def plotRelativeAbundanceCorrelations(infiles, outfile):
'''
plot the correlation between the estimated
relative abundance of species and the true
relative abundances - done on the shared set
'''
PipelineMetagenomeBenchmark.plotRelativeAbundanceCorrelations(infiles, outfile)
def plotRelativeAbundanceCorrelations(infiles, outfile):
'''
plot the correlation between the estimated
relative abundance of species and the true
relative abundances - done on the shared set
'''
PipelineMetagenomeBenchmark.plotRelativeAbundanceCorrelations(
infiles, outfile)
def buildTrueTaxonomicRelativeAbundances(infiles, outfile):
'''
get species level relative abundances for the simulateds
data. This involes creating maps between different identifiers
from the NCBI taxonomy. This is so that the results are comparable
to species level analysis from metaphlan
The gi_taxid_nucl is a huge table and therefore this function
takes an age to run - can think of optimising this somehow
'''
to_cluster = True
PipelineMetagenomeBenchmark.buildTrueTaxonomicRelativeAbundances(infiles, outfile)
def buildTrueTaxonomicRelativeAbundances(infiles, outfile):
'''
relative abundances for the simulateds at different levels of
the taxonomy.
This involes creating maps between different identifiers
from the NCBI taxonomy. This is so that the results are comparable
to species level analysis from metaphlan
The gi_taxid_nucl is a huge table and therefore this function
takes an age to run - can think of optimising this somehow
'''
to_cluster = True
PipelineMetagenomeBenchmark.buildTrueTaxonomicRelativeAbundances(
infiles, outfile)
def plotCoverageOverGenomes(infile, outfile):
'''
plot the percent coverage over each genome
'''
PipelineMetagenomeBenchmark.plotCoverageOverGenomes(infile, outfile)
def calculateFalsePositiveRate(infiles, outfile):
'''
calculate the false positive rate in taxonomic
abundances
'''
PipelineMetagenomeBenchmark.calculateFalsePositiveRate(infiles, outfile)
def calculateFalsePositiveRate(infiles, outfile):
'''
calculate the false positive rate in taxonomic
abundances
'''
PipelineMetagenomeBenchmark.calculateFalsePositiveRate(infiles, outfile)
def plotCoverageOverGenomes(infile, outfile):
'''
plot the percent coverage over each genome
'''
PipelineMetagenomeBenchmark.plotCoverageOverGenomes(infile, outfile)
