aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorZachary Sloan2013-01-08 14:46:07 -0600
committerZachary Sloan2013-01-08 14:46:07 -0600
commitc8a4719a83e3ee65a8c03b0b600a3cfea9ff17bf (patch)
tree40e1c27050964d4339ce631cea7553fd5dae52ab
parentf15e39f5251ff3689e4a065d11c1edd36f5e4811 (diff)
downloadgenenetwork2-c8a4719a83e3ee65a8c03b0b600a3cfea9ff17bf.tar.gz
Deleted some unnecessary code in marker_regression.py and fixed some bugs
Added a couple utility functions to the Chromosomes class in species.py
-rw-r--r--wqflask/base/species.py22
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py66
2 files changed, 30 insertions, 58 deletions
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 1fd76772..85f076ca 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -13,7 +13,8 @@ class TheSpecies(object):
self.dataset = dataset
print("self.dataset is:", pf(self.dataset.__dict__))
self.chromosomes = Chromosomes(self.dataset.group.name)
-
+ self.genome_length = self.chromosomes.get_genome_length()
+
#@property
#def chromosomes(self):
# chromosomes = [("All", -1)]
@@ -31,7 +32,7 @@ class TheSpecies(object):
class Chromosomes(object):
def __init__(self, group_name):
self.chromosomes = collections.OrderedDict()
-
+
results = g.db.execute("""
Select
Chr_Length.Name, Length from Chr_Length, InbredSet
@@ -46,3 +47,20 @@ class Chromosomes(object):
self.chromosomes[item.Name] = item.Length
print("self.chromosomes:", self.chromosomes)
+
+
+ def get_mb_length(self):
+ """Gets the chromosome length in megabases"""
+
+ mb_lengths = chr_length/1000000.0 for name, chr_length in self.chromosomes
+
+ return mb_lengths
+
+ def get_genome_length(self):
+ """Gets the sum of each chromosome's length"""
+
+ genome_length = 0
+ for name, value in self.chromosomes.items():
+ genome_length += value
+
+ return genome_length \ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index ace76411..0aad4e54 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -67,11 +67,9 @@ class MarkerRegression(object):
self.dataset.group.read_genotype_file()
self.genotype = self.dataset.group.genotype
- assert start_vars['display_all_vars'] in ('True', 'False')
+ assert start_vars['display_all_lrs'] in ('True', 'False')
self.display_all_lrs = True if start_vars['display_all_lrs'] == 'True' else False
- print("self.display_all_lrs is:", pf(self.display_all_lrs))
-
for sample in self.dataset.group.samplelist:
value = start_vars['value:' + sample]
variance = start_vars['variance:' + sample]
@@ -314,6 +312,7 @@ class MarkerRegression(object):
"""
Initializes all of the MarkerRegressionPage class parameters,
acquiring most values from the formdata (fd)
+
"""
###################################
# manhattam plot parameters
@@ -448,70 +447,23 @@ class MarkerRegression(object):
return rv, tblobj,bottomInfo
- #def GenReport(self, ChrNameOrderIdDict,fd, _genotype, _strains, _vals, _vars= []):
def gen_data(self):
"""Todo: Fill this in here"""
- #'Create an HTML division which reports any loci which are significantly associated with the submitted trait data.'
-
+
#calculate QTL for each trait
- #self.qtlresults = []
- #if webqtlUtil.ListNotNull(_vars):
-
- #strains =
- #vals =
- #variances =
-
- #if any(self.variances):
- # self.qtl_results = self.genotype.regression(strains = self.samples,
- # trait = self.vals,
- # variance = self.variances)
- # self.lrs_array = self.genotype.permutation(strains = self.samples,
- # trait = self.vals,
- # variance = self.variances,
- # nperm = self.num_perm)
- #else:
self.qtl_results = self.genotype.regression(strains = self.samples,
trait = self.vals)
self.lrs_array = self.genotype.permutation(strains = self.samples,
trait = self.vals,
nperm=self.num_perm)
- #print("[yellow] self.__dict__ is:", pf(self.__dict__))
-
- #self.qtlresults.append(qtlresults)
-
- #filename= webqtlUtil.genRandStr("GenomeAsscociation_")
-
-
-
- # set suggestive, significant and highly significant LRS
- #if fd.suggestive == None:
- #self.suggestive = self.lrs_array[int(self.num_perm*0.37-1)]
- ##else:
- ## fd.suggestive = float(fd.suggestive)
- ##if fd.significance == None:
- #self.significance = self.lrs_array[int(self.num_perm*0.95-1)]
- ##else:
- ## fd.significance = float(fd.significance)
- #
- ##self.significance =fd.significance
- ##self.suggestive = fd.suggestive
- #self.highlysignificant = LRSArray[int(fd.nperm*0.99-1)]
-
self.lrs_thresholds = Bunch(
suggestive = self.lrs_array[int(self.num_perm*0.37-1)],
significant = self.lrs_array[int(self.num_perm*0.95-1)],
- highly_significant = self.lrs_array[int(fd.nperm*0.99-1)]
+ highly_significant = self.lrs_array[int(self.num_perm*0.99-1)]
)
-
- #disp_all_lrs = False
- #if fd.formdata.getvalue('displayAllLRS'):
- # disp_all_lrs = True
-
- #if not self.disp_all_lrs:
-
- if self.disp_all_lrs:
+ if self.display_all_lrs:
filtered_results = self.qtl_results
else:
suggestive_results = []
@@ -587,7 +539,9 @@ class MarkerRegression(object):
# report = HT.Blockquote(HT.Font('No association ',color="#FF0000"),HT.Font('with a likelihood ratio statistic greater than %3.1f was found. Here are the top 10 LRSs.' % fd.suggestive,color="#000000"))
#else:
# report = HT.Blockquote('The following loci in the %s data set have associations with the above trait data.\n' % fd.RISet, HT.P())
- report.__setattr__("class","normalsize")
+
+
+ #report.__setattr__("class","normalsize")
#fpText = open('%s.txt' % (webqtlConfig.TMPDIR+filename), 'wb')
#fpText.write('Suggestive LRS =%3.2f\n'%self.suggestive)
@@ -610,11 +564,11 @@ class MarkerRegression(object):
#for ncol, item in enumerate(headerList):
# reportHeaderRow.append(THCell(HT.TD(item, Class=headerStyle, valign='bottom',nowrap='ON'),text=item, idx=ncol))
- for marker in filtered:
+ for marker in filtered_results:
if marker.lrs > webqtlConfig.MAXLRS:
marker.lrs = webqtlConfig.MAXLRS
- self.filtered = filtered
+ self.filtered_results = filtered_results
#if fd.genotype.type == 'intercross':
# ncol =len(headerList)