capalyzer.packet_builder.sub_factories package

Submodules

capalyzer.packet_builder.sub_factories.amr_factory module

class capalyzer.packet_builder.sub_factories.amr_factory.AMRFactory(dataFactory)[source]

Bases: capalyzer.packet_builder.sub_factories.subfactory.SubFactory

card_rpkm()[source]
card_rpkmg()[source]
classus(rpkmg=False)[source]
gene(rpkmg=False)[source]
generic_card(metric)[source]
generic_megares(result, rpkmg=False)[source]
group(rpkmg=False)[source]
mech(rpkmg=False)[source]

capalyzer.packet_builder.sub_factories.ave_genome_size_factory module

class capalyzer.packet_builder.sub_factories.ave_genome_size_factory.AGSFactory(dataFactory)[source]

Bases: capalyzer.packet_builder.sub_factories.subfactory.SubFactory

tbl()[source]
capalyzer.packet_builder.sub_factories.ave_genome_size_factory.get_ags_from_file(fname)[source]

capalyzer.packet_builder.sub_factories.constants module

capalyzer.packet_builder.sub_factories.hmp_comparison_factory module

class capalyzer.packet_builder.sub_factories.hmp_comparison_factory.HMPFactory(dataFactory)[source]

Bases: capalyzer.packet_builder.sub_factories.subfactory.SubFactory

dists()[source]
raw()[source]
raw_table()[source]
capalyzer.packet_builder.sub_factories.hmp_comparison_factory.as_dist(raw_vals)[source]
capalyzer.packet_builder.sub_factories.hmp_comparison_factory.jloads(fname)[source]

capalyzer.packet_builder.sub_factories.macrobes module

class capalyzer.packet_builder.sub_factories.macrobes.MacrobeFactory(dataFactory)[source]

Bases: capalyzer.packet_builder.sub_factories.subfactory.SubFactory

table()[source]
capalyzer.packet_builder.sub_factories.macrobes.jloads(fname)[source]

capalyzer.packet_builder.sub_factories.microbe_directory module

class capalyzer.packet_builder.sub_factories.microbe_directory.MicrobeDirectoryFactory(dataFactory)[source]

Bases: capalyzer.packet_builder.sub_factories.subfactory.SubFactory

raw()[source]
raw_table()[source]
capalyzer.packet_builder.sub_factories.microbe_directory.jloads(fname)[source]

capalyzer.packet_builder.sub_factories.pathway_factory module

class capalyzer.packet_builder.sub_factories.pathway_factory.PathwayFactory(dataFactory)[source]

Bases: capalyzer.packet_builder.sub_factories.subfactory.SubFactory

pathways(coverage=False, show_unmapped=False)[source]

Return a table of pathway abundances or coverages.

capalyzer.packet_builder.sub_factories.read_proportions module

class capalyzer.packet_builder.sub_factories.read_proportions.ReadPropsFactory(dataFactory)[source]

Bases: capalyzer.packet_builder.sub_factories.subfactory.SubFactory

table()[source]
capalyzer.packet_builder.sub_factories.read_proportions.jloads(fname)[source]

capalyzer.packet_builder.sub_factories.subfactory module

class capalyzer.packet_builder.sub_factories.subfactory.SubFactory(dataFactory)[source]

Bases: object

capalyzer.packet_builder.sub_factories.taxonomy_factory module

class capalyzer.packet_builder.sub_factories.taxonomy_factory.TaxonomyFactory(dataFactory)[source]

Bases: capalyzer.packet_builder.sub_factories.subfactory.SubFactory

bracken(rank='species')[source]
generic(mod_name, top_n=0, cutoff=0, rank='species', top_taxa='all', proportions=False, rname='mpa')[source]
kraken(top_n=0, cutoff=0, rank='species', top_taxa='all', proportions=False, level=None)[source]
krakenhll(top_n=0, cutoff=0, rank='species', top_taxa='all', proportions=False, level=None)[source]
krakenhll_angular(min_reads=3, min_kmers=64, slope=0.4)[source]
krakenhll_long()[source]
metaphlan2(top_n=0, cutoff=0, rank='species', top_taxa='all', proportions=True, level=None)[source]
parse_krakenhll_report(mod_name, top_n=0, cutoff=0, rank='species', top_taxa='all', proportions=False, rname='mpa')[source]
capalyzer.packet_builder.sub_factories.taxonomy_factory.clean_taxa(taxa)[source]
capalyzer.packet_builder.sub_factories.taxonomy_factory.get_top_n(vec, n)[source]
capalyzer.packet_builder.sub_factories.taxonomy_factory.is_rank(key, rank)[source]
capalyzer.packet_builder.sub_factories.taxonomy_factory.is_top_taxa(key, top_taxa)[source]

capalyzer.packet_builder.sub_factories.toxonomy_long_form module

capalyzer.packet_builder.sub_factories.toxonomy_long_form.add_to_tree(sample_name, report_file, root, min_rank=None, min_abundance=0, min_kmer=0, min_cov=0)[source]

Return a root node with the file as a tree.

capalyzer.packet_builder.sub_factories.toxonomy_long_form.build_table(report_files, features, rank, min_abundance=0, min_kmer=0, min_cov=0, wide=True)[source]

Return a pandas dataframe with data from all files.

capalyzer.packet_builder.sub_factories.toxonomy_long_form.get_mpa_str(node)[source]

Return an MPA string to this nodes lineage.

capalyzer.packet_builder.sub_factories.toxonomy_long_form.get_node(parent, sample_name, depth, tkns)[source]
capalyzer.packet_builder.sub_factories.toxonomy_long_form.get_sample_name(filename)[source]

Extract sample name from filename.

capalyzer.packet_builder.sub_factories.toxonomy_long_form.longform_taxa(report_filenames, min_abundance=0, min_kmer=64, min_cov=0, wide=False, rank=None, features='reads, kmers, dup, cov, percent, tax_reads')[source]

Return a longform taxa table as a pandas dataframe.

capalyzer.packet_builder.sub_factories.toxonomy_long_form.report_from_tree(root_node, features, rank, wide=True)[source]

Return a pandas dataframe with all requested info about child nodes of root.

capalyzer.packet_builder.sub_factories.toxonomy_long_form.tokenize(line)[source]

capalyzer.packet_builder.sub_factories.utils module

capalyzer.packet_builder.sub_factories.utils.parse_gene_table(gene_table, metric)[source]

Return a parsed gene quantification table.

Module contents