MGKit: Metagenomic framework
release/0.3.3
Introduction
Installation
Metagenomic Pipeline
Scripts Details
Example Notebooks
MGKit GFF Specifications
Library Reference
Changes
MGKit: Metagenomic framework
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Index
Edit on Bitbucket
Index
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A
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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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R
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S
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T
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U
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W
_
__contains__() (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)
_replace() (mgkit.taxon.UniprotTaxonTuple method)
A
add() (mgkit.snps.classes.GeneSNP method)
add_basic_options() (in module mgkit.workflow.utils)
add_coverage_info() (in module mgkit.align)
add_lineage() (mgkit.taxon.UniprotTaxonomy method)
add_module_compounds() (in module mgkit.graphs)
add_profiles_to_length() (in module mgkit.workflow.download_profiles)
add_significance_to_boxplot() (in module mgkit.plots.boxplot)
add_snp() (mgkit.snps.classes.GeneSNP method)
add_taxon() (mgkit.taxon.UniprotTaxonomy method)
add_values_to_boxplot() (in module mgkit.plots.boxplot)
aggr_filtered_list() (in module mgkit.filter.lists)
annotate_graph_nodes() (in module mgkit.graphs)
api_url (mgkit.kegg.KeggClientRest attribute)
apply_func_to_values() (in module mgkit.utils.dictionary)
apply_func_window() (in module mgkit.utils.common)
average_length() (in module mgkit.utils.common)
B
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)
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_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_version() (in module mgkit)
choose_annotation() (in module mgkit.filter.gff)
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)
cite() (in module mgkit)
CiteAction (class in mgkit.workflow.utils)
classes (mgkit.kegg.KeggModule attribute)
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)
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_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)
coverage (mgkit.snps.classes.GeneSNP attribute)
,
[1]
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)
dbfetch() (in module mgkit.net.embl)
dendrogram() (in module mgkit.plots.heatmap)
DependencyError
deprecated() (in module mgkit.utils.common)
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)
E
empty_cache() (mgkit.kegg.KeggClientRest method)
entry (mgkit.kegg.KeggModule attribute)
EntryNotFound
exit_script() (in module mgkit.workflow.utils)
exp_nonsyn (mgkit.snps.classes.GeneSNP attribute)
,
[1]
exp_syn (mgkit.snps.classes.GeneSNP attribute)
,
[1]
expected_error_rate() (in module mgkit.filter.reads)
F
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_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_ratios_by_numbers() (in module mgkit.utils.dictionary)
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)
FilterFails
find() (mgkit.kegg.KeggClientRest method)
find_by_name() (mgkit.taxon.UniprotTaxonomy method)
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)
from_gff() (in module mgkit.counts.func)
from_json() (mgkit.snps.classes.GeneSNP method)
from_kgml() (in module mgkit.graphs)
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.snps.classes.GeneSNP attribute)
,
[1]
GeneSNP (class in mgkit.snps.classes)
get_ancestor_map() (in module mgkit.taxon)
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_cp_names() (mgkit.kegg.KeggData method)
get_default_filters() (in module mgkit.snps.filter)
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_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_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_lineage_string() (mgkit.taxon.UniprotTaxonomy method)
get_mapping_level() (in module mgkit.mappings.enzyme)
get_mappings() (in module mgkit.net.uniprot)
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_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_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_rn_cp_links() (mgkit.kegg.KeggData method)
get_rn_names() (mgkit.kegg.KeggData method)
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_taxon_colors_new() (in module mgkit.plots.unused)
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)
group_annotation_by_mapping() (in module mgkit.mappings.utils)
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)
is_ancestor() (in module mgkit.taxon)
(mgkit.taxon.UniprotTaxonomy method)
K
Kegg2CazyMapper (class in mgkit.mappings.cazy)
Kegg2GOMapper (class in mgkit.mappings.go)
Kegg2NogMapper (class in mgkit.mappings.eggnog)
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)
left_cp (mgkit.kegg.KeggReaction attribute)
legend_patches() (in module mgkit.plots.utils)
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() (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_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_funccat() (mgkit.mappings.eggnog.NOGInfo method)
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)
lowest_common_ancestor() (in module mgkit.taxon)
M
main() (in module mgkit.workflow.download_data)
(in module mgkit.workflow.download_profiles)
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)
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.lists (module)
mgkit.filter.reads (module)
mgkit.filter.taxon (module)
mgkit.graphs (module)
mgkit.io (module)
mgkit.io.fasta (module)
mgkit.io.fastq (module)
mgkit.io.glimmer (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.trans_tables (module)
mgkit.workflow (module)
mgkit.workflow.download_data (module)
,
[1]
mgkit.workflow.download_profiles (module)
,
[1]
mgkit.workflow.utils (module)
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)
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_entry() (mgkit.kegg.KeggModule method)
parse_entry2() (mgkit.kegg.KeggModule method)
parse_expasy_file() (in module mgkit.mappings.enzyme)
parse_glimmer3() (in module mgkit.io.glimmer)
parse_gtdb_lineage() (mgkit.taxon.UniprotTaxonomy static method)
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_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)
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)
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)
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_samtools_depth() (in module mgkit.align)
read_taxonomy() (mgkit.taxon.UniprotTaxonomy method)
region_coverage() (mgkit.align.SamtoolsDepth method)
rename_graph_nodes() (in module mgkit.graphs)
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)
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)
set_parser() (in module mgkit.workflow.download_data)
(in module mgkit.workflow.download_profiles)
significance_test() (in module mgkit.snps.funcs)
snps (mgkit.snps.classes.GeneSNP attribute)
,
[1]
SNPType (class in mgkit.snps.classes)
split_dictionary_by_value() (in module mgkit.utils.dictionary)
split_fasta_file() (in module mgkit.io.fasta)
split_write() (in module mgkit.io.utils)
syn (mgkit.snps.classes.GeneSNP attribute)
(mgkit.snps.classes.SNPType attribute)
T
taxa_distance_matrix() (in module mgkit.taxon)
taxon_id (mgkit.snps.classes.GeneSNP attribute)
,
[1]
(mgkit.taxon.UniprotTaxonTuple attribute)
to_edges() (mgkit.kegg.KeggModule method)
to_json() (mgkit.snps.classes.GeneSNP method)
trim_by_ee() (in module mgkit.filter.reads)
U
uid (mgkit.snps.classes.GeneSNP attribute)
,
[1]
union_range() (in module mgkit.utils.common)
union_ranges() (in module mgkit.utils.common)
uniprot_mappings_to_dict() (in module mgkit.io.uniprot)
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)
W
write_association_file() (mgkit.mappings.go.Kegg2GOMapper method)
write_cache() (mgkit.kegg.KeggClientRest method)
write_fasta_sequence() (in module mgkit.io.fasta)
write_fastq_sequence() (in module mgkit.io.fastq)
write_ko_sequences() (in module mgkit.workflow.download_profiles)
write_sign_genes_table() (in module mgkit.snps.funcs)
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