diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 20 |
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)) |