def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) ctrldata = args[0].split(",") expdata = args[1].split(",") annotationPath = args[2] output_path = args[3] output_file = open(output_path, "w") normalization = kwargs.get("n", "TTR") samples = int(kwargs.get("s", 10000)) adaptive = kwargs.get("a", False) doHistogram = kwargs.get("h", False) replicates = kwargs.get("r", "Sum") includeZeros = kwargs.get("iz", False) pseudocount = float(kwargs.get("pc", 0.00)) LOESS = kwargs.get("l", False) ignoreCodon = True NTerminus = float(kwargs.get("iN", 0.00)) CTerminus = float(kwargs.get("iC", 0.00)) return self(ctrldata, expdata, annotationPath, output_file, normalization, samples, adaptive, doHistogram, includeZeros, pseudocount, replicates, LOESS, ignoreCodon, NTerminus, CTerminus)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) ctrldata = args[0].split(",") expdata = args[1].split(",") annotationPath = args[2] output_path = args[3] output_file = open(output_path, "w") normalization = kwargs.get("n", "TTR") includeZeros = kwargs.get("iz", False) replicates = None LOESS = kwargs.get("l", False) ignoreCodon = True NTerminus = float(kwargs.get("iN", 0.00)) CTerminus = float(kwargs.get("iC", 0.00)) return self(ctrldata, expdata, annotationPath, output_file, normalization, includeZeros, replicates, LOESS, ignoreCodon, NTerminus, CTerminus)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) resamplingFile = args[0] associations = args[1] pathways = args[2] output = args[3] method = kwargs.get("M", "FISHER") N = int(kwargs.get("N", "10000")) # for GSEA? p = int(kwargs.get("p", "1")) # for GSEA? PC = int(kwargs.get("PC", "2")) if method not in "FISHER GSEA ONT".split(): print("error: method %s not recognized" % method) print(self.usage_string()) sys.exit(0) if method == "ONT": print("error: Ontologizer is not implemented yet") sys.exit(0) return self(resamplingFile, associations, pathways, output, method, PC=PC, N=N, p=p)
def fromargs(self,rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) ctrldata = args[0].split(",") annotationPath = args[1] outpath = args[2] output_file = open(outpath, "w") samples = int(kwargs.get("s", 10000)) burnin = int(kwargs.get("b", 500)) trim = int(kwargs.get("t", 1)) minread = int(kwargs.get("m", 1)) replicates = kwargs.get("r", "Sum") normalization = None LOESS = False ignoreCodon = True NTerminus = float(kwargs.get("iN", 0.0)) CTerminus = float(kwargs.get("iC", 0.0)) return self(ctrldata, annotationPath, output_file, samples, burnin, trim, minread, replicates, normalization, LOESS, ignoreCodon, NTerminus, CTerminus)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) # ctrl-vs-exp = condition 1-vs-2 # originally, MAD defined order of CL args this way: strA/cond1, strB/cond1, strA/cond2, strB/cond #ctrldataA = args[0].split(",") #ctrldataB = args[1].split(",") #expdataA = args[2].split(",") #expdataB = args[3].split(",") # TRI changed order of args this way: strA/cond1, strA/cond2, strB/cond1, strB/cond ctrldataA = args[0].split(",") expdataA = args[1].split(",") ctrldataB = args[2].split(",") expdataB = args[3].split(",") annotationPath = args[4] output_path = args[5] output_file = open(output_path, "w") normalization = kwargs.get("n", "TTR") samples = int(kwargs.get("s", 10000)) rope = float(kwargs.get("-rope", 0.5)) # fixed! changed int to float replicates = kwargs.get("r", "Sum") includeZeros = kwargs.get("iz", False) LOESS = kwargs.get("l", False) ignoreCodon = True NTerminus = float(kwargs.get("iN", 0.00)) CTerminus = float(kwargs.get("iC", 0.00)) return self(ctrldataA, ctrldataB, expdataA, expdataB, annotationPath, output_file, normalization, samples, rope, includeZeros, replicates, LOESS, ignoreCodon, NTerminus, CTerminus)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) ctrldataA = args[0].split(",") ctrldataB = args[1].split(",") expdataA = args[2].split(",") expdataB = args[3].split(",") annotationPath = args[4] output_path = args[5] output_file = open(output_path, "w") normalization = kwargs.get("n", "TTR") samples = int(kwargs.get("s", 10000)) rope = int(kwargs.get("-rope", 0.5)) replicates = kwargs.get("r", "Sum") includeZeros = kwargs.get("iz", False) LOESS = kwargs.get("l", False) ignoreCodon = True NTerminus = float(kwargs.get("iN", 0.00)) CTerminus = float(kwargs.get("iC", 0.00)) return self(ctrldataA, ctrldataB, expdataA, expdataB, annotationPath, output_file, normalization, samples, rope, includeZeros, replicates, LOESS, ignoreCodon, NTerminus, CTerminus)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) if (len(args) != 3): # wigs prot_table output print("Error: Incorrect number of args. See usage") print(self.usage_string()) sys.exit(0) ctrldata = args[0].split(",") annotationPath = args[1] outpath = args[2] output_file = open(outpath, "w") normalization = kwargs.get("n", "TTR") LOESS = False ignoreCodon = True NTerminus = 0.0 CTerminus = 0.0 return self(ctrldata, annotationPath, output_file, normalization, LOESS, ignoreCodon, NTerminus, CTerminus)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) resamplingFile = args[0] associations = args[1] pathways = args[2] output = args[3] method = kwargs.get("M", "FET") PC = int(kwargs.get("PC", "2")) # for FET Nperm = int(kwargs.get("Nperm", "10000")) # for GSEA p = float(kwargs.get("p", "0")) # for GSEA ranking = kwargs.get("ranking", "SLPV") # for GSEA if method not in "FET GSEA ONT".split(): print("error: method %s not recognized" % method) print(self.usage_string()) sys.exit(0) return self(resamplingFile, associations, pathways, output, method, PC=PC, Nperm=Nperm, p=p, ranking=ranking)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) if len(args) < 3: raise base.InvalidArgumentException("Must provide all necessary arguments") ctrldata = args[0].split(",") annotationPath = args[1] outpath = args[2] output_file = open(outpath, "w") replicates = "Sum" normalization = kwargs.get("n", "TTR") LOESS = False ignoreCodon = True NTerminus = 0.0 CTerminus = 0.0 return self(ctrldata, annotationPath, output_file, replicates, normalization, LOESS, ignoreCodon, NTerminus, CTerminus)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) ctrldata = args[0].split(",") annotationPath = args[1] outpath = args[2] output_file = open(outpath, "w") replicates = kwargs.get("r", "Sum") minread = int(kwargs.get("m", 1)) normalization = None LOESS = False ignoreCodon = True NTerminus = 0.0 CTerminus = 0.0 return self(ctrldata, annotationPath, output_file, replicates, normalization, LOESS, ignoreCodon, minread, NTerminus, CTerminus)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) ctrldata = args[0].split(",") annotationPath = args[1] outpath = args[2] output_file = open(outpath, "w") replicates = kwargs.get("r", "Sum") minread = int(kwargs.get("m", 1)) normalization = None LOESS = False ignoreCodon = True NTerminus = float(kwargs.get("iN","0")) CTerminus = float(kwargs.get("iC","0")) return self(ctrldata, annotationPath, output_file, replicates, normalization, LOESS, ignoreCodon, minread, NTerminus, CTerminus)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) if (kwargs.get('-help', False) or kwargs.get('h', False)): print(AnovaMethod.usage_string()) sys.exit(0) combined_wig = args[0] annotation = args[2] metadata = args[1] output_file = args[3] normalization = kwargs.get("n", "TTR") NTerminus = float(kwargs.get("iN", 0.0)) CTerminus = float(kwargs.get("iC", 0.0)) PC = int(kwargs.get("PC", 5)) ignored_conditions = list(filter(None, kwargs.get("-ignore-conditions", "").split(","))) included_conditions = list(filter(None, kwargs.get("-include-conditions", "").split(","))) # check for unrecognized flags flags = "-n --ignore-conditions --include-conditions -iN -iC -PC".split() for arg in rawargs: if arg[0]=='-' and arg not in flags: self.transit_error("flag unrecognized: %s" % arg) print(AnovaMethod.usage_string()) sys.exit(0) return self(combined_wig, metadata, annotation, normalization, output_file, ignored_conditions, included_conditions, NTerminus, CTerminus, PC)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) if (kwargs.get('-help', False)): print(self.usage_string()); sys.exit(0) if len(args)<2: print(self.usage_string()); sys.exit(0) self.gene_means = args[0] self.outfile = args[1] self.filetype = "gene_means" if "-anova" in rawargs: self.filetype = "anova" if "-zinb" in rawargs: self.filetype = "zinb" return self(self.gene_means,outfile=self.outfile)
def fromargs(self, rawargs): if not hasR: print("Error: R and rpy2 (~= 3.0) required to run ZINB analysis.") print( "After installing R, you can install rpy2 using the command \"pip install 'rpy2~=3.0'\"" ) sys.exit(0) (args, kwargs) = transit_tools.cleanargs(rawargs) if (kwargs.get('-help', False) or kwargs.get('h', False)): print(ZinbMethod.usage_string()) sys.exit(0) if (kwargs.get('v', False)): global DEBUG DEBUG = True if (kwargs.get('-gene', False)): global GENE GENE = kwargs.get('-gene', None) combined_wig = args[0] metadata = args[1] annotation = args[2] output_file = args[3] normalization = kwargs.get("n", "TTR") NTerminus = float(kwargs.get("iN", 5.0)) CTerminus = float(kwargs.get("iC", 5.0)) PC = float(kwargs.get("PC", 5.0)) condition = kwargs.get("-condition", "Condition") covars = list(filter(None, kwargs.get("-covars", "").split(","))) interactions = list( filter(None, kwargs.get("-interactions", "").split(","))) winz = True if "w" in kwargs else False ignored_conditions = list( filter(None, kwargs.get("-ignore-conditions", "").split(","))) included_conditions = list( filter(None, kwargs.get("-include-conditions", "").split(","))) # check for unrecognized flags flags = "-n --ignore-conditions --include-conditions -iN -iC -PC --condition --covars --interactions --gene".split( ) for arg in rawargs: if arg[0] == '-' and arg not in flags: self.transit_error("flag unrecognized: %s" % arg) print(ZinbMethod.usage_string()) sys.exit(0) return self(combined_wig, metadata, annotation, normalization, output_file, ignored_conditions, included_conditions, winz, NTerminus, CTerminus, condition, covars, interactions, PC)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) if (len(args) < 2): print("Error: Please specify Input and Output paths") print(self.usage_string()) sys.exit(1) annotationPath = args[0] outpath = args[1] output_file = open(outpath, "w") return self(annotationPath, output_file)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) if (len(args) < 2): print "Error: Please specify Input and Output paths" print(self.usage_string()) sys.exit(1) annotationPath = args[0] outpath = args[1] output_file = open(outpath, "w") return self(annotationPath, output_file)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) p = int(kwargs.get("p", 1)) N = int(kwargs.get("S", 1000)) M = kwargs.get("M", "GSEA") resamplingFile = args[0] geneSetFile = args[1] outpath = args[2] output = open(outpath, "w") #The outputfile is opened here!!! return self(resamplingFile, geneSetFile, output, p, N, M)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) if len(args) < 2: raise base.InvalidArgumentException("Must provide all necessary arguments") self.infile = args[0] # only 1 input wig file self.outfile = args[1] # if no arg give, could print to screen self.normalization = kwargs.get("n", "TTR") # check if it is a legal method name self.combined_wig = kwargs.get("c",False) return self(self.infile,self.outfile,self.normalization)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) ctrldata = args[0].split(",") annotationPath = args[1] outpath = args[2] output_file = open(outpath, "w") samples = int(kwargs.get("s", 10000)) burnin = int(kwargs.get("b", 500)) replicates = "Sum" normalization = None LOESS = False ignoreCodon = True NTerminus = float(kwargs.get("iN", 0.0)) CTerminus = float(kwargs.get("iC", 0.0)) pi0 = float(kwargs.get("pi0", 0.5)) pi1 = float(kwargs.get("pi1", 0.5)) M0 = float(kwargs.get("M0", 1.0)) M1 = float(kwargs.get("M1", 1.0)) a0 = float(kwargs.get("a0", 10.0)) a1 = float(kwargs.get("a1", 10.0)) b0 = float(kwargs.get("b0", 1.0)) b1 = float(kwargs.get("b1", 1.0)) alpha_w = float(kwargs.get("aw", 0.5)) beta_w = float(kwargs.get("bw", 0.5)) return self(ctrldata, annotationPath, output_file, samples=samples, burnin=burnin, replicates=replicates, normalization=normalization, LOESS=LOESS, ignoreCodon=ignoreCodon, NTerminus=NTerminus, CTerminus=CTerminus, pi0=pi0, pi1=pi1, M0=M0, M1=M1, a0=a0, a1=a1, b0=b0, b1=b1, alpha_w=alpha_w, beta_w=beta_w)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) ctrldata = args[0].split(",") annotationPath = args[1] outpath = args[2] output_file = open(outpath, "w") samples = int(kwargs.get("s", 10000)) burnin = int(kwargs.get("b", 500)) replicates = "Sum" normalization = None LOESS = False ignoreCodon = True NTerminus = float(kwargs.get("iN", 0.0)) CTerminus = float(kwargs.get("iC", 0.0)) pi0 = float(kwargs.get("pi0", 0.5)) pi1 = float(kwargs.get("pi1", 0.5)) M0 = float(kwargs.get("M0", 1.0)) M1 = float(kwargs.get("M1", 1.0)) a0 = float(kwargs.get("a0", 10.0)) a1 = float(kwargs.get("a1", 10.0)) b0 = float(kwargs.get("b0", 1.0)) b1 = float(kwargs.get("b1", 1.0)) alpha_w = float(kwargs.get("aw", 0.5)) beta_w = float(kwargs.get("bw", 0.5)) return self(ctrldata, annotationPath, output_file, samples=samples, burnin=burnin, replicates=replicates, normalization=normalization, LOESS=LOESS, ignoreCodon=ignoreCodon, NTerminus=NTerminus, CTerminus=CTerminus, pi0=pi0, pi1=pi1, M0=M0, M1=M1, a0=a0, a1=a1, b0=b0, b1=b1, alpha_w=alpha_w, beta_w=beta_w)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) ctrldata = args[0].split(",") annotationPath = args[1] outpath = args[2] output_file = open(outpath, "w") normalization = kwargs.get("n", "TTR") LOESS = False ignoreCodon = True NTerminus = 0.0 CTerminus = 0.0 return self(ctrldata, annotationPath, output_file, normalization, LOESS, ignoreCodon, NTerminus, CTerminus)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) isCombinedWig = kwargs.has_key('c') if (not isCombinedWig and len(args) < 2) or (isCombinedWig and len(args) < 1): raise base.InvalidArgumentException("Must provide all necessary arguments") if isCombinedWig: self.infile = kwargs.get("c") # only 1 input wig file self.outfile = args[0] # if no arg give, could print to screen else: self.infile = args[0] # only 1 input wig file self.outfile = args[1] # if no arg give, could print to screen self.normalization = kwargs.get("n", "TTR") # check if it is a legal method name self.combined_wig = isCombinedWig return self(self.infile,self.outfile,self.normalization)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) if len(rawargs) < 3: print(self.usage_string()) sys.exit(-1) self.filetype = None if kwargs.get("anova", False): self.filetype = "anova" elif kwargs.get("zinb", False): self.filetype = "zinb" else: print(self.usage_string()) sys.exit(-1) self.infile = args[0] self.outfile = args[1] self.qval = float(kwargs.get("qval", 0.05)) self.topk = int(kwargs.get("topk", -1)) return self(self.infile, outfile=self.outfile)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) if (kwargs.get('-help', False)): print(self.usage_string()) sys.exit(0) self.wigs = args self.outfile = kwargs.get("o", None) self.combined_wig = kwargs.get("c", None) if self.combined_wig == None and len(self.wigs) == 0: print(self.usage_string()) sys.exit(0) return self(self.wigs, outfile=self.outfile)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) ctrldata = args[0].split(",") annotationPath = args[1] outpath = args[2] output_file = open(outpath, "w") replicates = kwargs.get("r", "Mean") normalization = kwargs.get("r", "TTR") LOESS = kwargs.get("l", False) ignoreCodon = True NTerminus = float(kwargs.get("iN", 0.0)) CTerminus = float(kwargs.get("iC", 0.0)) return self(ctrldata, annotationPath, output_file, replicates, normalization, LOESS, ignoreCodon, NTerminus, CTerminus)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) if (kwargs.get('-help', False) or kwargs.get('h', False)): print(AnovaMethod.usage_string()) sys.exit(0) combined_wig = args[0] annotation = args[1] metadata = args[2] output_file = args[3] normalization = kwargs.get("n", "TTR") ignored_conditions = set( kwargs.get("-ignore-conditions", "Unknown").split(",")) return self(combined_wig, metadata, annotation, normalization, output_file, ignored_conditions)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) if len(args) < 3: raise base.InvalidArgumentException( "Must provide all necessary arguments") ctrldata = args[0].split(",") annotationPath = args[1] outpath = args[2] output_file = open(outpath, "w") replicates = "Sum" normalization = kwargs.get("n", "TTR") LOESS = False ignoreCodon = True NTerminus = 0.0 CTerminus = 0.0 return self(ctrldata, annotationPath, output_file, replicates, normalization, LOESS, ignoreCodon, NTerminus, CTerminus)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) if (len(args) != 3): # wigs prot_table output print("Error: Incorrect number of args. See usage") print(self.usage_string()) sys.exit(0) ctrldata = args[0].split(",") annotationPath = args[1] outpath = args[2] output_file = open(outpath, "w") normalization = kwargs.get("n", "TTR") LOESS = False ignoreCodon = True NTerminus = 0.0 CTerminus = 0.0 return self(ctrldata, annotationPath, output_file, normalization, LOESS, ignoreCodon, NTerminus, CTerminus)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) ctrldataA = args[0].split(",") ctrldataB = args[1].split(",") expdataA = args[2].split(",") expdataB = args[3].split(",") annotationPath = args[4] output_path = args[5] output_file = open(output_path, "w") normalization = kwargs.get("n", "TTR") samples = int(kwargs.get("s", 10000)) rope = float(kwargs.get("-rope", 0.5)) # fixed! changed int to float replicates = kwargs.get("r", "Sum") includeZeros = kwargs.get("iz", False) LOESS = kwargs.get("l", False) ignoreCodon = True NTerminus = float(kwargs.get("iN", 0.00)) CTerminus = float(kwargs.get("iC", 0.00)) return self(ctrldataA, ctrldataB, expdataA, expdataB, annotationPath, output_file, normalization, samples, rope, includeZeros, replicates, LOESS, ignoreCodon, NTerminus, CTerminus)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) ctrldata = args[0].split(",") annotationPath = args[1] outpath = args[2] output_file = open(outpath, "w") normalization = kwargs.get("n", "TTR") LOESS = False ignoreCodon = True NTerminus = 0.0 CTerminus = 0.0 return self(ctrldata, annotationPath, output_file, normalization, LOESS, ignoreCodon, NTerminus, CTerminus)
def fromargs(self, rawargs): if not hasR: print("Error: R and rpy2 (< 2.9.0) required to run ZINB analysis.") print("After installing R, you can install rpy2 using the command \"pip install 'rpy2<2.9.0'\"") sys.exit(0) (args, kwargs) = transit_tools.cleanargs(rawargs) if (kwargs.get('-help', False) or kwargs.get('h', False)): print(ZinbMethod.usage_string()) sys.exit(0) if (kwargs.get('v', False)): global DEBUG DEBUG = True if (kwargs.get('-gene', False)): global GENE GENE = kwargs.get('-gene', None) combined_wig = args[0] metadata = args[1] annotation = args[2] output_file = args[3] normalization = kwargs.get("n", "TTR") NTerminus = float(kwargs.get("iN", 5.0)) CTerminus = float(kwargs.get("iC", 5.0)) condition = kwargs.get("-condition", "Condition") covars = filter(None, kwargs.get("-covars", "").split(",")) interactions = filter(None, kwargs.get("-interactions", "").split(",")) winz = True if kwargs.has_key("w") else False ignored_conditions = filter(None, kwargs.get("-ignore-conditions", "").split(",")) included_conditions = filter(None, kwargs.get("-include-conditions", "").split(",")) if len(included_conditions) > 0 and len(ignored_conditions) > 0: self.transit_error("Cannot use both include-conditions and ignore-conditions flags") print(ZinbMethod.usage_string()) sys.exit(0) return self(combined_wig, metadata, annotation, normalization, output_file, ignored_conditions, included_conditions, winz, NTerminus, CTerminus, condition, covars, interactions)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) ctrldata = args[0].split(",") expdata = args[1].split(",") annotationPath = args[2] output_path = args[3] output_file = open(output_path, "w") normalization = kwargs.get("n", "TTR") samples = int(kwargs.get("s", 100)) adaptive = kwargs.get("a", False) doHistogram = kwargs.get("h", False) replicates = kwargs.get("r", "Sum") LOESS = kwargs.get("l", False) ignoreCodon = True NTerminus = float(kwargs.get("iN", 0.00)) CTerminus = float(kwargs.get("iC", 0.00)) return self(ctrldata, expdata, annotationPath, output_file, normalization, samples, adaptive, doHistogram, replicates, LOESS, ignoreCodon, NTerminus, CTerminus)
def test_cleanargs_flag_arguments_with_double_dash(self): TEST_RAWARGS = ["a", "b", "c", "-d", "1", "--p", "test this"] args, kwargs = transit_tools.cleanargs(TEST_RAWARGS) self.assertFalse("p" in kwargs) self.assertFalse("--p" in kwargs) self.assertTrue("-p" in kwargs)
def test_cleanargs_flag_arguments_w_quotes(self): TEST_RAWARGS = ["a", "b", "c", "-d", "1", "-p", "test this"] args, kwargs = transit_tools.cleanargs(TEST_RAWARGS) self.assertEqual(kwargs.get("p"), "test this")
def run_main(): (args, kwargs) = transit_tools.cleanargs(sys.argv[1:]) main(*args, **kwargs)
def run_main(): (args, kwargs) = transit_tools.cleanargs(sys.argv[1:]) main(*args, **kwargs)
def test_cleanargs_positional_arguments(self): TEST_RAWARGS = ["a", "b", "c", "-d", "1", "e"] args, kwargs = transit_tools.cleanargs(TEST_RAWARGS) self.assertEqual(args, ["a", "b", "c", "e"])
def test_cleanargs_flag_arguments_w_quotes(self): TEST_RAWARGS = ["a", "b", "c", "-d", "1", "-p", "test this"] args, kwargs = transit_tools.cleanargs(TEST_RAWARGS) self.assertEqual(kwargs.get("p"), "test this")
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) isCombinedWig = True if kwargs.get('c', False) else False combinedWigParams = None if isCombinedWig: if (len(args) != 5): print("Error: Incorrect number of args. See usage") print(self.usage_string()) sys.exit(0) combinedWigParams = { "combined_wig": kwargs.get('c'), "samples_metadata": args[0], "conditions": [args[1].lower(), args[2].lower()] } annot_paths = args[3].split(",") ctrldata = "" expdata = "" output_path = args[4] else: if (len(args) != 4): print("Error: Incorrect number of args. See usage") print(self.usage_string()) sys.exit(0) ctrldata = args[0].split(",") expdata = args[1].split(",") annot_paths = args[2].split(",") output_path = args[3] annotationPath = annot_paths[0] diffStrains = False annotationPathExp = "" if len(annot_paths) == 2: annotationPathExp = annot_paths[1] diffStrains = True if (diffStrains and isCombinedWig): print("Error: Cannot have combined wig and different annotation files.") sys.exit(0) output_file = open(output_path, "w") # check for unrecognized flags flags = "-c -s -n -h -a -ez -PC -l -iN -iC --ctrl_lib --exp_lib -Z".split() for arg in rawargs: if arg[0]=='-' and arg not in flags: self.transit_error("flag unrecognized: %s" % arg) print(ZinbMethod.usage_string()) sys.exit(0) normalization = kwargs.get("n", "TTR") samples = int(kwargs.get("s", 10000)) adaptive = kwargs.get("a", False) doHistogram = kwargs.get("h", False) replicates = kwargs.get("r", "Sum") excludeZeros = kwargs.get("ez", False) includeZeros = not excludeZeros pseudocount = float(kwargs.get("PC", 1.0)) # use -PC (new semantics: for LFCs) instead of -pc (old semantics: fake counts) Z = True if "Z" in kwargs else False LOESS = kwargs.get("l", False) ignoreCodon = True NTerminus = float(kwargs.get("iN", 0.00)) # integer interpreted as percentage CTerminus = float(kwargs.get("iC", 0.00)) ctrl_lib_str = kwargs.get("-ctrl_lib", "") exp_lib_str = kwargs.get("-exp_lib", "") return self(ctrldata, expdata, annotationPath, output_file, normalization, samples, adaptive, doHistogram, includeZeros, pseudocount, replicates, LOESS, ignoreCodon, NTerminus, CTerminus, ctrl_lib_str, exp_lib_str, Z = Z, diffStrains = diffStrains, annotation_path_exp = annotationPathExp, combinedWigParams = combinedWigParams)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) isCombinedWig = True if kwargs.get('c', False) else False combinedWigParams = None if isCombinedWig: if (len(args) != 5): print("Error: Incorrect number of args. See usage") print(self.usage_string()) sys.exit(0) combinedWigParams = { "combined_wig": kwargs.get('c'), "samples_metadata": args[0], "conditions": [args[1].lower(), args[2].lower()] } annot_paths = args[3].split(",") ctrldata = "" expdata = "" output_path = args[4] else: if (len(args) != 4): print("Error: Incorrect number of args. See usage") print(self.usage_string()) sys.exit(0) ctrldata = args[0].split(",") expdata = args[1].split(",") annot_paths = args[2].split(",") output_path = args[3] annotationPath = annot_paths[0] diffStrains = False annotationPathExp = "" if len(annot_paths) == 2: annotationPathExp = annot_paths[1] diffStrains = True if (diffStrains and isCombinedWig): print( "Error: Cannot have combined wig and different annotation files." ) sys.exit(0) output_file = open(output_path, "w") normalization = kwargs.get("n", "TTR") samples = int(kwargs.get("s", 10000)) adaptive = kwargs.get("a", False) doHistogram = kwargs.get("h", False) replicates = kwargs.get("r", "Sum") excludeZeros = kwargs.get("ez", False) includeZeros = not excludeZeros pseudocount = float(kwargs.get("pc", 0.00)) Z = True if "Z" in kwargs else False LOESS = kwargs.get("l", False) ignoreCodon = True NTerminus = float(kwargs.get("iN", 0.00)) CTerminus = float(kwargs.get("iC", 0.00)) ctrl_lib_str = kwargs.get("-ctrl_lib", "") exp_lib_str = kwargs.get("-exp_lib", "") return self(ctrldata, expdata, annotationPath, output_file, normalization, samples, adaptive, doHistogram, includeZeros, pseudocount, replicates, LOESS, ignoreCodon, NTerminus, CTerminus, ctrl_lib_str, exp_lib_str, Z=Z, diffStrains=diffStrains, annotation_path_exp=annotationPathExp, combinedWigParams=combinedWigParams)
def test_cleanargs_flag_without_arguments(self): TEST_RAWARGS = ["test", "-p"] args, kwargs = transit_tools.cleanargs(TEST_RAWARGS) self.assertTrue(kwargs.get("p", False))
def test_cleanargs_positional_arguments_w_quotes(self): TEST_RAWARGS = ["a", "b", "c", "-d", "1", "test this"] args, kwargs = transit_tools.cleanargs(TEST_RAWARGS) self.assertEqual(args, ["a", "b", "c", "test this"])
def test_cleanargs_negative_arguments(self): TEST_RAWARGS = ["test", "-p", "-10"] args, kwargs = transit_tools.cleanargs(TEST_RAWARGS) self.assertEqual(int(kwargs.get("p",0)), -10)
def test_cleanargs_flag_without_arguments(self): TEST_RAWARGS = ["test", "-p"] args, kwargs = transit_tools.cleanargs(TEST_RAWARGS) self.assertTrue(kwargs.get("p",False))
-l := Perform LOESS Correction; Helps remove possible genomic position bias. Default: Turned Off. -iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0 -iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0 """ % (sys.argv[0]) if __name__ == "__main__": (args, kwargs) = transit_tools.cleanargs(sys.argv) #TODO: Figure out issue with inputs (transit requires initial method name, running as script does not !!!!) G = RankProductMethod.fromargs(sys.argv[1:]) G.console_message("Printing the member variables:") G.print_members() print "" print "Running:" G.Run()
def test_cleanargs_negative_arguments(self): TEST_RAWARGS = ["test", "-p", "-10"] args, kwargs = transit_tools.cleanargs(TEST_RAWARGS) self.assertEqual(int(kwargs.get("p", 0)), -10)
def fromargs(self, rawargs): (args, kwargs) = transit_tools.cleanargs(rawargs) isCombinedWig = True if kwargs.get('c', False) else False combinedWigParams = None if isCombinedWig: if (len(args) != 5): print("Error: Incorrect number of args. See usage") print(self.usage_string()) sys.exit(0) combinedWigParams = { "combined_wig": kwargs.get('c'), "samples_metadata": args[0], "conditions": [args[1].lower(), args[2].lower()] } annot_paths = args[3].split(",") ctrldata = "" expdata = "" output_path = args[4] else: if (len(args) != 4): print("Error: Incorrect number of args. See usage") print(self.usage_string()) sys.exit(0) ctrldata = args[0].split(",") expdata = args[1].split(",") annot_paths = args[2].split(",") output_path = args[3] annotationPath = annot_paths[0] diffStrains = False annotationPathExp = "" if len(annot_paths) == 2: annotationPathExp = annot_paths[1] diffStrains = True if (diffStrains and isCombinedWig): print("Error: Cannot have combined wig and different annotation files.") sys.exit(0) output_file = open(output_path, "w") normalization = kwargs.get("n", "TTR") samples = int(kwargs.get("s", 10000)) adaptive = kwargs.get("a", False) doHistogram = kwargs.get("h", False) replicates = kwargs.get("r", "Sum") excludeZeros = kwargs.get("ez", False) includeZeros = not excludeZeros pseudocount = float(kwargs.get("pc", 0.00)) Z = True if "Z" in kwargs else False LOESS = kwargs.get("l", False) ignoreCodon = True NTerminus = float(kwargs.get("iN", 0.00)) CTerminus = float(kwargs.get("iC", 0.00)) ctrl_lib_str = kwargs.get("-ctrl_lib", "") exp_lib_str = kwargs.get("-exp_lib", "") return self(ctrldata, expdata, annotationPath, output_file, normalization, samples, adaptive, doHistogram, includeZeros, pseudocount, replicates, LOESS, ignoreCodon, NTerminus, CTerminus, ctrl_lib_str, exp_lib_str, Z = Z, diffStrains = diffStrains, annotation_path_exp = annotationPathExp, combinedWigParams = combinedWigParams)
"#ORF\tName\tNumber of TA Sites\tMean count (Strain A Time 1)\tMean count (Strain A Time 2)\tMean count (Strain B Time 1)\tMean count (Strain B Time 2)\tMean logFC (Strain A)\tMean logFC (Strain B) \tMean delta logFC\tLower Bound delta logFC\tUpper Bound delta logFC\tProb. of delta-logFC being within ROPE\tAdjusted Probability (%s)\tIs HDI outside ROPE?\tType of Interaction\n" % adjusted_label) # Write gene results for i, row in enumerate(data): #1 2 3 4 5 6 7 8 9 10 11 12 13 14 orf, name, n, mean_muA1_post, mean_muA2_post, mean_muB1_post, mean_muB2_post, mean_logFC_A, mean_logFC_B, mean_delta_logFC, l_delta_logFC, u_delta_logFC, probROPE, not_HDI_overlap_bit = row type_of_interaction = "No Interaction" if ((doBFDR or doFWER) and adjusted_prob[i] < 0.05): type_of_interaction = classify_interaction(mean_delta_logFC, mean_logFC_B, mean_logFC_A) elif not (doBFDR or doFWER) and not_HDI_overlap_bit: type_of_interaction = classify_interaction(mean_delta_logFC, mean_logFC_B, mean_logFC_A) new_row = tuple( list(row[:-1]) + [adjusted_prob[i], not_HDI_overlap_bit, type_of_interaction]) sys.stdout.write( "%s\t%s\t%d\t%1.2f\t%1.2f\t%1.2f\t%1.2f\t%1.2f\t%1.2f\t%1.2f\t%1.2f\t%1.2f\t%1.8f\t%1.8f\t%s\t%s\n" % new_row) if __name__ == "__main__": (args, kwargs) = transit_tools.cleanargs(sys.argv[1:]) (data, adjusted_prob, adjusted_label) = main(args, kwargs) print_results(args, kwargs, data, adjusted_prob, adjusted_label)
def test_cleanargs_flag_arguments_with_double_dash(self): TEST_RAWARGS = ["a", "b", "c", "-d", "1", "--p", "test this"] args, kwargs = transit_tools.cleanargs(TEST_RAWARGS) self.assertFalse("p" in kwargs) self.assertFalse("--p" in kwargs) self.assertTrue("-p" in kwargs)