pytransit.analysis package¶

Submodules¶

pytransit.analysis.base module¶

class pytransit.analysis.base.AnalysisGUI[source]¶

Enable()[source]¶

Hide()[source]¶

Show()[source]¶

definePanel(wxobj)[source]¶

class pytransit.analysis.base.AnalysisMethod(short_name, long_name, description, output, annotation_path, wxobj=None)[source]¶

Basic class for analysis methods. Inherited by SingleMethod and ComparisonMethod.

Run()[source]¶

add_file(path=None, filetype=None)[source]¶

console_message(text)[source]¶

console_message_inplace(text)[source]¶

finish()[source]¶

classmethod fromGUI(wxobj)[source]¶

classmethod fromargs(rawargs)[source]¶

classmethod fromconsole()[source]¶

print_members()[source]¶

progress_range(count)[source]¶

progress_update(text, count)[source]¶

status_message(text)[source]¶

transit_error(text)[source]¶

transit_message(text)[source]¶

transit_message_inplace(text)[source]¶

transit_warning(text)[source]¶

classmethod usage_string()[source]¶

class pytransit.analysis.base.DualConditionMethod(short_name, long_name, description, ctrldata, expdata, annotation_path, output, normalization, replicates='Sum', LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, wxobj=None)[source]¶

Bases: pytransit.analysis.base.AnalysisMethod

Class to be inherited by analysis methods that determine changes in essentiality between two conditions (e.g. Resampling, DEHMM).

class pytransit.analysis.base.SingleConditionMethod(short_name, long_name, description, ctrldata, annotation_path, output, replicates='Sum', normalization=None, LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, wxobj=None)[source]¶

Bases: pytransit.analysis.base.AnalysisMethod

Class to be inherited by analysis methods that determine essentiality in a single condition (e.g. Gumbel, Binomial, HMM).

class pytransit.analysis.base.TransitAnalysis(sn, ln, desc, tn, method_class=<class pytransit.analysis.base.AnalysisMethod at 0x4ef39a8>, gui_class=<class pytransit.analysis.base.AnalysisGUI at 0x4ef3940>, filetypes=[<class pytransit.analysis.base.TransitFile at 0x4ef3870>])[source]¶

fullname()[source]¶

getDescriptionText()[source]¶

getInstructionsText()[source]¶

getTransposonsText()[source]¶

class pytransit.analysis.base.TransitFile(identifier='#Unknown', colnames=[])[source]¶

displayInTrackView(displayFrame, event)[source]¶

getData(path, colnames)[source]¶

getHeader(path)[source]¶

getMenus()[source]¶

pytransit.analysis.binomial module¶

class pytransit.analysis.binomial.BinomialAnalysis[source]¶

Bases: pytransit.analysis.base.TransitAnalysis

class pytransit.analysis.binomial.BinomialFile[source]¶

Bases: pytransit.analysis.base.TransitFile

getHeader(path)[source]¶

class pytransit.analysis.binomial.BinomialGUI[source]¶

Bases: pytransit.analysis.base.AnalysisGUI

definePanel(wxobj)[source]¶

class pytransit.analysis.binomial.BinomialMethod(ctrldata, annotation_path, output_file, samples=10000, burnin=500, replicates='Sum', normalization=None, LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, wxobj=None)[source]¶

Bases: pytransit.analysis.base.SingleConditionMethod

binomial

Run()[source]¶

classmethod fromGUI(wxobj)[source]¶

classmethod fromargs(rawargs)[source]¶

classmethod usage_string()[source]¶

pytransit.analysis.example module¶

class pytransit.analysis.example.ExampleAnalysis[source]¶

Bases: pytransit.analysis.base.TransitAnalysis

class pytransit.analysis.example.ExampleFile[source]¶

Bases: pytransit.analysis.base.TransitFile

getHeader(path)[source]¶

class pytransit.analysis.example.ExampleGUI[source]¶

Bases: pytransit.analysis.base.AnalysisGUI

class pytransit.analysis.example.ExampleMethod(ctrldata, annotation_path, output_file, replicates='Sum', normalization=None, LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, wxobj=None)[source]¶

Bases: pytransit.analysis.base.SingleConditionMethod

Example

Run()[source]¶

classmethod fromGUI(wxobj)[source]¶

classmethod fromargs(rawargs)[source]¶

classmethod usage_string()[source]¶

pytransit.analysis.griffin module¶

class pytransit.analysis.griffin.GriffinAnalysis[source]¶

Bases: pytransit.analysis.base.TransitAnalysis

class pytransit.analysis.griffin.GriffinFile[source]¶

Bases: pytransit.analysis.base.TransitFile

getHeader(path)[source]¶

class pytransit.analysis.griffin.GriffinGUI[source]¶

Bases: pytransit.analysis.base.AnalysisGUI

definePanel(wxobj)[source]¶

class pytransit.analysis.griffin.GriffinMethod(ctrldata, annotation_path, output_file, replicates='Sum', normalization=None, LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, wxobj=None)[source]¶

Bases: pytransit.analysis.base.SingleConditionMethod

griffin

Run()[source]¶

classmethod fromGUI(wxobj)[source]¶

classmethod fromargs(rawargs)[source]¶

classmethod usage_string()[source]¶

pytransit.analysis.gumbel module¶

class pytransit.analysis.gumbel.GumbelAnalysis[source]¶

Bases: pytransit.analysis.base.TransitAnalysis

class pytransit.analysis.gumbel.GumbelFile[source]¶

Bases: pytransit.analysis.base.TransitFile

getHeader(path)[source]¶

class pytransit.analysis.gumbel.GumbelGUI[source]¶

Bases: pytransit.analysis.base.AnalysisGUI

definePanel(wxobj)[source]¶

class pytransit.analysis.gumbel.GumbelMethod(ctrldata, annotation_path, output_file, samples=10000, burnin=500, trim=1, minread=1, replicates='Sum', normalization=None, LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, wxobj=None)[source]¶

Bases: pytransit.analysis.base.SingleConditionMethod

Gumbel

F_non(p, N, R)[source]¶

Run()[source]¶

classify(n, r, p)[source]¶

classmethod fromGUI(wxobj)[source]¶

classmethod fromargs(rawargs)[source]¶

good_orf(gene)[source]¶

sample_Z(p, w1, N, R, S, T, mu_s, sigma_s, SIG)[source]¶

sigmoid(d, n)[source]¶

classmethod usage_string()[source]¶

pytransit.analysis.hmm module¶

class pytransit.analysis.hmm.HMMAnalysis[source]¶

Bases: pytransit.analysis.base.TransitAnalysis

class pytransit.analysis.hmm.HMMGUI[source]¶

Bases: pytransit.analysis.base.AnalysisGUI

definePanel(wxobj)[source]¶

class pytransit.analysis.hmm.HMMGenesFile[source]¶

Bases: pytransit.analysis.base.TransitFile

getHeader(path)[source]¶

class pytransit.analysis.hmm.HMMMethod(ctrldata, annotation_path, output_file, replicates='TTRMean', normalization=None, LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, wxobj=None)[source]¶

Bases: pytransit.analysis.base.SingleConditionMethod

HMM

Run()[source]¶

backward_procedure(A, B, PI, O, C=None)[source]¶

calculate_pins(reads)[source]¶

forward_procedure(A, B, PI, O)[source]¶

classmethod fromGUI(wxobj)[source]¶

classmethod fromargs(rawargs)[source]¶

post_process_genes(data, position, states, output_path)[source]¶

classmethod usage_string()[source]¶

viterbi(A, B, PI, O)[source]¶

class pytransit.analysis.hmm.HMMSitesFile[source]¶

Bases: pytransit.analysis.base.TransitFile

getHeader(path)[source]¶

pytransit.analysis.rankproduct module¶

class pytransit.analysis.rankproduct.RankProductAnalysis[source]¶

Bases: pytransit.analysis.base.TransitAnalysis

class pytransit.analysis.rankproduct.RankProductFile[source]¶

Bases: pytransit.analysis.base.TransitFile

class pytransit.analysis.rankproduct.RankProductGUI[source]¶

Bases: pytransit.analysis.base.AnalysisGUI

definePanel(wxobj)[source]¶

class pytransit.analysis.rankproduct.RankProductMethod(ctrldata, expdata, annotation_path, output_file, normalization='TTR', samples=10000, adaptive=False, doHistogram=False, replicates='Sum', LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, wxobj=None)[source]¶

Bases: pytransit.analysis.base.DualConditionMethod

rankproduct

Run()[source]¶

classmethod fromGUI(wxobj)[source]¶

classmethod fromargs(rawargs)[source]¶

classmethod usage_string()[source]¶

pytransit.analysis.resampling module¶

class pytransit.analysis.resampling.ResamplingAnalysis[source]¶

Bases: pytransit.analysis.base.TransitAnalysis

class pytransit.analysis.resampling.ResamplingFile[source]¶

Bases: pytransit.analysis.base.TransitFile

displayHistogram(displayFrame, event)[source]¶

getHeader(path)[source]¶

getMenus()[source]¶

class pytransit.analysis.resampling.ResamplingGUI[source]¶

Bases: pytransit.analysis.base.AnalysisGUI

definePanel(wxobj)[source]¶

class pytransit.analysis.resampling.ResamplingMethod(ctrldata, expdata, annotation_path, output_file, normalization='TTR', samples=10000, adaptive=False, doHistogram=False, includeZeros=False, replicates='Sum', LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, wxobj=None)[source]¶

Bases: pytransit.analysis.base.DualConditionMethod

resampling

Run()[source]¶

classmethod fromGUI(wxobj)[source]¶

classmethod fromargs(rawargs)[source]¶

classmethod usage_string()[source]¶

pytransit.analysis.tn5gaps module¶

class pytransit.analysis.tn5gaps.Tn5GapsAnalysis[source]¶

Bases: pytransit.analysis.base.TransitAnalysis

class pytransit.analysis.tn5gaps.Tn5GapsFile[source]¶

Bases: pytransit.analysis.base.TransitFile

getHeader(path)[source]¶

class pytransit.analysis.tn5gaps.Tn5GapsGUI[source]¶

Bases: pytransit.analysis.base.AnalysisGUI

definePanel(wxobj)[source]¶

class pytransit.analysis.tn5gaps.Tn5GapsMethod(ctrldata, annotation_path, output_file, replicates='Sum', normalization=None, LOESS=False, ignoreCodon=True, minread=1, NTerminus=0.0, CTerminus=0.0, wxobj=None)[source]¶

Bases: pytransit.analysis.base.SingleConditionMethod

Example

Run()[source]¶

calc_overlap(run_interv, gene_interv)[source]¶

classmethod fromGUI(wxobj)[source]¶

classmethod fromargs(rawargs)[source]¶

intersect_size(intv1, intv2)[source]¶

classmethod usage_string()[source]¶

Module contents¶