aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/utility/Plot.py10
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py19
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py63
3 files changed, 49 insertions, 43 deletions
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 372e0ac5..d60e2bb2 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -43,6 +43,8 @@ import svg
import webqtlUtil
from base import webqtlConfig
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
def cformat(d, rank=0):
'custom string format'
@@ -294,10 +296,10 @@ def find_outliers(vals):
"""
- print("xerxes vals is:", pf(vals))
+ logger.debug("xerxes vals is:", pf(vals))
if vals:
- #print("vals is:", pf(vals))
+ #logger.debug("vals is:", pf(vals))
stats = corestats.Stats(vals)
low_hinge = stats.percentile(25)
up_hinge = stats.percentile(75)
@@ -310,7 +312,7 @@ def find_outliers(vals):
upper_bound = None
lower_bound = None
- print(pf(locals()))
+ logger.debug(pf(locals()))
return upper_bound, lower_bound
@@ -433,7 +435,7 @@ def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabe
canvas.drawCross(XCoord, plotHeight + yTopOffset - (catMean-Yll)*plotHeight/(Yur - Yll), \
color=pid.blue,size=3)
- #print (catMean, catMedian, cat25per, cat75per)
+ #print(catMean, catMedian, cat25per, cat75per)
pass
XCoord += stepX
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 363b1efe..4f8f9e64 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -12,6 +12,9 @@ from pprint import pformat as pf
import itertools
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
class SampleList(object):
def __init__(self,
dataset,
@@ -29,7 +32,7 @@ class SampleList(object):
self.sample_attribute_values = {}
self.get_attributes()
- print("camera: attributes are:", pf(self.attributes))
+ logger.debug("camera: attributes are:", pf(self.attributes))
if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
self.get_extra_attribute_values()
@@ -41,7 +44,7 @@ class SampleList(object):
try:
sample = self.this_trait.data[sample_name]
except KeyError:
- print("No sample %s, let's create it now" % sample_name)
+ logger.debug("No sample %s, let's create it now" % sample_name)
sample = webqtlCaseData.webqtlCaseData(sample_name)
#sampleNameAdd = ''
@@ -52,7 +55,7 @@ class SampleList(object):
sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
sample.extra_info['css_class'] = "fs12"
- print(" type of sample:", type(sample))
+ logger.debug(" type of sample:", type(sample))
if sample_group_type == 'primary':
sample.this_id = "Primary_" + str(counter)
@@ -62,17 +65,17 @@ class SampleList(object):
#### For extra attribute columns; currently only used by several datasets - Zach
if self.sample_attribute_values:
sample.extra_attributes = self.sample_attribute_values.get(sample_name, {})
- print("sample.extra_attributes is", pf(sample.extra_attributes))
+ logger.debug("sample.extra_attributes is", pf(sample.extra_attributes))
self.sample_list.append(sample)
- print("self.attributes is", pf(self.attributes))
+ logger.debug("self.attributes is", pf(self.attributes))
self.do_outliers()
#do_outliers(the_samples)
- print("*the_samples are [%i]: %s" % (len(self.sample_list), pf(self.sample_list)))
+ logger.debug("*the_samples are [%i]: %s" % (len(self.sample_list), pf(self.sample_list)))
for sample in self.sample_list:
- print("apple:", type(sample), sample)
+ logger.debug("apple:", type(sample), sample)
#return the_samples
def __repr__(self):
@@ -105,7 +108,7 @@ class SampleList(object):
self.attributes = {}
for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)):
key, name = attr
- print("radish: %s - %s" % (key, name))
+ logger.debug("radish: %s - %s" % (key, name))
self.attributes[key] = Bunch()
self.attributes[key].name = name
self.attributes[key].distinct_values = [item.Value for item in values]
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 73acde22..a8ff0fdf 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -26,6 +26,9 @@ from pprint import pformat as pf
from utility.tools import flat_files
MAPPING_PATH = flat_files("mapping")
+from utility.logger import getLogger
+logger = getLogger(__name__ )
+
###############################################
#
# Todo: Put in security to ensure that user has permission to access confidential data sets
@@ -36,7 +39,7 @@ MAPPING_PATH = flat_files("mapping")
class ShowTrait(object):
def __init__(self, kw):
- print("in ShowTrait, kw are:", kw)
+ logger.debug("in ShowTrait, kw are:", kw)
if kw['trait_id'] != None:
self.temp_trait = False
@@ -97,7 +100,7 @@ class ShowTrait(object):
#Get nearest marker for composite mapping
- print("self.dataset.type:", self.dataset.type)
+ logger.debug("self.dataset.type:", self.dataset.type)
if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
self.nearest_marker = get_nearest_marker(self.this_trait, self.dataset)
#self.nearest_marker1 = get_nearest_marker(self.this_trait, self.dataset)[0]
@@ -143,7 +146,7 @@ class ShowTrait(object):
else:
self.sample_group_types['samples_primary'] = self.dataset.group.name
sample_lists = [group.sample_list for group in self.sample_groups]
- print("sample_lists is:", pf(sample_lists))
+ logger.debug("sample_lists is:", pf(sample_lists))
self.get_mapping_methods()
@@ -204,7 +207,7 @@ class ShowTrait(object):
except ValueError:
return None
- print("bottle samplelist is:", samplelist)
+ logger.debug("bottle samplelist is:", samplelist)
if traitfiledata:
tt = traitfiledata.split()
values = map(webqtlUtil.StringAsFloat, tt)
@@ -212,17 +215,17 @@ class ShowTrait(object):
tt = traitpastedata.split()
values = map(webqtlUtil.StringAsFloat, tt)
else:
- print("mapping formdataasfloat")
+ logger.debug("mapping formdataasfloat")
#values = map(self.FormDataAsFloat, samplelist)
values = [to_float(getattr(self, key)) for key in samplelist]
- print("rocket values is:", values)
+ logger.debug("rocket values is:", values)
if len(values) < len(samplelist):
values += [None] * (len(samplelist) - len(values))
elif len(values) > len(samplelist):
values = values[:len(samplelist)]
- print("now values is:", values)
+ logger.debug("now values is:", values)
if variancefiledata:
@@ -253,7 +256,7 @@ class ShowTrait(object):
if values[i] != None:
self.allTraitData[_sample] = webqtlCaseData(
_sample, values[i], variances[i], nsamples[i])
- print("allTraitData is:", pf(self.allTraitData))
+ logger.debug("allTraitData is:", pf(self.allTraitData))
def dispTraitInformation(self, args, title1Body, hddn, this_trait):
@@ -504,7 +507,7 @@ class ShowTrait(object):
txst = int(txst*1000000)
txen = int(txen*1000000)
if self.species_name == "mouse":
- print("this_trait.symbol:", this_trait.symbol)
+ logger.debug("this_trait.symbol:", this_trait.symbol)
result = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone()
if result != None:
this_chr, txst, txen = result[0], result[1], result[2]
@@ -752,14 +755,14 @@ class ShowTrait(object):
primary_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_samples #XZ: note that fd.f1list and fd.parlist are added.
all_samples = primary_samples + other_samples
other_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + other_samples #XZ: note that fd.f1list and fd.parlist are added.
- print("ac1") # This is the one used for first sall3
+ logger.debug("ac1") # This is the one used for first sall3
self.MDP_menu.append(('All Cases','0'))
self.MDP_menu.append(('%s Only' % fd.group, '1'))
self.MDP_menu.append(('Non-%s Only' % fd.group, '2'))
else:
if (len(other_samples) > 0) and (len(primary_samples) + len(other_samples) > 3):
- print("ac2")
+ logger.debug("ac2")
self.MDP_menu.append(('All Cases','0'))
self.MDP_menu.append(('%s Only' % fd.group,'1'))
self.MDP_menu.append(('Non-%s Only' % fd.group,'2'))
@@ -768,7 +771,7 @@ class ShowTrait(object):
all_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + all_samples
primary_samples = map(lambda X:"_2nd_"+X, fd.f1list + fd.parlist) + primary_samples
else:
- print("ac3")
+ logger.debug("ac3")
all_samples = samplelist
other_samples.sort(key=webqtlUtil.natsort_key)
@@ -785,18 +788,18 @@ class ShowTrait(object):
for sampleNameOrig in all_samples:
sampleName = sampleNameOrig.replace("_2nd_", "")
- print("* type of this_trait:", type(this_trait))
- print(" name:", this_trait.__class__.__name__)
- print(" this_trait:", this_trait)
- print(" type of this_trait.data[sampleName]:", type(this_trait.data[sampleName]))
- print(" name:", this_trait.data[sampleName].__class__.__name__)
- print(" this_trait.data[sampleName]:", this_trait.data[sampleName])
+ logger.debug("* type of this_trait:", type(this_trait))
+ logger.debug(" name:", this_trait.__class__.__name__)
+ logger.debug(" this_trait:", this_trait)
+ logger.debug(" type of this_trait.data[sampleName]:", type(this_trait.data[sampleName]))
+ logger.debug(" name:", this_trait.data[sampleName].__class__.__name__)
+ logger.debug(" this_trait.data[sampleName]:", this_trait.data[sampleName])
thisval = this_trait.data[sampleName].value
- print(" thisval:", thisval)
+ logger.debug(" thisval:", thisval)
thisvar = this_trait.data[sampleName].variance
- print(" thisvar:", thisvar)
+ logger.debug(" thisvar:", thisvar)
thisValFull = [sampleName, thisval, thisvar]
- print(" thisValFull:", thisValFull)
+ logger.debug(" thisValFull:", thisValFull)
vals1.append(thisValFull)
@@ -1202,9 +1205,9 @@ class ShowTrait(object):
this_trait=this_trait,
sample_group_type='primary',
header="%s Only" % (self.dataset.group.name))
- print("primary_samples is: ", pf(primary_samples))
+ logger.debug("primary_samples is: ", pf(primary_samples))
- print("other_sample_names2:", other_sample_names)
+ logger.debug("other_sample_names2:", other_sample_names)
if other_sample_names and self.dataset.group.species != "human":
parent_f1_samples = None
if self.dataset.group.parlist and self.dataset.group.f1list:
@@ -1214,7 +1217,7 @@ class ShowTrait(object):
if parent_f1_samples:
other_sample_names = parent_f1_samples + other_sample_names
- print("other_sample_names:", other_sample_names)
+ logger.debug("other_sample_names:", other_sample_names)
other_samples = SampleList(dataset=self.dataset,
sample_names=other_sample_names,
@@ -1229,14 +1232,14 @@ class ShowTrait(object):
#TODO: Figure out why this if statement is written this way - Zach
#if (other_sample_names or (fd.f1list and this_trait.data.has_key(fd.f1list[0]))
# or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))):
- # print("hjs")
+ # logger.debug("hjs")
self.dataset.group.allsamples = all_samples_ordered
def get_nearest_marker(this_trait, this_db):
this_chr = this_trait.locus_chr
- print("this_chr:", this_chr)
+ logger.debug("this_chr:", this_chr)
this_mb = this_trait.locus_mb
- print("this_mb:", this_mb)
+ logger.debug("this_mb:", this_mb)
#One option is to take flanking markers, another is to take the two (or one) closest
query = """SELECT Geno.Name
FROM Geno, GenoXRef, GenoFreeze
@@ -1245,10 +1248,10 @@ def get_nearest_marker(this_trait, this_db):
GenoFreeze.Id = GenoXRef.GenoFreezeId AND
GenoFreeze.Name = '{}'
ORDER BY ABS( Geno.Mb - {}) LIMIT 1""".format(this_chr, this_db.group.name+"Geno", this_mb)
- print("query:", query)
+ logger.debug("query:", query)
result = g.db.execute(query).fetchall()
- print("result:", result)
+ logger.debug("result:", result)
if result == []:
return ""
@@ -1267,5 +1270,3 @@ def get_trait_table_width(sample_groups):
table_width += len(sample_groups[0].attributes)*10
return table_width
-
-
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 23:57:46 +0000