snps.funcs) build_weighted_graph() (in module mgkit.graphs)

C

c_name (mgkit.taxon.UniprotTaxonTuple attribute) cache (mgkit.kegg.KeggClientRest attribute) cache_dict_file (class in mgkit.utils.dictionary) calc_coefficient_of_variation() (in module mgkit.mappings.pandas_map) calc_n50() (in module mgkit.utils.sequence) calc_pn() (mgkit.snps.classes.RatioMixIn method) calc_ps() (mgkit.snps.classes.RatioMixIn method) calc_ratio() (mgkit.snps.classes.RatioMixIn method) calc_ratio_flag() (mgkit.snps.classes.RatioMixIn method) CASAVA_HEADER_NEW (in module mgkit.io.fastq) CASAVA_HEADER_OLD (in module mgkit.io.fastq) CAZY_FAMILIES (in module mgkit.mappings.cazy) change_mapping_level() (in module mgkit.mappings.enzyme) check_fastq_type() (in module mgkit.io.fastq) check_snp_in_seq() (in module mgkit.utils.sequence) check_snp_in_set() (in module mgkit.workflow.pnps_gen) (in module mgkit.workflow.snp_parser) check_version() (in module mgkit) choose_annotation() (in module mgkit.filter.gff) choose_header_type() (in module mgkit.io.fastq) chr_name (mgkit.io.snpdat.SNPDatRow attribute), [1] chr_pos (mgkit.io.snpdat.SNPDatRow attribute), [1] cite() (in module mgkit) cite_callback() (in module mgkit.workflow.utils) CiteAction (class in mgkit.workflow.utils) classes (mgkit.kegg.KeggModule attribute) closed (mgkit.align.SamtoolsDepth attribute) cmp_compounds() (mgkit.graphs.Reaction method) codon (mgkit.io.snpdat.SNPDatRow attribute), [1] col_func_firstel() (in module mgkit.plots.abund) col_func_name() (in module mgkit.plots.abund)

col_func_taxon() (in module mgkit.plots.abund) ColorFormatter (class in mgkit.logger) colors (mgkit.logger.ColorFormatter attribute) combine_dict() (in module mgkit.utils.dictionary) combine_dict_one_value() (in module mgkit.utils.dictionary) combine_sample_snps() (in module mgkit.snps.funcs) compare_header() (in module mgkit.workflow.sampling_utils) complement_ranges() (in module mgkit.utils.common) compounds (mgkit.kegg.KeggModule attribute) compressed_handle() (in module mgkit.io.utils) concatenate_and_rename_tables() (in module mgkit.mappings.pandas_map) config_log() (in module mgkit.logger) config_log_to_file() (in module mgkit.logger) conn (mgkit.db.mongo.GFFDB attribute) contact (mgkit.kegg.KeggClientRest attribute) conv() (mgkit.kegg.KeggClientRest method) convert_aa_to_nuc_coord() (in module mgkit.utils.sequence) convert_gff_to_gtf() (in module mgkit.io.gff) convert_record() (mgkit.db.mongo.GFFDB method) convert_seqid_to_new() (in module mgkit.io.fastq) convert_seqid_to_old() (in module mgkit.io.fastq) copy_edges() (in module mgkit.graphs) copy_nodes() (in module mgkit.graphs) count_genes_in_mapping() (in module mgkit.mappings.utils) counts() (mgkit.io.gff.Annotation property) coverage (mgkit.snps.classes.GeneSNP attribute), [1] coverage() (mgkit.io.gff.Annotation property) covered_annotation_bp() (in module mgkit.align) cpd_desc_re (mgkit.kegg.KeggClientRest attribute) cpd_re (mgkit.kegg.KeggClientRest attribute) create_gff_dbm() (in module mgkit.db.dbm) cursor() (mgkit.db.mongo.GFFDB method)

D

data (mgkit.align.SamtoolsDepth attribute) datawarehouse_search() (in module mgkit.net.embl) db (mgkit.db.dbm.GFFDB attribute) (mgkit.db.mongo.GFFDB attribute) db() (mgkit.io.gff.Annotation property) dbfetch() (in module mgkit.net.embl) dbq() (mgkit.io.gff.Annotation property) DEBUG (in module mgkit) DEFAULT_SNP_FILTER (in module mgkit.consts) del_attr() (mgkit.io.gff.Annotation method) dendrogram() (in module mgkit.plots.heatmap) density (mgkit.align.SamtoolsDepth attribute) DependencyError

deprecated() (in module mgkit.utils.common) dict_to_text() (in module mgkit.utils.dictionary) diff_gff() (in module mgkit.io.gff) distance_taxa_ancestor() (in module mgkit.taxon) distance_two_taxa() (in module mgkit.taxon) draw_1d_grid() (in module mgkit.plots.abund) draw_axis_internal_triangle() (in module mgkit.plots.abund) draw_circles() (in module mgkit.plots.abund) draw_triangle_grid() (in module mgkit.plots.abund) drop_sequence() (mgkit.align.SamtoolsDepth method) drop_taxon() (mgkit.taxon.Taxonomy method) DRS_MIT (in module mgkit.utils.trans_tables) DuplicateKeyError

E

EDGE_LINKS (in module mgkit.graphs) edit-gff command line option --cite --version edit-gff-add command line option --attributes <attributes> --only-edited --overwrite --uids <uids> --verbose -a -f -o -v -w INPUT_FILE OUTPUT_FILE edit-gff-fields command line option --num-ann <num_ann> --verbose -n -v GFF_FILE TXT_FILE edit-gff-remove command line option --attributes <attributes> --uids <uids> --verbose -a -f -v INPUT_FILE OUTPUT_FILE edit-gff-rename command line option --attributes <attributes> --strict --verbose -a -s -v INPUT_FILE OUTPUT_FILE edit-gff-table command line option --attr-index <attr_index> --attribute <attribute> --comment <comment> --default-value <default_value> --key <key> --key-index <key_index> --only-edited --prodigal-gene --separator <separator> --skip-rows <skip_rows> --strip-kegg --table-file <table_file> --verbose -a -ai -c -d -k -ki -o -p -r -s -t -v INPUT_FILE OUTPUT_FILE

edit-gff-view command line option --attributes <attributes> --header --keep-empty --separator <separator> --verbose -a -h -k -s -v INPUT_FILE OUTPUT_FILE EGGNOG_CAT (in module mgkit.mappings.eggnog) EGGNOG_CAT_KEYS (in module mgkit.mappings.eggnog) EGGNOG_CAT_MAP (in module mgkit.mappings.eggnog) EGGNOG_CAT_NAMES (in module mgkit.mappings.eggnog) elongate_annotations() (in module mgkit.io.gff) EMBL_DBID (in module mgkit.net.embl) empty_cache() (mgkit.kegg.KeggClientRest method) end (mgkit.io.gff.GenomicRange attribute) entry (mgkit.kegg.KeggModule attribute) EntryNotFound ENZCLASS_REGEX (in module mgkit.mappings.enzyme) exit_script() (in module mgkit.workflow.utils) exon (mgkit.io.snpdat.SNPDatRow attribute), [1] exp_nonsyn (mgkit.snps.classes.GeneSNP attribute), [1] exp_nonsyn() (mgkit.io.gff.Annotation property) exp_syn (mgkit.snps.classes.GeneSNP attribute), [1] exp_syn() (mgkit.io.gff.Annotation property) expand_from_list() (mgkit.io.gff.GenomicRange method) expected_error_rate() (in module mgkit.filter.reads) extract_nuc_seqs() (in module mgkit.io.gff) extrapolate_model() (in module mgkit.utils.sequence)

F

fasta-utils command line option --cite --version fasta-utils-filter command line option --header-contains <header_contains> --header-file <header_file> --len-gt <len_gt> --len-lt <len_lt> --seq-pattern <seq_pattern> --trim-tail --verbose --wrap -f -s -v -w FASTA_FILE OUTPUT_FILE fasta-utils-info command line option --gc-content --hash-type <hash_type> --header --include-seq --no-rename --out-gff --verbose -a -g -gc -h -r -s -v FASTA_FILE OUTPUT_FILE fasta-utils-rename command line option --file-name --prefix <prefix> --separator <separator> --suffix-len <suffix_len> --verbose -f -l -p -s -v FASTA_FILE OUTPUT_FILE fasta-utils-split command line option --gzip --number <number> --prefix <prefix> --verbose -n -p -v -z FASTA_FILE fasta-utils-translate command line option --no-wrap --one-seq --progress --trans-table <trans_table> --verbose -1 -t -v -w FASTA_FILE OUTPUT_FILE fasta-utils-uid command line option --table <table> --verbose -t -v FASTA_FILE OUTPUT_FILE FASTA_FILE fasta-utils-filter command line option fasta-utils-info command line option fasta-utils-rename command line option fasta-utils-split command line option fasta-utils-translate command line option fasta-utils-uid command line option fastq-utils-convert command line option get-gff-info-sequence command line option fastq-utils command line option --cite --version fastq-utils-convert command line option --verbose -v FASTA_FILE FASTQ_FILE fastq-utils-di command line option --strip --verbose -s -v FASTQ_FILE MATE1_FILE MATE2_FILE fastq-utils-il command line option --verbose -v FASTQ_FILE MATE1_FILE MATE2_FILE fastq-utils-sort command line option --verbose -v MATE1_INPUT MATE1_OUTPUT MATE2_INPUT MATE2_OUTPUT FASTQ_FILE fastq-utils-convert command line option fastq-utils-di command line option fastq-utils-il command line option

feat_dist (mgkit.io.snpdat.SNPDatRow attribute), [1] feat_end (mgkit.io.snpdat.SNPDatRow attribute), [1] feat_num (mgkit.io.snpdat.SNPDatRow attribute), [1] feat_start (mgkit.io.snpdat.SNPDatRow attribute), [1] feat_type (mgkit.io.gff.Annotation attribute) feature (mgkit.io.snpdat.SNPDatRow attribute), [1] file_handle (mgkit.align.SamtoolsDepth attribute) filter-gff command line option --cite --version filter-gff-cov command line option --min-coverage <min_coverage> --progress --reference <reference> --rename --sorted --strand-specific --verbose -c -f -r -s -t -v INPUT_FILE OUTPUT_FILE filter-gff-overlap command line option --choose-func <choose_func> --iterations <iterations> --no-strand --progress --size <size> --sort-attr <sort_attr> --sorted --verbose -a -c -d -n -s -t -v INPUT_FILE OUTPUT_FILE filter-gff-sequence command line option --attribute <attribute> --comparison <comparison> --function <function> --progress --sorted --value <value> --verbose -a -c -f -l -t -v INPUT_FILE OUTPUT_FILE filter-gff-values command line option --num-eq <num_eq> --num-ge <num_ge> --num-gt <num_gt> --num-le <num_le> --num-lt <num_lt> --progress --str-eq <str_eq> --str-in <str_in> --verbose -v INPUT_FILE OUTPUT_FILE filter_annotations() (in module mgkit.filter.gff) filter_attr_num() (in module mgkit.filter.gff) filter_attr_num_s() (in module mgkit.filter.gff) filter_attr_str() (in module mgkit.filter.gff) filter_base() (in module mgkit.filter.gff) filter_base_num() (in module mgkit.filter.gff) filter_by_ancestor() (in module mgkit.filter.taxon) filter_counts() (in module mgkit.counts.func) filter_eq() (in module mgkit.workflow.filter_gff) filter_genesyn_by_coverage() (in module mgkit.snps.filter) filter_genesyn_by_gene_id() (in module mgkit.snps.filter) filter_genesyn_by_taxon_id() (in module mgkit.snps.filter) filter_graph() (in module mgkit.graphs) filter_gt() (in module mgkit.workflow.filter_gff) filter_in() (in module mgkit.workflow.filter_gff) filter_len() (in module mgkit.filter.gff) filter_lt() (in module mgkit.workflow.filter_gff) filter_nan() (in module mgkit.utils.dictionary) filter_ratios_by_numbers() (in module mgkit.utils.dictionary) filter_taxon_by_id_list() (in module mgkit.filter.taxon) FilterFails find() (mgkit.kegg.KeggClientRest method) find_annotation() (mgkit.db.mongo.GFFDB method) find_by_name() (mgkit.taxon.Taxonomy method) find_comparison() (in module mgkit.workflow.filter_gff) find_id_in_dict() (in module mgkit.utils.dictionary) find_submodules() (mgkit.kegg.KeggModule method) first_cp() (mgkit.kegg.KeggModule property) fit_lowess_interpolate() (in module mgkit.counts.glm) flat_sample_snps() (in module mgkit.snps.funcs) float_to_hex_color() (in module mgkit.plots.colors) format() (mgkit.logger.ColorFormatter method) fpkms() (mgkit.io.gff.Annotation property) frame (mgkit.io.snpdat.SNPDatRow attribute), [1] from_aa_blast_frag() (in module mgkit.io.gff) from_gff() (in module mgkit.counts.func) (in module mgkit.io.gff) from_glimmer3() (in module mgkit.io.gff) from_hmmer() (in module mgkit.io.gff) from_json() (in module mgkit.io.gff) (mgkit.snps.classes.GeneSNP method) from_kgml() (in module mgkit.graphs) from_mongodb() (in module mgkit.io.gff) from_nuc_blast() (in module mgkit.io.gff) from_nuc_blast_frag() (in module mgkit.io.gff) from_prodigal_frag() (in module mgkit.io.gff) from_sequence() (in module mgkit.io.gff)

G

gen_alt_map() (mgkit.taxon.Taxonomy method) gen_name_map() (mgkit.taxon.Taxonomy method) gene_id (mgkit.io.snpdat.SNPDatRow attribute), [1] (mgkit.snps.classes.GeneSNP attribute), [1] gene_id() (mgkit.io.gff.Annotation property) gene_name (mgkit.io.snpdat.SNPDatRow attribute), [1] GeneSNP (class in mgkit.snps.classes) GenomicRange (class in mgkit.io.gff) get-gff-info command line option --cite --version get-gff-info-cov command line option --json-out --progress --reference <reference> --rename --strand-specific --verbose -f -j -r -s -v GFF_FILE OUTPUT_FILE get-gff-info-dbm command line option --output-dir <output_dir> --verbose -d -v GFF_FILE get-gff-info-gtf command line option --gene-id <gene_id> --verbose -g -v GFF_FILE GTF_FILE get-gff-info-mongodb command line option --indent <indent> --no-cache --progress --taxonomy <taxonomy> --verbose -c -i -t -v GFF_FILE OUTPUT_FILE get-gff-info-sequence command line option --no-wrap --progress --reference <reference> --reverse --split --verbose -f -r -s -v -w FASTA_FILE GFF_FILE get-gff-info-split command line option --gzip --number <number> --prefix <prefix> --verbose -n -p -v -z GFF_FILE get_aa_data() (in module mgkit.workflow.hmmer2gff) get_aa_seq() (mgkit.io.gff.Annotation method) get_ancestor_map() (in module mgkit.taxon) get_annotation_map() (in module mgkit.io.gff) get_attr() (mgkit.io.gff.Annotation method) get_by_lineage() (mgkit.taxon.Taxonomy method) get_consensus() (mgkit.utils.sequence.Alignment method)

get_contigs_info() (in module mgkit.utils.sequence) get_default_filters() (in module mgkit.snps.filter) get_ec() (mgkit.io.gff.Annotation method) get_entry() (mgkit.kegg.KeggClientRest method) get_enzyme_full_name() (in module mgkit.mappings.enzyme) get_enzyme_level() (in module mgkit.mappings.enzyme) get_fc() (mgkit.io.gff.Annotation method) get_full_dataframe() (in module mgkit.snps.conv_func) get_gene_funccat() (mgkit.mappings.eggnog.NOGInfo method) get_gene_info() (in module mgkit.net.uniprot) get_gene_info_iter() (in module mgkit.net.uniprot) get_gene_map_dataframe() (in module mgkit.snps.conv_func) get_gene_nog() (mgkit.mappings.eggnog.NOGInfo method) get_gene_taxon_dataframe() (in module mgkit.snps.conv_func) get_general_eggnog_cat() (in module mgkit.mappings.eggnog) get_grid_figure() (in module mgkit.plots.utils) get_ids_names() (mgkit.kegg.KeggClientRest method) get_ko_to_eggnog_mappings() (in module mgkit.net.uniprot) get_lineage() (in module mgkit.taxon) (in module mgkit.workflow.pnps_gen) (mgkit.taxon.Taxonomy method) get_lineage_string() (mgkit.taxon.Taxonomy method) get_mapping() (mgkit.io.gff.Annotation method) get_mapping_level() (in module mgkit.mappings.enzyme) get_mappings() (in module mgkit.net.uniprot) (mgkit.io.gff.Annotation method) get_name_map() (mgkit.taxon.Taxonomy method) get_nog_funccat() (mgkit.mappings.eggnog.NOGInfo method) get_nog_gencat() (mgkit.mappings.eggnog.NOGInfo method) get_nogs_funccat() (mgkit.mappings.eggnog.NOGInfo method) get_nuc_seq() (mgkit.io.gff.Annotation method) get_number_of_samples() (mgkit.io.gff.Annotation method) get_ortholog_pathways() (mgkit.kegg.KeggClientRest method) get_pathway_links() (mgkit.kegg.KeggClientRest method) get_pfam_families() (in module mgkit.net.pfam) get_position() (mgkit.utils.sequence.Alignment method) get_range() (mgkit.io.gff.GenomicRange method) get_rank_dataframe() (in module mgkit.snps.conv_func) get_ranked_id() (mgkit.taxon.Taxonomy method) get_ranked_taxon() (mgkit.taxon.Taxonomy method) get_reaction_equations() (mgkit.kegg.KeggClientRest method) get_region_coverage() (in module mgkit.align) get_relative_pos() (mgkit.io.gff.GenomicRange method) get_seq_expected_syn_count() (in module mgkit.utils.sequence) get_seq_len() (mgkit.utils.sequence.Alignment method) get_seq_number_of_syn() (in module mgkit.utils.sequence) get_sequences_by_ids() (in module mgkit.net.embl) get_sequences_by_ko() (in module mgkit.net.uniprot) get_single_figure() (in module mgkit.plots.utils) get_snps() (mgkit.utils.sequence.Alignment method) get_syn_matrix() (in module mgkit.utils.sequence) get_syn_matrix_all() (in module mgkit.utils.sequence) get_taxon_colors_new() (in module mgkit.plots.unused) get_taxon_info() (in module mgkit.workflow.taxon_utils) get_uid_info() (in module mgkit.counts.func) get_uid_info_ann() (in module mgkit.counts.func) get_uniprot_ec_mappings() (in module mgkit.net.uniprot) get_variant_sequence() (in module mgkit.utils.sequence) GFF_FILE blast2gff-blastdb command line option blast2gff-uniprot command line option edit-gff-fields command line option get-gff-info-cov command line option get-gff-info-dbm command line option get-gff-info-gtf command line option get-gff-info-mongodb command line option get-gff-info-sequence command line option get-gff-info-split command line option json2gff-mongodb command line option taxon-utils-lca command line option GFFDB (class in mgkit.db.dbm) (class in mgkit.db.mongo) group_annotation_by_mapping() (in module mgkit.mappings.utils) group_annotations() (in module mgkit.io.gff) group_annotations_by_ancestor() (in module mgkit.io.gff) group_annotations_sorted() (in module mgkit.io.gff) group_dataframe_by_mapping() (in module mgkit.mappings.pandas_map) group_rank_matrix() (in module mgkit.snps.funcs) group_tuples_by_key() (in module mgkit.io.utils) grouped_spine() (in module mgkit.plots.heatmap) GTF_FILE get-gff-info-gtf command line option

H

has_attr() (mgkit.io.gff.Annotation method)

HDFDict (class in mgkit.utils.dictionary) heatmap_clustered() (in module mgkit.plots.heatmap)

I

id_prefix (mgkit.kegg.KeggClientRest attribute) IMPORT_FILE taxon-utils-import command line option in_feat (mgkit.io.snpdat.SNPDatRow attribute), [1] infer_parameters() (in module mgkit.workflow.sampling_utils) init_count_set() (in module mgkit.workflow.pnps_gen) (in module mgkit.workflow.snp_parser) init_count_set_sample_files() (in module mgkit.workflow.pnps_gen) INPUT_FILE add-gff-info-addtaxa command line option add-gff-info-bins command line option add-gff-info-counts command line option add-gff-info-cov_samtools command line option add-gff-info-coverage command line option add-gff-info-exp_syn command line option add-gff-info-kegg command line option add-gff-info-pfam command line option add-gff-info-unipfile command line option add-gff-info-uniprot command line option edit-gff-add command line option edit-gff-remove command line option edit-gff-rename command line option edit-gff-table command line option edit-gff-view command line option filter-gff-cov command line option filter-gff-overlap command line option filter-gff-sequence command line option filter-gff-values command line option json2gff-mongodb command line option sampling-utils-sample command line option sampling-utils-sample_stream command line option sampling-utils-sync command line option taxon-utils-filter command line option taxon-utils-lca_line command line option taxon-utils-to_hdf command line option

insert_many() (mgkit.db.mongo.GFFDB method) insert_one() (mgkit.db.mongo.GFFDB method) intersect() (mgkit.io.gff.GenomicRange method) INV_MIT (in module mgkit.utils.trans_tables) irreversible_paths (mgkit.graphs.Reaction attribute) is_ancestor() (in module mgkit.taxon) (mgkit.taxon.Taxonomy method) is_ranked_below() (mgkit.taxon.Taxonomy method) is_syn() (mgkit.io.gff.Annotation method) items() (mgkit.db.dbm.GFFDB method) (mgkit.db.mongo.GFFDB method) iter_ids() (mgkit.taxon.Taxonomy method) iteritems() (mgkit.db.dbm.GFFDB method) (mgkit.db.mongo.GFFDB method) itervalues() (mgkit.db.dbm.GFFDB method) (mgkit.db.mongo.GFFDB method)

J

json2gff command line option --cite --version json2gff-mongodb command line option --verbose -v GFF_FILE INPUT_FILE

K

kegg_id (mgkit.graphs.Reaction attribute) KeggClientRest (class in mgkit.kegg) KeggModule (class in mgkit.kegg)

keys() (mgkit.db.mongo.GFFDB method) ko_desc_re (mgkit.kegg.KeggClientRest attribute) ko_to_mapping() (in module mgkit.net.uniprot)

L

last_common_ancestor() (in module mgkit.taxon) last_common_ancestor_multiple() (in module mgkit.taxon) last_cp() (mgkit.kegg.KeggModule property) legend_patches() (in module mgkit.plots.utils) length() (mgkit.io.gff.Annotation property) LEVEL1_NAMES (in module mgkit.mappings.enzyme) lineage (mgkit.taxon.UniprotTaxonTuple attribute) lineplot_values_on_second_axis() (in module mgkit.plots.unused) link() (mgkit.kegg.KeggClientRest method) link_graph() (in module mgkit.graphs) link_ids() (in module mgkit.utils.dictionary) (mgkit.kegg.KeggClientRest method) link_nodes() (in module mgkit.graphs) list_ids() (mgkit.kegg.KeggClientRest method) load_cache() (mgkit.kegg.KeggClientRest method) load_counts_from_gff() (in module mgkit.counts.func) load_data() (mgkit.taxon.Taxonomy method) load_description() (mgkit.mappings.eggnog.NOGInfo method) load_deseq2_results() (in module mgkit.counts.func) load_fasta() (in module mgkit.io.fasta)

load_fasta_file() (in module mgkit.workflow.blast2gff) load_fasta_files() (in module mgkit.io.fasta) load_fasta_prodigal() (in module mgkit.io.fasta) load_fasta_rename() (in module mgkit.io.fasta) load_fastq() (in module mgkit.io.fastq) load_fastq_rename() (in module mgkit.io.fastq) load_featurecounts_files() (in module mgkit.workflow.add_gff_info) load_funccat() (mgkit.mappings.eggnog.NOGInfo method) load_gff_base_info() (in module mgkit.io.gff) load_gff_mappings() (in module mgkit.io.gff) load_htseq_count_files() (in module mgkit.workflow.add_gff_info) load_htseq_counts() (in module mgkit.counts.func) load_members() (mgkit.mappings.eggnog.NOGInfo method) load_sample_counts() (in module mgkit.counts.func) load_sample_counts_to_genes() (in module mgkit.counts.func) load_sample_counts_to_taxon() (in module mgkit.counts.func) load_trans_table() (in module mgkit.workflow.fasta_utils) LOG (in module mgkit.net.embl) lowess_ci_bootstrap() (in module mgkit.counts.glm) lowest_common_ancestor() (in module mgkit.taxon)

M

main() (in module mgkit.workflow.hmmer2gff) (in module mgkit.workflow.snp_parser) make_choose_func() (in module mgkit.workflow.filter_gff) make_reverse_table() (in module mgkit.utils.sequence) make_stat_table() (in module mgkit.mappings.pandas_map) manual_callback() (in module mgkit.workflow.add_gff_info) map_counts() (in module mgkit.counts.func) map_counts_to_category() (in module mgkit.counts.func) map_gene_id() (in module mgkit.snps.mapper) map_gene_id_to_map() (in module mgkit.counts.func) map_taxon_by_id_list() (in module mgkit.mappings.taxon) map_taxon_id_to_ancestor() (in module mgkit.snps.mapper) map_taxon_id_to_rank() (in module mgkit.counts.func) (in module mgkit.snps.mapper) map_taxon_to_colours() (in module mgkit.plots.unused) MAPPINGS (in module mgkit.io.uniprot) MATE1_FILE fastq-utils-di command line option fastq-utils-il command line option MATE1_INPUT fastq-utils-sort command line option MATE1_OUTPUT fastq-utils-sort command line option MATE2_FILE fastq-utils-di command line option fastq-utils-il command line option MATE2_INPUT fastq-utils-sort command line option MATE2_OUTPUT fastq-utils-sort command line option max_id() (mgkit.taxon.Taxonomy property) max_size (mgkit.align.SamtoolsDepth attribute) max_size_dict (mgkit.align.SamtoolsDepth attribute) memoize (class in mgkit.simple_cache) merge_dictionaries() (in module mgkit.utils.dictionary) merge_kgmls() (in module mgkit.graphs) messages (mgkit.io.snpdat.SNPDatRow attribute), [1] mgkit module mgkit.align module mgkit.consts module mgkit.counts module mgkit.counts.func module mgkit.counts.glm module mgkit.counts.scaling module mgkit.db module mgkit.db.dbm module mgkit.db.mongo module mgkit.filter module mgkit.filter.common module mgkit.filter.gff module mgkit.filter.lists module mgkit.filter.reads module mgkit.filter.taxon module mgkit.graphs module mgkit.io module mgkit.io.blast module mgkit.io.fasta module mgkit.io.fastq module mgkit.io.gff module mgkit.io.glimmer module mgkit.io.snpdat module mgkit.io.uniprot module mgkit.io.utils module mgkit.kegg module mgkit.logger module mgkit.mappings module mgkit.mappings.cazy module mgkit.mappings.eggnog module mgkit.mappings.enzyme module mgkit.mappings.go module mgkit.mappings.pandas_map module mgkit.mappings.taxon module mgkit.mappings.utils module mgkit.net module mgkit.net.embl module mgkit.net.pfam module mgkit.net.uniprot module mgkit.net.utils module mgkit.plots module mgkit.plots.abund module mgkit.plots.boxplot module mgkit.plots.colors module mgkit.plots.heatmap module mgkit.plots.unused module mgkit.plots.utils module mgkit.simple_cache module mgkit.snps module mgkit.snps.classes module

mgkit.snps.conv_func module mgkit.snps.filter module mgkit.snps.funcs module mgkit.snps.mapper module mgkit.taxon module mgkit.utils module mgkit.utils.common module mgkit.utils.dictionary module mgkit.utils.sequence module mgkit.utils.trans_tables module mgkit.workflow module mgkit.workflow.add_gff_info module, [1] mgkit.workflow.alg_utils module mgkit.workflow.blast2gff module, [1] mgkit.workflow.count_utils module mgkit.workflow.dict_utils module mgkit.workflow.edit_gff module, [1] mgkit.workflow.extract_gff_info module, [1] mgkit.workflow.fasta_utils module, [1] mgkit.workflow.fastq_utils module, [1] mgkit.workflow.filter_gff module, [1] mgkit.workflow.hmmer2gff module, [1] mgkit.workflow.json2gff module, [1] mgkit.workflow.pnps_gen module, [1] mgkit.workflow.sampling_utils module, [1] mgkit.workflow.snp_parser module, [1] mgkit.workflow.taxon_utils module, [1] mgkit.workflow.utils module MIN_COV (in module mgkit.consts) min_id() (mgkit.taxon.Taxonomy property) MIN_NUM (in module mgkit.consts) module mgkit mgkit.align mgkit.consts mgkit.counts mgkit.counts.func mgkit.counts.glm mgkit.counts.scaling mgkit.db mgkit.db.dbm mgkit.db.mongo mgkit.filter mgkit.filter.common mgkit.filter.gff mgkit.filter.lists mgkit.filter.reads mgkit.filter.taxon mgkit.graphs mgkit.io mgkit.io.blast mgkit.io.fasta mgkit.io.fastq mgkit.io.gff mgkit.io.glimmer mgkit.io.snpdat mgkit.io.uniprot mgkit.io.utils mgkit.kegg mgkit.logger mgkit.mappings mgkit.mappings.cazy mgkit.mappings.eggnog mgkit.mappings.enzyme mgkit.mappings.go mgkit.mappings.pandas_map mgkit.mappings.taxon mgkit.mappings.utils mgkit.net mgkit.net.embl mgkit.net.pfam mgkit.net.uniprot mgkit.net.utils mgkit.plots mgkit.plots.abund mgkit.plots.boxplot mgkit.plots.colors mgkit.plots.heatmap mgkit.plots.unused mgkit.plots.utils mgkit.simple_cache mgkit.snps mgkit.snps.classes mgkit.snps.conv_func mgkit.snps.filter mgkit.snps.funcs mgkit.snps.mapper mgkit.taxon mgkit.utils mgkit.utils.common mgkit.utils.dictionary mgkit.utils.sequence mgkit.utils.trans_tables mgkit.workflow mgkit.workflow.add_gff_info, [1] mgkit.workflow.alg_utils mgkit.workflow.blast2gff, [1] mgkit.workflow.count_utils mgkit.workflow.dict_utils mgkit.workflow.edit_gff, [1] mgkit.workflow.extract_gff_info, [1] mgkit.workflow.fasta_utils, [1] mgkit.workflow.fastq_utils, [1] mgkit.workflow.filter_gff, [1] mgkit.workflow.hmmer2gff, [1] mgkit.workflow.json2gff, [1] mgkit.workflow.pnps_gen, [1] mgkit.workflow.sampling_utils, [1] mgkit.workflow.snp_parser, [1] mgkit.workflow.taxon_utils, [1] mgkit.workflow.utils

N

name (mgkit.kegg.KeggModule attribute) next() (mgkit.utils.dictionary.cache_dict_file method) NoEntryFound NOGInfo (class in mgkit.mappings.eggnog) NoLcaFound NONE_FOUND (in module mgkit.net.embl) nonsyn (mgkit.snps.classes.SNPType attribute)

nonsyn() (mgkit.snps.classes.GeneSNP property) NOT_FOUND (in module mgkit.net.embl) not_found (mgkit.align.SamtoolsDepth attribute) nuc_change (mgkit.io.snpdat.SNPDatRow attribute), [1] nuc_ref (mgkit.io.snpdat.SNPDatRow attribute), [1] num_features (mgkit.io.snpdat.SNPDatRow attribute), [1] num_stops (mgkit.io.snpdat.SNPDatRow attribute), [1]

O

open_file() (in module mgkit.io.utils) optimise_alpha_scipy() (in module mgkit.counts.glm) optimise_alpha_scipy_function() (in module mgkit.counts.glm) order_ratios() (in module mgkit.snps.funcs) orthologs (mgkit.graphs.Reaction attribute) OUTPUT_FILE add-gff-info-addtaxa command line option add-gff-info-bins command line option add-gff-info-counts command line option add-gff-info-cov_samtools command line option add-gff-info-coverage command line option add-gff-info-exp_syn command line option add-gff-info-kegg command line option add-gff-info-pfam command line option add-gff-info-unipfile command line option add-gff-info-uniprot command line option edit-gff-add command line option edit-gff-remove command line option edit-gff-rename command line option edit-gff-table command line option edit-gff-view command line option fasta-utils-filter command line option fasta-utils-info command line option fasta-utils-rename command line option fasta-utils-translate command line option fasta-utils-uid command line option filter-gff-cov command line option filter-gff-overlap command line option filter-gff-sequence command line option filter-gff-values command line option get-gff-info-cov command line option get-gff-info-mongodb command line option pnps-gen-full command line option pnps-gen-vcf command line option pnps-gen-vcf_alt command line option sampling-utils-rand_seq command line option sampling-utils-sample_stream command line option sampling-utils-sync command line option taxon-utils-filter command line option taxon-utils-get command line option taxon-utils-lca command line option taxon-utils-lca_line command line option taxon-utils-to_hdf command line option

output_taxon_line() (in module mgkit.workflow.taxon_utils)

P

palette_float_to_hex() (in module mgkit.plots.colors) parent_id (mgkit.taxon.UniprotTaxonTuple attribute) parse_accession_taxa_table() (in module mgkit.io.blast) parse_blast_tab() (in module mgkit.io.blast) parse_domain_table_contigs() (in module mgkit.workflow.hmmer2gff) parse_entry() (mgkit.kegg.KeggModule method) parse_entry2() (mgkit.kegg.KeggModule method) parse_expasy_dat() (in module mgkit.mappings.enzyme) parse_expasy_dat_section() (in module mgkit.mappings.enzyme) parse_expasy_file() (in module mgkit.mappings.enzyme) parse_fragment_blast() (in module mgkit.io.blast) parse_gff() (in module mgkit.io.gff) parse_gff_files() (in module mgkit.io.gff) parse_glimmer3() (in module mgkit.io.glimmer) parse_gtdb_lineage() (mgkit.taxon.Taxonomy static method) parse_hdf5_arg() (in module mgkit.workflow.add_gff_info) parse_kgml_reactions() (in module mgkit.graphs) parse_ncbi_taxonomy_merged_file() (in module mgkit.taxon) parse_ncbi_taxonomy_names_file() (in module mgkit.taxon) parse_ncbi_taxonomy_nodes_file() (in module mgkit.taxon) parse_phylophlan_lineage() (mgkit.taxon.Taxonomy static method) parse_reaction() (in module mgkit.kegg) (mgkit.kegg.KeggModule static method) parse_uniprot_blast() (in module mgkit.io.blast) parse_uniprot_mappings() (in module mgkit.io.uniprot) parse_uniprot_response() (in module mgkit.net.uniprot) parse_uniprot_taxon() (in module mgkit.taxon) parse_vcf() (in module mgkit.workflow.pnps_gen) (in module mgkit.workflow.snp_parser) pathways() (mgkit.graphs.Reaction property) perseq_calc_threshold() (in module mgkit.workflow.filter_gff) phase (mgkit.io.gff.Annotation attribute) phylophlan_results_parser() (in module mgkit.workflow.add_gff_info) pipe_filters() (in module mgkit.snps.filter) plot_contig_assignment_bar() (in module mgkit.plots.unused) plot_scatter_2d() (in module mgkit.plots.unused) plot_scatter_3d() (in module mgkit.plots.unused) pnps-gen command line option --cite --version pnps-gen-full command line option --gene-map <gene_map> --lineage --min-cov <min_cov> --min-num <min_num> --only-pn --only-ps --parquet --rank <rank> --separator <separator> --snp-data <snp_data> --taxon-ids <taxon_ids> --taxonomy <taxonomy> --two-columns --use-uid --verbose -2 -c -e -g -i -l -m -p -pn -ps -r -s -t -u -v OUTPUT_FILE pnps-gen-rank command line option --lineage --min-cov <min_cov> --min-num <min_num> --only-pn --only-ps --rank <rank> --snp-data <snp_data> --taxon_ids <taxon_ids> --taxonomy <taxonomy> --unstack --verbose -c -i -l -m -pn -ps -r -s -t -u -v TXT_FILE

pnps-gen-vcf command line option --fasta-file <fasta_file> --feature <feature> --gff-file <gff_file> --min-freq <min_freq> --min-qual <min_qual> --min-reads <min_reads> --num-lines <num_lines> --sample-ids <sample_ids> --verbose -a -f -ft -g -m -n -q -r -v OUTPUT_FILE VCF_FILE pnps-gen-vcf_alt command line option --fasta-file <fasta_file> --feature <feature> --file-list <file_list> --gff-file <gff_file> --min-freq <min_freq> --min-qual <min_qual> --min-reads <min_reads> --num-lines <num_lines> --sample-file <sample_file> --uid-map <uid_map> --verbose -a -f -ft -g -l -n -q -r -s -u -v OUTPUT_FILE VCF_FILE PrintManAction (class in mgkit.workflow.utils) products (mgkit.graphs.Reaction attribute) project_point() (in module mgkit.plots.abund) protein_id (mgkit.io.snpdat.SNPDatRow attribute), [1] PRT_MIT (in module mgkit.utils.trans_tables) put_gaps_in_nuc_seq() (in module mgkit.utils.sequence)

Q

qualities_model_constant() (in module mgkit.utils.sequence)

qualities_model_decrease() (in module mgkit.utils.sequence) query_uniprot() (in module mgkit.net.uniprot)

R

random_qualities() (in module mgkit.utils.sequence) random_sequences() (in module mgkit.utils.sequence) random_sequences_codon() (in module mgkit.utils.sequence) range_intersect() (in module mgkit.utils.common) range_substract() (in module mgkit.utils.common) ranges_length() (in module mgkit.utils.common) rank (mgkit.taxon.UniprotTaxonTuple attribute) RatioMixIn (class in mgkit.snps.classes) Reaction (class in mgkit.graphs) reactions (mgkit.kegg.KeggModule attribute) read_from_gtdb_taxonomy() (mgkit.taxon.Taxonomy method) read_from_ncbi_dump() (mgkit.taxon.Taxonomy method) read_from_phylophlan_taxonomy() (mgkit.taxon.Taxonomy method) read_gene_map_default() (in module mgkit.workflow.pnps_gen) read_gene_map_two_columns() (in module mgkit.workflow.pnps_gen)

read_samtools_depth() (in module mgkit.align) read_taxonomy() (mgkit.taxon.Taxonomy method) region (mgkit.io.snpdat.SNPDatRow attribute), [1] region() (mgkit.io.gff.Annotation property) region_coverage() (mgkit.align.SamtoolsDepth method) rename_graph_nodes() (in module mgkit.graphs) report_counts() (in module mgkit.workflow.fastq_utils) REV_COMP (in module mgkit.utils.sequence) reverse_aa_coord() (in module mgkit.utils.sequence) reverse_complement() (in module mgkit.utils.sequence) reverse_complement_old() (in module mgkit.utils.sequence) reverse_mapping() (in module mgkit.utils.dictionary) reversible() (mgkit.graphs.Reaction property) reversible_paths (mgkit.graphs.Reaction attribute) rn_eq_re (mgkit.kegg.KeggClientRest attribute) rn_name_re (mgkit.kegg.KeggClientRest attribute)

S

s_name (mgkit.taxon.UniprotTaxonTuple attribute) sample_coverage() (mgkit.io.gff.Annotation property) sampling-utils command line option --cite --version sampling-utils-rand_seq command line option --coding-prop <coding_prop> --const-model --dist-loc <dist_loc> --fastq --gc-content <gc_content> --infer-params <infer_params> --length <length> --num-seqs <num_seqs> --progress --read-model <read_model> --save-model <save_model> --verbose -a -d -gc -i -l -m -n -q -r -v -x OUTPUT_FILE sampling-utils-sample command line option --fastq --gzip --max-seq <max_seq> --number <number> --prefix <prefix> --prob <prob> --verbose -n -p -q -r -v -x -z INPUT_FILE sampling-utils-sample_stream command line option --fastq --max-seq <max_seq> --prob <prob> --verbose -q -r -v -x INPUT_FILE OUTPUT_FILE

sampling-utils-sync command line option --master-file <master_file> --verbose -m -v INPUT_FILE OUTPUT_FILE SamtoolsDepth (class in mgkit.align) save_data() (in module mgkit.workflow.pnps_gen) (in module mgkit.workflow.snp_parser) (mgkit.taxon.Taxonomy method) scale_deseq() (in module mgkit.counts.scaling) scale_factor_deseq() (in module mgkit.counts.scaling) scale_rpkm() (in module mgkit.counts.scaling) scatter_gene_values() (in module mgkit.plots.unused) score (mgkit.io.gff.Annotation attribute) seq_id (mgkit.io.gff.GenomicRange attribute) sequence_composition() (in module mgkit.utils.sequence) sequence_gc_content() (in module mgkit.utils.sequence) sequence_gc_ratio() (in module mgkit.utils.sequence) set_attr() (mgkit.io.gff.Annotation method) set_mapping() (mgkit.io.gff.Annotation method) set_parser() (in module mgkit.workflow.hmmer2gff) (in module mgkit.workflow.snp_parser) setup_filters() (in module mgkit.workflow.filter_gff) significance_test() (in module mgkit.snps.funcs) snpdat_reader() (in module mgkit.io.snpdat) SNPDatRow (class in mgkit.io.snpdat) snps (mgkit.snps.classes.GeneSNP attribute), [1] SNPType (class in mgkit.snps.classes) source (mgkit.io.gff.Annotation attribute) split_dictionary_by_value() (in module mgkit.utils.dictionary) split_fasta_file() (in module mgkit.io.fasta) split_gff_file() (in module mgkit.io.gff) split_sample_alg() (in module mgkit.workflow.add_gff_info) split_write() (in module mgkit.io.utils) start (mgkit.io.gff.GenomicRange attribute) strand (mgkit.io.gff.GenomicRange attribute) (mgkit.io.snpdat.SNPDatRow attribute), [1] stream_feature_counts() (in module mgkit.workflow.count_utils) substrates (mgkit.graphs.Reaction attribute) syn (mgkit.snps.classes.SNPType attribute) syn() (mgkit.snps.classes.GeneSNP property) synonymous (mgkit.io.snpdat.SNPDatRow attribute), [1]

T

taxa_distance_matrix() (in module mgkit.taxon) taxon-utils command line option --cite --version taxon-utils-filter command line option --exclude-taxon-id <exclude_taxon_id> --exclude-taxon-name <exclude_taxon_name> --include-taxon-id <include_taxon_id> --include-taxon-name <include_taxon_name> --progress --table --taxonomy <taxonomy> --verbose -e -en -i -in -p -t -v INPUT_FILE OUTPUT_FILE taxon-utils-get command line option --header --id-file <id_file> --include-children --name-file <name_file> --no-fuzzy --only-ids <only_ids> --only-names <only_names> --partial --separator <separator> --tax-sep <tax_sep> --use-cname --verbose -a -c -d -i -o -p -s -v -x -z OUTPUT_FILE TAXONOMY_FILE taxon-utils-import command line option --tax-type <tax_type> --verbose -t -v IMPORT_FILE TAXONOMY_FILE taxon-utils-lca command line option --bitscore <bitscore> --feat-type <feat_type> --group-by-attr <group_by_attr> --krona-total <krona_total> --no-lca <no_lca> --only-ranked --out-format <out_format> --progress --reference <reference> --rename --simple-table --sorted --taxonomy <taxonomy> --verbose -a -b -f -ft -g -kt -m -n -p -r -s -t -v GFF_FILE OUTPUT_FILE

taxon-utils-lca_line command line option --no-lca <no_lca> --only-ranked --separator <separator> --taxonomy <taxonomy> --verbose -a -n -s -t -v INPUT_FILE OUTPUT_FILE taxon-utils-to_hdf command line option --chunk-size <chunk_size> --index-size <index_size> --overwrite --progress --table-name <table_name> --verbose -c -n -s -v -w INPUT_FILE OUTPUT_FILE TAXON_COLOURS (in module mgkit.plots.unused) taxon_db() (mgkit.io.gff.Annotation property) taxon_id (mgkit.snps.classes.GeneSNP attribute), [1] (mgkit.taxon.UniprotTaxonTuple attribute) taxon_id() (mgkit.io.gff.Annotation property) TAXON_RANKS (in module mgkit.taxon) TAXON_ROOTS (in module mgkit.taxon) Taxonomy (class in mgkit.taxon) TAXONOMY_FILE taxon-utils-get command line option taxon-utils-import command line option TaxonTuple (in module mgkit.taxon) text_to_dict() (in module mgkit.utils.dictionary) to_dict() (mgkit.io.gff.Annotation method) to_edges() (mgkit.graphs.Reaction method) (mgkit.kegg.KeggModule method) to_edges_compounds() (mgkit.graphs.Reaction method) to_file() (mgkit.io.gff.Annotation method) to_gff() (mgkit.io.gff.Annotation method) to_gtf() (mgkit.io.gff.Annotation method) to_json() (mgkit.io.gff.Annotation method) (mgkit.snps.classes.GeneSNP method) to_mongodb() (mgkit.io.gff.Annotation method) to_nodes() (mgkit.graphs.Reaction method) TRANS_TABLE (in module mgkit.utils.sequence) transcript_id (mgkit.io.snpdat.SNPDatRow attribute), [1] transcript_name (mgkit.io.snpdat.SNPDatRow attribute), [1] translate_seq() (in module mgkit.workflow.fasta_utils) translate_sequence() (in module mgkit.utils.sequence) trim_by_ee() (in module mgkit.filter.reads) TXT_FILE edit-gff-fields command line option pnps-gen-rank command line option

U

uid (mgkit.snps.classes.GeneSNP attribute), [1] uid() (mgkit.io.gff.Annotation property) union() (mgkit.io.gff.GenomicRange method) union_range() (in module mgkit.utils.common) union_ranges() (in module mgkit.utils.common) UNIPROT_GET (in module mgkit.net.uniprot) UNIPROT_MAP (in module mgkit.net.uniprot) uniprot_mappings_to_dict() (in module mgkit.io.uniprot) UNIPROT_TAXONOMY (in module mgkit.net.uniprot)

UniprotTaxonomy (in module mgkit.taxon) UniprotTaxonTuple (class in mgkit.taxon) UNIVERSAL (in module mgkit.utils.trans_tables) unknown (mgkit.snps.classes.SNPType attribute) UnsupportedFormat update() (mgkit.graphs.Reaction method) update_annotation_coverage() (in module mgkit.workflow.add_gff_info) url_open() (in module mgkit.net.utils) url_read() (in module mgkit.net.utils) URL_REST (in module mgkit.net.embl)

V

validate_params() (in module mgkit.workflow.blast2gff) (in module mgkit.workflow.filter_gff) validate_taxon_ids() (in module mgkit.workflow.taxon_utils) validate_taxon_names() (in module mgkit.workflow.taxon_utils) values() (mgkit.db.dbm.GFFDB method) (mgkit.db.mongo.GFFDB method)

variance_to_alpha() (in module mgkit.counts.glm) VCF_FILE pnps-gen-vcf command line option pnps-gen-vcf_alt command line option

W

write_cache() (mgkit.kegg.KeggClientRest method) write_fasta_sequence() (in module mgkit.io.fasta) write_fastq_sequence() (in module mgkit.io.fastq) write_gff() (in module mgkit.io.gff) write_json() (in module mgkit.workflow.taxon_utils)

write_krona() (in module mgkit.workflow.taxon_utils) write_lca_gff() (in module mgkit.workflow.taxon_utils) write_lca_tab() (in module mgkit.workflow.taxon_utils) write_lca_tab_simple() (in module mgkit.workflow.taxon_utils) write_no_lca() (in module mgkit.workflow.taxon_utils) write_sign_genes_table() (in module mgkit.snps.funcs)

Y

YST_ALT (in module mgkit.utils.trans_tables)