Module ImportFrom alias Import alias Import alias ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Assign NameStore Str Return Call AttributeLoad NameLoad attr NameLoad decorator_list decorator_list ClassDef bases NameLoad body Expr Str Assign NameStore Str FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Expr Str Assign NameStore ListLoad Assign NameStore BinOpMod Str NameLoad For NameStore Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad attr body Expr Call AttributeLoad NameLoad attr BinOpMult Call NameLoad SubscriptLoad NameLoad Index Num Num Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Return Dict Str NameLoad decorator_list decorator_list ClassDef bases NameLoad body Expr Str Assign NameStore Str FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Expr Str Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore ListLoad Str Str Str Str Str Str For NameStore NameLoad body Assign SubscriptStore NameLoad Index NameLoad Dict For NameStore Call AttributeLoad NameLoad attr body Assign NameStore BinOpMod Str TupleLoad NameLoad NameLoad For TupleStore NameStore NameStore Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad attr body If CompareGt Call NameLoad NameLoad Num body Assign SubscriptStore SubscriptLoad NameLoad Index NameLoad Index NameLoad BinOpMult Call NameLoad NameLoad Num Return NameLoad decorator_list decorator_list ClassDef bases NameLoad body Expr Str Assign NameStore Str FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Expr Str Assign NameStore Call AttributeLoad NameLoad attr Str Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore BinOpMod Str NameLoad For NameStore Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad attr body Assign TupleStore NameStore NameStore NameStore NameStore NameStore NameStore Call NameLoad NameLoad ListLoad SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num Assign TupleStore SubscriptStore NameLoad Index Str SubscriptStore NameLoad Index Str SubscriptStore NameLoad Index Str SubscriptStore NameLoad Index Str SubscriptStore NameLoad Index Str SubscriptStore NameLoad Index Str TupleLoad NameLoad NameLoad NameLoad NameLoad NameLoad NameLoad Return NameLoad decorator_list decorator_list
N/A SphinxReport.Tracker * N/A sqlite3 N/A collections LcaContributingReads N/A TrackerSQL N/A N/A 
    returns the proportion of reads 
    that contribute to the relative abundance
    estimations. 
     __call__ N/A N/A self track slice N/A None N/A N/A statement SELECT * FROM test_control_R1_taxa_readcounts N/A N/A N/A self getAll statement N/A N/A LcaSpeciesAbundanceDistribution N/A TrackerSQL N/A N/A 
    summarise the relative abundance distribution of 
    species
     N/A pattern (.*)_taxa_count __call__ N/A N/A self track slice N/A None N/A N/A 
        return species relative abundance distribution
         N/A species N/A N/A statement N/A SELECT proportion FROM %s_taxa_count
                   WHERE level == 'species' track N/A rel N/A N/A N/A N/A self execute statement fetchall N/A N/A N/A N/A species append N/A N/A float N/A rel N/A 0 100 N/A N/A N/A species sort N/A N/A N/A species reverse N/A N/A species species N/A N/A LcaRelativeAbundance N/A TrackerSQL N/A N/A 
    summarises the relative abundance at
    different taxonomic levels - results
    from lcamapper
     N/A pattern (.*)_taxa_count __call__ N/A N/A self track slice N/A None N/A N/A 
        only displays those above 1% relative abundance
         N/A result N/A N/A collections OrderedDict N/A taxon_levels N/A phylum class order family genus species N/A taxon taxon_levels N/A N/A N/A result N/A taxon N/A N/A taxon N/A N/A result keys N/A N/A statement N/A SELECT taxa, proportion FROM %s_taxa_count
                           WHERE level == '%s' N/A track taxon N/A N/A tax rel N/A N/A N/A N/A self execute statement fetchall N/A N/A N/A N/A float rel 0.01 N/A N/A N/A N/A result N/A taxon N/A tax N/A N/A float rel 100 N/A result N/A N/A LcaTotalTaxa N/A TrackerSQL N/A N/A 
    Summarises the total number of groups at
    each level that were detected in the samples
     N/A pattern (.*)_level_count __call__ N/A N/A self track slice N/A None N/A N/A 
        number of taxa found at each level
         N/A dbh N/A N/A sqlite3 connect csvdb N/A cc N/A N/A dbh cursor N/A result N/A N/A collections OrderedDict N/A statement N/A SELECT nphylum, nclass, norder, nfamily, ngenus, nspecies FROM %s_level_count track N/A data N/A N/A N/A N/A cc execute statement fetchall N/A N/A N/A phylum _class order family genus species N/A map int N/A N/A data N/A 0 N/A data N/A 1 N/A data N/A 2 N/A data N/A 3 N/A data N/A 4 N/A data N/A 5 N/A N/A N/A result N/A phylum N/A result N/A class N/A result N/A order N/A result N/A family N/A result N/A genus N/A result N/A species N/A phylum _class order family genus species N/A result N/A N/A