MGKit: Metagenomic framework
0.3.2
Introduction
Installation
Metagenomic Pipeline
Scripts Details
Example Notebooks
MGKit GFF Specifications
Library Reference
Changes
MGKit: Metagenomic framework
Docs
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Index
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Index
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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V
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W
_
__contains__() (mgkit.io.gff.GenomicRange method)
(mgkit.taxon.UniprotTaxonomy method)
__eq__() (mgkit.kegg.KeggCompound method)
(mgkit.kegg.KeggOrtholog method)
(mgkit.kegg.KeggPathway method)
__getitem__() (mgkit.taxon.UniprotTaxonomy method)
__getnewargs__() (mgkit.taxon.UniprotTaxonTuple method)
__getstate__() (mgkit.taxon.UniprotTaxonTuple method)
__iter__() (mgkit.taxon.UniprotTaxonomy method)
__len__() (mgkit.taxon.UniprotTaxonomy method)
__ne__() (mgkit.kegg.KeggCompound method)
(mgkit.kegg.KeggOrtholog method)
(mgkit.kegg.KeggPathway method)
__repr__() (mgkit.taxon.UniprotTaxonomy method)
(mgkit.taxon.UniprotTaxonTuple method)
_asdict() (mgkit.taxon.UniprotTaxonTuple method)
_get_kmers() (in module mgkit.utils.sequence)
_replace() (mgkit.taxon.UniprotTaxonTuple method)
_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_basic_options() (in module mgkit.workflow.utils)
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.UniprotTaxonomy method)
add_module_compounds() (in module mgkit.graphs)
add_profiles_to_length() (in module mgkit.workflow.download_profiles)
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.UniprotTaxonomy method)
add_uniprot_info() (in module mgkit.workflow.add_gff_info)
add_values_to_boxplot() (in module mgkit.plots.boxplot)
addtaxa_command() (in module mgkit.workflow.add_gff_info)
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)
assign_contigs_to_taxa() (in module mgkit.workflow.assembly)
attr (mgkit.io.gff.Annotation attribute)
AttributeNotFound
average_length() (in module mgkit.utils.common)
B
barchart_categories() (in module mgkit.plots.unused)
baseheatmap() (in module mgkit.plots.heatmap)
basic_stats() (in module mgkit.workflow.assembly)
batch_load_htseq_counts() (in module mgkit.counts.func)
between() (in module mgkit.utils.common)
bitscore (mgkit.io.gff.Annotation attribute)
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_ratio() (mgkit.snps.classes.RatioMixIn method)
calc_ratio_flag() (mgkit.snps.classes.RatioMixIn method)
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_version() (in module mgkit)
choose_annotation() (in module mgkit.filter.gff)
(in module mgkit.filter.gff_old)
choose_by_lca() (in module mgkit.workflow.add_gff_info)
choose_by_score() (in module mgkit.filter.gff_old)
(in module mgkit.workflow.add_gff_info)
choose_header_type() (in module mgkit.io.fastq)
choose_ko_ids() (in module mgkit.workflow.download_profiles)
choose_taxa() (in module mgkit.workflow.download_profiles)
chr_name (mgkit.io.snpdat.SNPDatRow attribute)
,
[1]
chr_pos (mgkit.io.snpdat.SNPDatRow attribute)
,
[1]
cite() (in module mgkit)
CiteAction (class in mgkit.workflow.utils)
classes (mgkit.kegg.KeggModule attribute)
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)
columns_string (mgkit.mappings.cazy.Kegg2CazyMapper attribute)
(mgkit.mappings.eggnog.Kegg2NogMapper attribute)
(mgkit.mappings.go.Kegg2GOMapper 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)
common_options() (in module mgkit.workflow.filter_gff)
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)
contact (mgkit.kegg.KeggClientRest attribute)
conv() (mgkit.kegg.KeggClientRest method)
convert_aa_to_nuc_coord() (in module mgkit.utils.sequence)
convert_from_blastdb() (in module mgkit.workflow.blast2gff)
convert_from_uniprot() (in module mgkit.workflow.blast2gff)
convert_gff_to_gtf() (in module mgkit.io.gff)
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 attribute)
counts_command() (in module mgkit.workflow.add_gff_info)
coverage (mgkit.io.gff.Annotation attribute)
(mgkit.snps.classes.GeneSNP attribute)
,
[1]
coverage_command() (in module mgkit.workflow.add_gff_info)
(in module mgkit.workflow.filter_gff)
covered_annotation_bp() (in module mgkit.align)
cpd_desc_re (mgkit.kegg.KeggClientRest attribute)
cpd_re (mgkit.kegg.KeggClientRest attribute)
D
data (mgkit.align.SamtoolsDepth attribute)
datawarehouse_search() (in module mgkit.net.embl)
db (mgkit.io.gff.Annotation attribute)
dbfetch() (in module mgkit.net.embl)
dbq (mgkit.io.gff.Annotation attribute)
dendrogram() (in module mgkit.plots.heatmap)
DependencyError
deprecated() (in module mgkit.utils.common)
diff_gff() (in module mgkit.io.gff)
distance_taxa_ancestor() (in module mgkit.taxon)
distance_two_taxa() (in module mgkit.taxon)
download_data() (in module mgkit.kegg)
(in module mgkit.mappings.cazy)
(in module mgkit.mappings.eggnog)
(in module mgkit.mappings.go)
download_ko_sequences() (in module mgkit.workflow.download_profiles)
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_taxon() (mgkit.taxon.UniprotTaxonomy method)
DuplicateKeyError
E
eggnog_command() (in module mgkit.workflow.add_gff_info)
elongate_annotations() (in module mgkit.io.gff)
empty_cache() (mgkit.kegg.KeggClientRest method)
end (mgkit.io.gff.GenomicRange attribute)
entry (mgkit.kegg.KeggModule attribute)
EntryNotFound
exit_script() (in module mgkit.workflow.utils)
exon (mgkit.io.snpdat.SNPDatRow attribute)
,
[1]
exp_nonsyn (mgkit.io.gff.Annotation attribute)
(mgkit.snps.classes.GeneSNP attribute)
,
[1]
exp_syn (mgkit.io.gff.Annotation attribute)
(mgkit.snps.classes.GeneSNP attribute)
,
[1]
exp_syn_command() (in module mgkit.workflow.add_gff_info)
expand_from_list() (mgkit.io.gff.GenomicRange method)
expected_error_rate() (in module mgkit.filter.reads)
extract_nuc_seqs() (in module mgkit.io.gff)
F
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_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_by_bit_score() (in module mgkit.filter.gff_old)
filter_by_description() (in module mgkit.filter.gff_old)
filter_by_hit_length() (in module mgkit.filter.gff_old)
filter_by_ko_id() (in module mgkit.filter.gff_old)
filter_by_ko_idx() (in module mgkit.filter.gff_old)
filter_by_reviewed() (in module mgkit.filter.gff_old)
filter_by_score() (in module mgkit.filter.gff_old)
filter_by_seq_id() (in module mgkit.filter.gff_old)
filter_by_strand() (in module mgkit.filter.gff_old)
filter_by_taxon() (in module mgkit.filter.gff_old)
filter_contig_assignments() (in module mgkit.workflow.assembly)
filter_counts() (in module mgkit.counts.func)
filter_found_taxa() (in module mgkit.workflow.download_profiles)
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_len() (in module mgkit.filter.gff)
filter_nan() (in module mgkit.utils.dictionary)
filter_overlapping() (in module mgkit.filter.gff_old)
filter_overlaps() (in module mgkit.workflow.filter_gff)
filter_perseq() (in module mgkit.workflow.filter_gff)
filter_ratios_by_numbers() (in module mgkit.utils.dictionary)
filter_taxa_command() (in module mgkit.workflow.taxon_utils)
filter_taxon_by_id_list() (in module mgkit.filter.taxon)
filter_taxonomy_by_lineage() (in module mgkit.workflow.download_profiles)
filter_taxonomy_by_rank() (in module mgkit.workflow.download_profiles)
filter_values() (in module mgkit.workflow.filter_gff)
FilterFails
find() (mgkit.kegg.KeggClientRest method)
find_by_name() (mgkit.taxon.UniprotTaxonomy method)
find_comparison() (in module mgkit.workflow.filter_gff)
find_function() (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 attribute)
flat_sample_snps() (in module mgkit.snps.funcs)
float_to_hex_color() (in module mgkit.plots.colors)
fpkms (mgkit.io.gff.Annotation attribute)
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_ko_map() (mgkit.kegg.KeggData method)
gen_ko_to_cat() (mgkit.mappings.eggnog.Kegg2NogMapper method)
gen_maps() (mgkit.kegg.KeggData method)
gen_name_map() (mgkit.taxon.UniprotTaxonomy method)
gene_id (mgkit.io.gff.Annotation attribute)
(mgkit.io.snpdat.SNPDatRow attribute)
,
[1]
(mgkit.snps.classes.GeneSNP attribute)
,
[1]
gene_name (mgkit.io.snpdat.SNPDatRow attribute)
,
[1]
GeneSNP (class in mgkit.snps.classes)
GenomicRange (class in mgkit.io.gff)
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_cat_ko_dict() (mgkit.mappings.eggnog.Kegg2NogMapper method)
get_cat_mapping() (mgkit.mappings.eggnog.Kegg2NogMapper method)
get_cat_mapping_from_file() (mgkit.mappings.eggnog.Kegg2NogMapper method)
get_consensus() (mgkit.utils.sequence.Alignment method)
get_contigs_info() (in module mgkit.utils.sequence)
get_cp_names() (mgkit.kegg.KeggData method)
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_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_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_gids() (in module mgkit.workflow.add_gff_info)
get_grid_figure() (in module mgkit.plots.utils)
get_id_map() (mgkit.kegg.KeggMapperBase method)
get_id_names() (mgkit.kegg.KeggMapperBase method)
get_ids_names() (mgkit.kegg.KeggClientRest method)
get_ko_cat() (mgkit.mappings.eggnog.Kegg2NogMapper method)
get_ko_cat_dict() (mgkit.mappings.eggnog.Kegg2NogMapper method)
get_ko_cp_links() (mgkit.kegg.KeggData method)
get_ko_cp_links_alt() (mgkit.kegg.KeggData method)
get_ko_map() (mgkit.kegg.KeggMapperBase method)
(mgkit.mappings.eggnog.Kegg2NogMapper method)
get_ko_names() (mgkit.kegg.KeggData method)
get_ko_pathway_map() (mgkit.kegg.KeggData method)
get_ko_pathways() (mgkit.kegg.KeggData method)
get_ko_rn_links() (mgkit.kegg.KeggData method)
get_ko_to_eggnog_mappings() (in module mgkit.net.uniprot)
get_lineage() (in module mgkit.taxon)
(mgkit.taxon.UniprotTaxonomy 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.UniprotTaxonomy 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_ko_map() (mgkit.kegg.KeggData 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_taxon() (mgkit.taxon.UniprotTaxonomy method)
get_reaction_equations() (mgkit.kegg.KeggClientRest method)
get_region_coverage() (in module mgkit.align)
get_relative_pos() (mgkit.io.gff.GenomicRange method)
get_rn_cp_links() (mgkit.kegg.KeggData method)
get_rn_names() (mgkit.kegg.KeggData 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)
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_by_root() (in module mgkit.taxon)
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)
H
HDFDict (class in mgkit.utils.dictionary)
heatmap_clustered() (in module mgkit.plots.heatmap)
I
id_prefix (mgkit.kegg.KeggClientRest attribute)
in_feat (mgkit.io.snpdat.SNPDatRow attribute)
,
[1]
intersect() (mgkit.io.gff.GenomicRange method)
is_ancestor() (in module mgkit.taxon)
(mgkit.taxon.UniprotTaxonomy method)
is_syn() (mgkit.io.gff.Annotation method)
K
Kegg2CazyMapper (class in mgkit.mappings.cazy)
Kegg2GOMapper (class in mgkit.mappings.go)
Kegg2NogMapper (class in mgkit.mappings.eggnog)
kegg_command() (in module mgkit.workflow.add_gff_info)
KeggClientRest (class in mgkit.kegg)
KeggCompound (class in mgkit.kegg)
KeggData (class in mgkit.kegg)
KeggMapperBase (class in mgkit.kegg)
KeggModule (class in mgkit.kegg)
KeggOrtholog (class in mgkit.kegg)
KeggPathway (class in mgkit.kegg)
KeggReaction (class in mgkit.kegg)
ko_desc_re (mgkit.kegg.KeggClientRest attribute)
ko_to_mapping() (in module mgkit.net.uniprot)
(mgkit.kegg.KeggMapperBase static method)
L
last_common_ancestor() (in module mgkit.taxon)
last_common_ancestor_multiple() (in module mgkit.taxon)
last_cp (mgkit.kegg.KeggModule attribute)
lca_contig_command() (in module mgkit.workflow.taxon_utils)
lca_line_command() (in module mgkit.workflow.taxon_utils)
lca_options() (in module mgkit.workflow.taxon_utils)
left_cp (mgkit.kegg.KeggReaction attribute)
legend_patches() (in module mgkit.plots.utils)
length (mgkit.io.gff.Annotation attribute)
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() (in module mgkit.workflow.add_gff_info)
load_counts_from_gff() (in module mgkit.counts.func)
load_data() (in module mgkit.workflow.download_profiles)
(mgkit.kegg.KeggData method)
(mgkit.kegg.KeggMapperBase method)
(mgkit.mappings.eggnog.Kegg2NogMapper method)
(mgkit.taxon.UniprotTaxonomy 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_prodigal() (in module mgkit.io.fasta)
load_fasta_rename() (in module mgkit.io.fasta)
load_fastq() (in module mgkit.io.fastq)
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_go_names() (mgkit.mappings.go.Kegg2GOMapper method)
load_goslim_mapping() (mgkit.mappings.go.Kegg2GOMapper method)
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_taxonomy_map() (in module mgkit.taxon)
load_trans_table() (in module mgkit.workflow.fasta_utils)
(in module mgkit.workflow.nuc2aa)
lowest_common_ancestor() (in module mgkit.taxon)
M
main() (in module mgkit.workflow.add_coverage)
(in module mgkit.workflow.add_gff_info)
(in module mgkit.workflow.blast2gff)
(in module mgkit.workflow.download_data)
(in module mgkit.workflow.download_profiles)
(in module mgkit.workflow.fasta_utils)
(in module mgkit.workflow.filter_gff)
(in module mgkit.workflow.hmmer2gff)
(in module mgkit.workflow.json2gff)
(in module mgkit.workflow.nuc2aa)
(in module mgkit.workflow.sampling_utils)
(in module mgkit.workflow.taxon_utils)
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)
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_ko_to_eggnog() (mgkit.mappings.eggnog.Kegg2NogMapper method)
map_ko_to_uniprot() (in module mgkit.workflow.download_profiles)
map_kos_cazy() (mgkit.mappings.cazy.Kegg2CazyMapper method)
map_kos_eggnog() (mgkit.mappings.eggnog.Kegg2NogMapper method)
map_kos_go() (mgkit.mappings.go.Kegg2GOMapper method)
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)
maps (mgkit.kegg.KeggData attribute)
memoize (class in mgkit.simple_cache)
merge_dictionaries() (in module mgkit.utils.dictionary)
messages (mgkit.io.snpdat.SNPDatRow attribute)
,
[1]
mgkit (module)
mgkit.align (module)
mgkit.consts (module)
mgkit.counts (module)
mgkit.counts.func (module)
mgkit.counts.scaling (module)
mgkit.db (module)
mgkit.filter (module)
mgkit.filter.common (module)
mgkit.filter.gff (module)
mgkit.filter.gff_old (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_coverage (module)
mgkit.workflow.add_gff_info (module)
,
[1]
mgkit.workflow.assembly (module)
mgkit.workflow.blast2gff (module)
,
[1]
mgkit.workflow.download_data (module)
,
[1]
mgkit.workflow.download_profiles (module)
,
[1]
mgkit.workflow.fasta_utils (module)
,
[1]
mgkit.workflow.filter_gff (module)
,
[1]
mgkit.workflow.hmmer2gff (module)
,
[1]
mgkit.workflow.json2gff (module)
,
[1]
mgkit.workflow.nuc2aa (module)
,
[1]
mgkit.workflow.sampling_utils (module)
,
[1]
mgkit.workflow.taxon_utils (module)
,
[1]
mgkit.workflow.utils (module)
mongodb_command() (in module mgkit.workflow.json2gff)
N
name (mgkit.kegg.KeggModule attribute)
next() (mgkit.utils.dictionary.cache_dict_file method)
NoEntryFound
NOGInfo (class in mgkit.mappings.eggnog)
NoLcaFound
nonsyn (mgkit.snps.classes.GeneSNP attribute)
(mgkit.snps.classes.SNPType 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)
order_ratios() (in module mgkit.snps.funcs)
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_attr_arg() (in module mgkit.workflow.blast2gff)
(in module mgkit.workflow.filter_gff)
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_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_hdf5_arg() (in module mgkit.workflow.add_gff_info)
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_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)
pathways (mgkit.kegg.KeggData attribute)
perseq_calc_threshold() (in module mgkit.workflow.filter_gff)
pfam_command() (in module mgkit.workflow.add_gff_info)
phase (mgkit.io.gff.Annotation attribute)
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)
print_ko_to_cat() (in module mgkit.mappings.eggnog)
PrintManAction (class in mgkit.workflow.utils)
project_point() (in module mgkit.plots.abund)
protein_id (mgkit.io.snpdat.SNPDatRow attribute)
,
[1]
put_gaps_in_nuc_seq() (in module mgkit.utils.sequence)
Q
query_string (mgkit.mappings.cazy.Kegg2CazyMapper attribute)
(mgkit.mappings.eggnog.Kegg2NogMapper attribute)
(mgkit.mappings.go.Kegg2GOMapper attribute)
query_uniprot() (in module mgkit.net.uniprot)
R
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)
rank_annotations_by_attr() (in module mgkit.workflow.assembly)
RatioMixIn (class in mgkit.snps.classes)
reactions (mgkit.kegg.KeggModule attribute)
read_from_gtdb_taxonomy() (mgkit.taxon.UniprotTaxonomy method)
read_from_ncbi_dump() (mgkit.taxon.UniprotTaxonomy method)
read_lines_from_files() (in module mgkit.workflow.add_gff_info)
read_samtools_depth() (in module mgkit.align)
read_taxonomy() (mgkit.taxon.UniprotTaxonomy method)
region (mgkit.io.gff.Annotation attribute)
(mgkit.io.snpdat.SNPDatRow attribute)
,
[1]
region_coverage() (mgkit.align.SamtoolsDepth method)
rename_graph_nodes() (in module mgkit.graphs)
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)
right_cp (mgkit.kegg.KeggReaction attribute)
rn_eq_re (mgkit.kegg.KeggClientRest attribute)
rn_id (mgkit.kegg.KeggReaction attribute)
rn_name_re (mgkit.kegg.KeggClientRest attribute)
S
s_name (mgkit.taxon.UniprotTaxonTuple attribute)
sample_command() (in module mgkit.workflow.sampling_utils)
sample_coverage (mgkit.io.gff.Annotation attribute)
samtools_depth_command() (in module mgkit.workflow.add_gff_info)
SamtoolsDepth (class in mgkit.align)
save_data() (mgkit.kegg.KeggData method)
(mgkit.kegg.KeggMapperBase method)
(mgkit.mappings.eggnog.Kegg2NogMapper method)
(mgkit.taxon.UniprotTaxonomy 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_addtaxa_parser() (in module mgkit.workflow.add_gff_info)
set_attr() (mgkit.io.gff.Annotation method)
set_blast_taxonomy_parser() (in module mgkit.workflow.add_gff_info)
set_blastdb_parser() (in module mgkit.workflow.blast2gff)
set_common_options() (in module mgkit.workflow.add_gff_info)
(in module mgkit.workflow.blast2gff)
(in module mgkit.workflow.json2gff)
(in module mgkit.workflow.taxon_utils)
set_counts_parser() (in module mgkit.workflow.add_gff_info)
set_coverage_parser() (in module mgkit.workflow.add_gff_info)
(in module mgkit.workflow.filter_gff)
set_eggnog_parser() (in module mgkit.workflow.add_gff_info)
set_exp_syn_parser() (in module mgkit.workflow.add_gff_info)
set_filter_taxa_parser() (in module mgkit.workflow.taxon_utils)
set_kegg_parser() (in module mgkit.workflow.add_gff_info)
set_lca_contig_parser() (in module mgkit.workflow.taxon_utils)
set_lca_line_parser() (in module mgkit.workflow.taxon_utils)
set_mapping() (mgkit.io.gff.Annotation method)
set_mongodb_parser() (in module mgkit.workflow.json2gff)
set_overlap_parser() (in module mgkit.workflow.filter_gff)
set_parser() (in module mgkit.workflow.add_coverage)
(in module mgkit.workflow.add_gff_info)
(in module mgkit.workflow.blast2gff)
(in module mgkit.workflow.download_data)
(in module mgkit.workflow.download_profiles)
(in module mgkit.workflow.fasta_utils)
(in module mgkit.workflow.filter_gff)
(in module mgkit.workflow.hmmer2gff)
(in module mgkit.workflow.json2gff)
(in module mgkit.workflow.nuc2aa)
(in module mgkit.workflow.sampling_utils)
(in module mgkit.workflow.taxon_utils)
set_perseq_parser() (in module mgkit.workflow.filter_gff)
set_pfam_parser() (in module mgkit.workflow.add_gff_info)
set_sample_parser() (in module mgkit.workflow.sampling_utils)
set_samtools_depth_parser() (in module mgkit.workflow.add_gff_info)
set_split_parser() (in module mgkit.workflow.fasta_utils)
set_taxa_table_parser() (in module mgkit.workflow.taxon_utils)
set_translate_parser() (in module mgkit.workflow.fasta_utils)
set_uid_parser() (in module mgkit.workflow.fasta_utils)
set_uniprot_offline_parser() (in module mgkit.workflow.add_gff_info)
set_uniprot_parser() (in module mgkit.workflow.add_gff_info)
(in module mgkit.workflow.blast2gff)
set_values_parser() (in module mgkit.workflow.filter_gff)
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_command() (in module mgkit.workflow.fasta_utils)
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]
syn (mgkit.snps.classes.GeneSNP attribute)
(mgkit.snps.classes.SNPType attribute)
synonymous (mgkit.io.snpdat.SNPDatRow attribute)
,
[1]
T
taxa_distance_matrix() (in module mgkit.taxon)
taxa_table_command() (in module mgkit.workflow.taxon_utils)
taxon_db (mgkit.io.gff.Annotation attribute)
taxon_id (mgkit.io.gff.Annotation attribute)
(mgkit.snps.classes.GeneSNP attribute)
,
[1]
(mgkit.taxon.UniprotTaxonTuple attribute)
taxonomy_command() (in module mgkit.workflow.add_gff_info)
to_dict() (mgkit.io.gff.Annotation method)
to_edges() (mgkit.kegg.KeggModule 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)
transcript_id (mgkit.io.snpdat.SNPDatRow attribute)
,
[1]
transcript_name (mgkit.io.snpdat.SNPDatRow attribute)
,
[1]
translate_buff() (in module mgkit.workflow.nuc2aa)
translate_command() (in module mgkit.workflow.fasta_utils)
translate_seq() (in module mgkit.workflow.fasta_utils)
(in module mgkit.workflow.nuc2aa)
translate_sequence() (in module mgkit.utils.sequence)
trim_by_ee() (in module mgkit.filter.reads)
U
uid (mgkit.io.gff.Annotation attribute)
(mgkit.snps.classes.GeneSNP attribute)
,
[1]
uid_command() (in module mgkit.workflow.fasta_utils)
union() (mgkit.io.gff.GenomicRange method)
union_range() (in module mgkit.utils.common)
union_ranges() (in module mgkit.utils.common)
uniprot_command() (in module mgkit.workflow.add_gff_info)
uniprot_mappings_to_dict() (in module mgkit.io.uniprot)
uniprot_offline_command() (in module mgkit.workflow.add_gff_info)
UniprotTaxonomy (class in mgkit.taxon)
UniprotTaxonTuple (class in mgkit.taxon)
unknown (mgkit.snps.classes.SNPType attribute)
UnsupportedFormat
url_open() (in module mgkit.net.utils)
url_read() (in module mgkit.net.utils)
V
validate_taxon_ids() (in module mgkit.workflow.taxon_utils)
validate_taxon_names() (in module mgkit.workflow.taxon_utils)
W
write_association_file() (mgkit.mappings.go.Kegg2GOMapper method)
write_cache() (mgkit.kegg.KeggClientRest method)
write_fasta_sequence() (in module mgkit.io.fasta)
write_fasta_summary() (in module mgkit.workflow.assembly)
write_fastq_sequence() (in module mgkit.io.fastq)
write_gff() (in module mgkit.io.gff)
write_json() (in module mgkit.workflow.taxon_utils)
write_ko_sequences() (in module mgkit.workflow.download_profiles)
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_no_lca() (in module mgkit.workflow.taxon_utils)
write_sign_genes_table() (in module mgkit.snps.funcs)
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