hatchet.bin package

Submodules

hatchet.bin.HATCHet module

class hatchet.bin.HATCHet.ProgressBar(total, length, counter=0, verbose=False, decimals=1, fill='█', prefix='Progress:', suffix='Complete')

Bases: object

Methods

progress

progress(advance=True, msg='')

hatchet.bin.HATCHet.argmax(d)

hatchet.bin.HATCHet.argmin(d)

hatchet.bin.HATCHet.backward(f, i, g, limit)

hatchet.bin.HATCHet.central(f, i, g, limit)

hatchet.bin.HATCHet.computeSizes(seg, bbc, samples)

hatchet.bin.HATCHet.debug(msg)

hatchet.bin.HATCHet.estimate_forward(f, i, g, knw, limit)

hatchet.bin.HATCHet.execute(args, basecmd, n, outprefix)

hatchet.bin.HATCHet.execute_python(solver, args, n, outprefix)

hatchet.bin.HATCHet.filtering(bbc, seg, size, ts, tc, mB, mR, samples, v)

hatchet.bin.HATCHet.findClonalClusters(fseg, neutral, size, tB, tR, samples, v)

hatchet.bin.HATCHet.findNeutralCluster(seg, size, td, samples, v)

hatchet.bin.HATCHet.forward(f, i, g, limit)

hatchet.bin.HATCHet.info(msg)

hatchet.bin.HATCHet.isfloat(value)

hatchet.bin.HATCHet.logArgs(args, width)

hatchet.bin.HATCHet.main(args=None)

hatchet.bin.HATCHet.makeBaseCMD(args, e)

hatchet.bin.HATCHet.parseClonalClusters(clonal, fseg, size, samples, v)

hatchet.bin.HATCHet.parse_clonal_diploid(clonal)

Given a list of clonal cluster copy numbers, this function tries to order them to be compatible with the HATCHet C++ factorization module. For diploid scaling, this module requires: -the first cluster is indicated with copy-number 1,1 -the second cluster has a total copy number different from 2

hatchet.bin.HATCHet.parse_clonal_tetraploid(clonal)

Given a list of clonal cluster copy numbers, this function tries to order them to be compatible with the HATCHet C++ factorization module. For tetraploid scaling, this module requires: -the first cluster is indicated with copy-number 2,2 -the second cluster has a total copy number different from 4

hatchet.bin.HATCHet.parsing_arguments(args=None)

Parse command line arguments Returns:

hatchet.bin.HATCHet.readBBC(filename)

hatchet.bin.HATCHet.readSEG(filename)

hatchet.bin.HATCHet.runningDiploid(neutral, args, clonal=None)

hatchet.bin.HATCHet.runningTetraploid(clonal, scale, size, args)

hatchet.bin.HATCHet.safediv(v)

hatchet.bin.HATCHet.select(diploid, tetraploid, v, rundir, g, limit)

hatchet.bin.HATCHet.selectDiploid(diploid, v, rundir, g, limit)

hatchet.bin.HATCHet.selectTetraploid(tetraploid, v, rundir, g, limit)

hatchet.bin.HATCHet.t2s(x)

hatchet.bin.HATCHet.warning(msg)

hatchet.bin.HATCHet-preprocess module

Module contents