WrapperCodeML.py -

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Code

exception WrapperCodeML.Error

Bases: Exception

Base class for exceptions in this module.

exception WrapperCodeML.ParsingError(message, line=None)

Bases: WrapperCodeML.Error

Exception raised for errors while parsing

message -- explanation of the error

exception WrapperCodeML.UsageError(message)

Bases: WrapperCodeML.Error

Exception raised for errors while starting

message -- explanation of the error

class WrapperCodeML.CodeMLBranchInfo(branch1, branch2, kaks, ka, ks, ndn, sds, n, s)

Bases: object

result with branch information.

class WrapperCodeML.BaseMLResult

Bases: WrapperCodeML.CodeMLResult

result object for BaseML.

class WrapperCodeML.CodeMLResultSites(num_sequences, model)

Bases: WrapperCodeML.CodeMLResult

result with site specific information.

class WrapperCodeML.CodeMLResultPairs

Bases: WrapperCodeML.CodeMLResult

results for a pairwise codeml run.

fromResult(result)

build pairwise results from tree.

class WrapperCodeML.CodeMLResultPair

Bases: WrapperCodeML.CodeMLResult

results for a pairwise comparison.

class WrapperCodeML.CodeMLAncestralSequence(sequence, accuracy_per_site, accuracy_per_sequence)

Bases: object

an ancestral sequence.

class WrapperCodeML.CodeML

Bases: object

GetOptions()

return options in pretty format

AddOptions(parser)

add options to an OptionParser object.

SetOptions(options)

set options from the command line.

WriteAlignment(mali)

write alignment in Phylip format.

WriteTree(tree)

write tree to file. The root of the tree is removed.

writeControlFile(outfile, filename_sequences='input', filename_output='output', filename_tree=None, options={})

write a codeml.ctl file into outfile.

parseRst(inlines, result)

parse lines from rst file.

checkSection(lines, section_start)

check if section starts with string section_start.

getSection(lines, *args)

check if section starts with string section_start.

parseLog(lines_log, result)

parse log output.

parseOutput(lines, lines_log=None, rst_lines=None)

parse CodeML output. This is rather tricky, as paml output is as freeformat as it can get. Also, there is a log file and an output file. Proceed sequentially through file.

class WrapperCodeML.CodeMLSites

Bases: WrapperCodeML.CodeML

parseOutput(lines, lines_log=None, rst_lines=None)

parse codeml output for site-specific analysis.

parseGrids(lines, result)

parse grid information.

parseSites(lines, result)

parse site specific model results.

class WrapperCodeML.CodeMLPairwise

Bases: WrapperCodeML.CodeML

parseLog(lines_log, result)

parse log output.

This routine collects the rho values for each pair.

parseOutput(lines, lines_log=None, rst_lines=None)

parse codeml output for pairwise rate calculation.

parsePairs(lines, result)

parse pairwise results.

class WrapperCodeML.BaseML

Bases: WrapperCodeML.CodeML

AddOptions(parser)

add options to an OptionParser object.

SetOptions(options)

set options from the command line.

parseOutput(lines, lines_log=None, rst_lines=None)

parse BASEML output. This is rather tricky, as paml output is as freeformat as it can get. Also, there is a log file and an output file. Proceed sequentially through file.

parseFrequencies(inlines, result)

parse frequency section.

class WrapperCodeML.Evolver

Bases: object

interface class for running evolver.

writeControlFile(outfile)

write control file to outfile.

fromMali(mali)

compute codon table from a multiple alignment.

setUniformFrequencies()

use uniform codon frequencies.

calculateScale(ds)

calculate tree scale for a given dS value.

The branch scale is given by:

t = 3 dS * ps + 3 omega * dS * (1-ps) t = 3 dS * (ps + omega (1 - ps )

setTree(tree)

set tree.

run(ds=None, tree=None, test=False, dump=False)

run evolver.

class WrapperCodeML.EvolverBaseml(*args, **kwargs)

Bases: WrapperCodeML.Evolver

interface class for running evolver for nucleotides.

setUniformFrequencies()

use uniform codon frequencies.

fromMali(mali)

compute frequencies from a multiple alignment.

getParameters()

get parameters for a model.

From the MCbase.dat: Parameter kappa or rate parameters in the substituton model: For TN93, two kappa values are required, while for REV, 5 values (a,b,c,d,e) are required (see Yang 1994 for the definition of these parameters). The kappa parameter is defined differently under HKY85 (when k=1 means no transition bias) and under F84 (when k=0 means no bias). JC69 and F81 are considered species cases of HKY85, so use 1 for kappa for those two models. Notation is from my two papers in JME in 1994.

writeControlFile(outfile)

write control file to outfile.

WrapperCodeML.getOptions(options)

translate command line options to PAML options.

WrapperCodeML.runEvolver(options)

run evolver.