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-rwxr-xr-xwqflask/base/webqtlFormData.py57
1 files changed, 29 insertions, 28 deletions
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
index 710c9f53..ff1db0e8 100755
--- a/wqflask/base/webqtlFormData.py
+++ b/wqflask/base/webqtlFormData.py
@@ -44,9 +44,9 @@ from utility import webqtlUtil
-class webqtlFormData:
+class webqtlFormData(object):
'Represents data from a WebQTL form page, needed to generate the next page'
-
+
attrs = ('formID','RISet','genotype','samplelist','allsamplelist', 'display_variance'
'suggestive','significance','submitID','identification', 'enablevariance',
'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo')
@@ -62,7 +62,7 @@ class webqtlFormData:
print("in webqtlFormData start_vars are:", pf(start_vars))
for item in webqtlFormData.attrs:
self.__dict__[item] = None
-
+
#ZS: This is only used in DataEditingPage.py (as far as I know)
self.varianceDispName = None
@@ -103,7 +103,7 @@ class webqtlFormData:
self.ppolar = None
self.mpolar = None
-
+
print("[yellow] self.RISet is:", self.RISet)
if self.RISet:
#try:
@@ -112,13 +112,13 @@ class webqtlFormData:
#except:
# f1 = f12 = self.mpolar = self.ppolar = None
-
+
def set_number(stringy):
return int(stringy) if stringy else 2000 # Rob asked to change the default value to 2000
self.nperm = set_number(self.nperm)
self.nboot = set_number(self.nboot)
-
+
#if self.allsamplelist:
# self.allsamplelist = map(string.strip, string.split(self.allsamplelist))
@@ -134,6 +134,7 @@ class webqtlFormData:
def __getitem__(self, key):
+ print("in __getitem__")
return self.__dict__[key]
def get(self, key, default=None):
@@ -154,22 +155,22 @@ class webqtlFormData:
'''read genotype from .geno file'''
if self.RISet == 'BXD300':
self.RISet = 'BXD'
-
+
assert self.RISet, "self.RISet needs to be set"
-
+
#genotype_1 is Dataset Object without parents and f1
#genotype_2 is Dataset Object with parents and f1 (not for intercross)
-
+
self.genotype_1 = reaper.Dataset()
-
+
full_filename = os.path.join(webqtlConfig.GENODIR, self.RISet + '.geno')
-
+
# reaper barfs on unicode filenames, so here we ensure it's a string
full_filename = str(full_filename)
self.genotype_1.read(full_filename)
-
+
print("Got to after read")
-
+
try:
# NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
_f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.RISet]
@@ -186,16 +187,16 @@ class webqtlFormData:
else:
self.incparentsf1 = 0
self.genotype = self.genotype_1
-
+
self.samplelist = list(self.genotype.prgy)
self.f1list = []
self.parlist = []
-
+
if _f1 and _f12:
self.f1list = [_f1, _f12]
if _mat and _pat:
self.parlist = [_mat, _pat]
-
+
def readData(self, samplelist, incf1=None):
'''read user input data or from trait data and analysis form'''
@@ -213,11 +214,11 @@ class webqtlFormData:
#print("before traitfiledata self.traitfile is:", pf(self.traitfile))
- traitfiledata = getattr(self, "traitfile", None)
- traitpastedata = getattr(self, "traitpaste", None)
- variancefiledata = getattr(self, "variancefile", None)
- variancepastedata = getattr(self, "variancepaste", None)
- Nfiledata = getattr(self, "Nfile", None)
+ traitfiledata = getattr(self, "traitfile", None)
+ traitpastedata = getattr(self, "traitpaste", None)
+ variancefiledata = getattr(self, "variancefile", None)
+ variancepastedata = getattr(self, "variancepaste", None)
+ Nfiledata = getattr(self, "Nfile", None)
#### Todo: Rewrite below when we get to someone submitting their own trait #####
@@ -246,7 +247,7 @@ class webqtlFormData:
elif len(values) > len(samplelist):
values = values[:len(samplelist)]
print("now values is:", values)
-
+
if variancefiledata:
tt = variancefiledata.split()
@@ -282,16 +283,16 @@ class webqtlFormData:
def informativeStrains(self, samplelist=None, include_variances = None):
'''if readData was called, use this to output informative samples (sample with values)'''
-
+
if not samplelist:
samplelist = self.samplelist
-
+
samples = []
values = []
variances = []
-
+
#print("self.allTraitData is:", pf(self.allTraitData))
-
+
for sample in samplelist:
if sample in self.allTraitData:
_val, _var = self.allTraitData[sample].value, self.allTraitData[sample].variance
@@ -305,13 +306,13 @@ class webqtlFormData:
samples.append(sample)
values.append(_val)
variances.append(None)
-
+
return samples, values, variances, len(samples)
#def FormDataAsFloat(self, key):
- #
+ #
# #try:
# # return float(self.key)
# #except: