aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py4
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py20
2 files changed, 16 insertions, 8 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index d2b27991..d7c78db0 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -41,6 +41,9 @@ from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMM
from utility.external import shell
from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
class MarkerRegression(object):
def __init__(self, start_vars, temp_uuid):
@@ -194,6 +197,7 @@ class MarkerRegression(object):
self.control_marker = start_vars['control_marker']
self.do_control = start_vars['do_control']
+ logger.info("Running qtlreaper")
results = self.gen_reaper_results()
elif self.mapping_method == "plink":
results = self.run_plink()
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 9cef3cec..bc147f75 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -44,6 +44,9 @@ from utility import Plot
from wqflask.interval_analyst import GeneUtil
from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR, GENERATED_IMAGE_DIR
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
#########################################
# Inteval Mapping Plot Page
#########################################
@@ -159,6 +162,7 @@ class MarkerRegression(object):
#if not self.openMysql():
# return
+ logger.info("Running qtlreaper")
#helper_functions.get_species_dataset_trait(self, start_vars)
@@ -211,7 +215,7 @@ class MarkerRegression(object):
self.plotScale = start_vars['mapping_scale']
else:
self.plotScale = "physic"
-
+
self.manhattan_plot = start_vars['manhattan_plot']
if 'permCheck' in start_vars.keys():
@@ -514,13 +518,13 @@ class MarkerRegression(object):
if self.dataset.group.species == "mouse":
if self.selectedChr == 20:
- chrName = "X"
+ chrName = "X"
else:
chrName = self.selectedChr
self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "mouse")
elif self.dataset.group.species == "rat":
if self.selectedChr == 21:
- chrName = "X"
+ chrName = "X"
else:
chrName = self.selectedChr
self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "rat")
@@ -860,7 +864,7 @@ class MarkerRegression(object):
BootCoord = []
i = 0
startX = xLeftOffset
-
+
if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes
for j, _chr in enumerate(self.genotype):
BootCoord.append( [])
@@ -883,8 +887,8 @@ class MarkerRegression(object):
else:
Xc = startX + (_locus.cM-_chr[0].cM)*plotXScale
BootCoord[-1].append([Xc, self.bootResult[i]])
- i += 1
-
+ i += 1
+
#reduce bootResult
if self.selectedChr > -1:
maxBootBar = 80.0
@@ -1851,7 +1855,7 @@ class MarkerRegression(object):
if j == 0:
canvas.drawLine(startPosX,yZero,startPosX,yZero+40, color=lineColor)
startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale
-
+
centimorganLabelFont = pid.Font(ttf="verdana", size=18*zoom*1.5, bold=0)
canvas.drawString("Centimorgans", xLeftOffset + (plotWidth - canvas.stringWidth("Megabases", font=centimorganLabelFont))/2,
strYLoc + canvas.fontHeight(MBLabelFont)+ 10*(zoom%2) + 10, font=centimorganLabelFont, color=pid.black)
@@ -2963,7 +2967,7 @@ class MarkerRegression(object):
chr_as_int = 20
else:
chr_as_int = int(theGO["Chromosome"]) - 1
-
+
geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"]))
#geneLengthURL = "javascript:centerIntervalMapOnRange2('%s', %f, %f, document.changeViewForm)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1))
geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1))