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)
