pytransit.analysis package

Submodules

pytransit.analysis.base module

class pytransit.analysis.base.AnalysisGUI[source]
Enable()[source]
GlobalDisable()[source]
GlobalEnable()[source]
GlobalHide()[source]
GlobalShow()[source]
Hide()[source]
Show()[source]
defineCheckBox(panel, labelText='', widgetCheck=False, tooltipText='', widgetSize=None)[source]
defineChoiceBox(panel, labelText='', widgetChoice=[''], tooltipText='', labSize=None, widgetSize=None)[source]
definePanel(wxobj)[source]
defineTextBox(panel, labelText='', widgetText='', tooltipText='', labSize=None, widgetSize=None)[source]
class pytransit.analysis.base.AnalysisMethod(short_name, long_name, short_desc, long_desc, 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, time=-1)[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, short_desc, long_desc, 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).

exception pytransit.analysis.base.InvalidArgumentException(message)[source]

Bases: exceptions.Exception

class pytransit.analysis.base.MultiConditionMethod(short_name, long_name, short_desc, long_desc, combined_wig, metadata, annotation_path, output, normalization=None, LOESS=False, ignoreCodon=True, wxobj=None)[source]

Bases: pytransit.analysis.base.AnalysisMethod

Class to be inherited by analysis methods that compare essentiality between multiple conditions (e.g Anova).

class pytransit.analysis.base.QuadConditionMethod(short_name, long_name, short_desc, long_desc, ctrldataA, ctrldataB, expdataA, expdataB, 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 four conditions (e.g. GI).

class pytransit.analysis.base.SingleConditionMethod(short_name, long_name, short_desc, long_desc, 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, short_desc, long_desc, tn, method_class=<class pytransit.analysis.base.AnalysisMethod>, gui_class=<class pytransit.analysis.base.AnalysisGUI>, filetypes=[<class pytransit.analysis.base.TransitFile>])[source]
fullname()[source]
getDescriptionText()[source]
getInstructionsText()[source]
getTransposonsText()[source]
class pytransit.analysis.base.TransitFile(identifier='#Unknown', colnames=[])[source]

Bases: pytransit.analysis.base.TransitGUIBase

displayInTrackView(displayFrame, event)[source]
getData(path, colnames)[source]
getHeader(path)[source]
getMenus()[source]
class pytransit.analysis.base.TransitGUIBase[source]
console_message(text)[source]
console_message_inplace(text)[source]
status_message(text, time=-1)[source]
transit_error(text)[source]
transit_message(text)[source]
transit_message_inplace(text)[source]
transit_warning(text)[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, pi0=0.5, pi1=0.5, M0=1.0, M1=1.0, a0=10.0, a1=10.0, b0=1.0, b1=1.0, alpha_w=0.5, beta_w=0.5, 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, minread=1, 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

ExpectedRuns_cached(n, q)[source]
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='Mean', 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=array([], dtype=float64))[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

GlobalDisable()[source]
GlobalEnable()[source]
definePanel(wxobj)[source]
class pytransit.analysis.resampling.ResamplingMethod(ctrldata, expdata, annotation_path, output_file, normalization='TTR', samples=10000, adaptive=False, doHistogram=False, includeZeros=False, pseudocount=0.0, replicates='Sum', LOESS=False, ignoreCodon=True, NTerminus=0.0, CTerminus=0.0, ctrl_lib_str='', exp_lib_str='', 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]

pytransit.analysis.anova module

class pytransit.analysis.anova.AnovaAnalysis[source]

Bases: pytransit.analysis.base.TransitAnalysis

class pytransit.analysis.anova.AnovaMethod(combined_wig, metadata, annotation, normalization, output_file, ignored_conditions=set([]))[source]

Bases: pytransit.analysis.base.MultiConditionMethod

anova

Run()[source]
filter_by_conditions_blacklist(data, conditions, ignored_conditions)[source]

Filters out wigfiles, with ignored conditions. ([[Wigdata]], [Condition]) -> Tuple([[Wigdata]], [Condition])

classmethod fromargs(rawargs)[source]
group_by_condition(wigList, conditions)[source]

Returns array of datasets, where each dataset corresponds to one condition. ([[Wigdata]], [Condition]) -> [[DataForCondition]] Wigdata :: [Number] Condition :: String DataForCondition :: [Number]

means_by_condition_for_gene(sites, conditions, data)[source]

Returns a dictionary of {Condition: Mean} for each condition. ([Site], [Condition]) -> {Condition: Number} Site :: Number Condition :: String

means_by_rv(data, RvSiteindexesMap, genes, conditions)[source]

Returns Dictionary of mean values by condition ([[Wigdata]], {Rv: SiteIndex}, [Gene], [Condition]) -> {Rv: {Condition: Number}} Wigdata :: [Number] SiteIndex :: Number Gene :: {start, end, rv, gene, strand} Condition :: String

read_samples_metadata(metadata_file)[source]

Filename -> ConditionMap ConditionMap :: {Filename: Condition}

run_anova(data, genes, MeansByRv, RvSiteindexesMap, conditions)[source]

Runs Anova (grouping data by condition) and returns p and q values ([[Wigdata]], [Gene], {Rv: {Condition: Mean}}, {Rv: [SiteIndex]}, [Condition]) -> Tuple([Number], [Number]) Wigdata :: [Number] Gene :: {start, end, rv, gene, strand} Mean :: Number SiteIndex: Integer Condition :: String

classmethod usage_string()[source]
wigs_to_conditions(conditionsByFile, filenamesInCombWig)[source]

Returns list of conditions corresponding to given wigfiles. ({FileName: Condition}, [FileName]) -> [Condition] Condition :: [String]

pytransit.analysis.anova.main()[source]

Module contents