diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/display_mapping_results.py | 164 |
1 files changed, 131 insertions, 33 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py index 5104bd06..8e6d344a 100644 --- a/wqflask/wqflask/marker_regression/display_mapping_results.py +++ b/wqflask/wqflask/marker_regression/display_mapping_results.py @@ -143,7 +143,10 @@ class DisplayMappingResults(object): DRAW_DETAIL_MB = 4 DRAW_UTR_LABELS_MB = 4 - qmarkImg = HT.Image('/images/qmarkBoxBlue.gif', width=10, height=13, border=0, alt='Glossary') + qmarkImg = HtmlGenWrapper.create_image_tag( + src='/images/qmarkBoxBlue.gif', + width="10", height="13", border="0", alt='Glossary' + ) # Note that "qmark.gif" is a similar, smaller, rounded-edges # question mark. It doesn't look like the ones on the image, @@ -543,7 +546,11 @@ class DisplayMappingResults(object): "{}.png".format( os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename)), format='png') - intImg=HT.Image('/image/'+self.filename+'.png', border=0, usemap='#WebQTLImageMap') + intImg = HtmlGenWrapper.create_image_tag( + src="/image/{}.png".format(self.filename), + border="0", usemap='#WebQTLImageMap' + ) + self.intImg = intImg #Scales plot differently for high resolution if self.draw2X: @@ -560,11 +567,16 @@ class DisplayMappingResults(object): ################################################################ #this form is used for opening Locus page or trait page, only available for genetic mapping if showLocusForm: - showLocusForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', - name=showLocusForm, submit=HT.Input(type='hidden')) + showLocusForm = HtmlGenWrapper.create_form_tag( + cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), + enctype='multipart/form-data', + name=showLocusForm, + submit=HtmlGenWrapper.create_input_tag(type='hidden')) + hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'} for key in hddn.keys(): - showLocusForm.append(HT.Input(name=key, value=hddn[key], type='hidden')) + showLocusForm.append(HtmlGenWrapper.create_input_tag( + name=key, value=hddn[key], type='hidden')) showLocusForm.append(intImg) else: showLocusForm = intImg @@ -636,8 +648,8 @@ class DisplayMappingResults(object): if zoom == 2: drawAreaHeight -= 60 - #Image map - gifmap = HT.Map(name = "WebQTLImageMap") + # Image map + gifmap = HtmlGenWrapper.create_map_tag(name="WebQTLImageMap") newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset) # Draw the alternating-color background first and get plotXScale @@ -985,8 +997,8 @@ class DisplayMappingResults(object): if thisTrait.db: COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift,yPaddingTop+kstep*15,rectWidth+2+rightShift+nameWidth,yPaddingTop+10+kstep*15,) HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name) - Areas = HT.Area(shape='rect',coords=COORDS,href=HREF) - gifmap.areas.append(Areas) + Areas = HtmlGenWrapper.create_area_tag(shape='rect',coords=COORDS,href=HREF) + gifmap.areas.append(Areas) ### TODO def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1): im_drawer = ImageDraw.Draw(canvas) @@ -1388,7 +1400,13 @@ class DisplayMappingResults(object): COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT)) # NL: 06-02-2011 Rob required to display NCBI info in a new window - gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE,target="_blank")) + gifmap.areas.append( + HtmlGenWrapper.create_area_tag( + shape='rect', + coords=COORDS, + href=HREF, + title=TITLE, + target="_blank")) ## BEGIN HaplotypeAnalyst def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None): @@ -1556,7 +1574,12 @@ class DisplayMappingResults(object): COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation+ind*self.EACH_GENE_HEIGHT, geneEndPix+1, (geneYLocation + ind*self.EACH_GENE_HEIGHT)) TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart)) HREF = '' - gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE)) + gifmap.areas.append( + HtmlGenWrapper.create_area_tag( + shape='rect', + coords=COORDS, + href=HREF, + title=TITLE)) # if there are no more markers in a chromosome, the plotRight value calculated above will be before the plotWidth # resulting in some empty space on the right side of the plot area. This draws an "unknown" bar from plotRight to the edge. @@ -1675,7 +1698,12 @@ class DisplayMappingResults(object): WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0) WEBQTL_TITLE = "Click to view this section of the genome in WebQTL" - gifmap.areas.append(HT.Area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE)) + gifmap.areas.append( + HtmlGenWrapper.create_area_tag( + shape='rect', + coords=WEBQTL_COORDS, + href=WEBQTL_HREF, + title=WEBQTL_TITLE)) im_drawer.rectangle( xy=((xBrowse1, paddingTop), (xBrowse2, (paddingTop + self.BAND_HEIGHT))), @@ -1692,7 +1720,12 @@ class DisplayMappingResults(object): else: PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen" - gifmap.areas.append(HT.Area(shape='rect',coords=PHENOGEN_COORDS,href=PHENOGEN_HREF, title=PHENOGEN_TITLE)) + gifmap.areas.append( + HtmlGenWrapper.create_area_tag( + shape='rect', + coords=PHENOGEN_COORDS, + href=PHENOGEN_HREF, + title=PHENOGEN_TITLE)) im_drawer.rectangle( xy=((xBrowse1, phenogenPaddingTop), (xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT))), @@ -1708,7 +1741,12 @@ class DisplayMappingResults(object): else: UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser" - gifmap.areas.append(HT.Area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE)) + gifmap.areas.append( + HtmlGenWrapper.create_area_tag( + shape='rect', + coords=UCSC_COORDS, + href=UCSC_HREF, + title=UCSC_TITLE)) im_drawer.rectangle( xy=((xBrowse1, ucscPaddingTop), (xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))), @@ -1725,7 +1763,11 @@ class DisplayMappingResults(object): else: ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases) ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser" - gifmap.areas.append(HT.Area(shape='rect',coords=ENSEMBL_COORDS,href=ENSEMBL_HREF, title=ENSEMBL_TITLE)) + gifmap.areas.append(HtmlGenWrapper.create_area_tag( + shape='rect', + coords=ENSEMBL_COORDS, + href=ENSEMBL_HREF, + title=ENSEMBL_TITLE)) im_drawer.rectangle( xy=((xBrowse1, ensemblPaddingTop), (xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT))), @@ -1957,9 +1999,14 @@ class DisplayMappingResults(object): outline=rectColor,fill=rectColor,width = 0) COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\ xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth) - HREF="/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name+"Geno") + HREF = "/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name+"Geno") #HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname) - Areas=HT.Area(shape='rect', coords=COORDS, href=HREF, target="_blank", title="Locus : " + Lname) + Areas = HtmlGenWrapper.create_area_tag( + shape='rect', + coords=COORDS, + href=HREF, + target="_blank", + title="Locus : {}".format(Lname)) gifmap.areas.append(Areas) ##piddle bug if j == 0: @@ -2168,8 +2215,14 @@ class DisplayMappingResults(object): else: sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive/4.61) sig_title = "Significant LOD = %0.2f" % (self.significant/4.61) - Areas1 = HT.Area(shape='rect',coords=sugg_coords,title=sugg_title) - Areas2 = HT.Area(shape='rect',coords=sig_coords,title=sig_title) + Areas1 = HtmlGenWrapper.create_area_tag( + shape='rect', + coords=sugg_coords, + title=sugg_title) + Areas2 = HtmlGenWrapper.create_area_tag( + shape='rect', + coords=sig_coords, + title=sig_title) gifmap.areas.append(Areas1) gifmap.areas.append(Areas2) @@ -2621,7 +2674,10 @@ class DisplayMappingResults(object): #add by NL 09-03-2010 HREF = "javascript:chrView(%d,%s);" % (i,self.ChrLengthMbList) #HREF = "javascript:changeView(%d,%s);" % (i,self.ChrLengthMbList) - Areas = HT.Area(shape='rect', coords=COORDS, href=HREF) + Areas = HtmlGenWrapper.create_area_tag( + shape='rect', + coords=COORDS, + href=HREF) gifmap.areas.append(Areas) startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale @@ -2707,7 +2763,11 @@ class DisplayMappingResults(object): tableIterationsCnt = tableIterationsCnt + 1 this_row = [] #container for the cells of each row - selectCheck = HT.Input(type="checkbox", name="selectCheck", value=theGO["GeneSymbol"], Class="checkbox trait_checkbox") #checkbox for each row + selectCheck = HtmlGenWrapper.create_input_tag( + type="checkbox", + name="selectCheck", + value=theGO["GeneSymbol"], + Class="checkbox trait_checkbox") # checkbox for each row geneLength = (theGO["TxEnd"] - theGO["TxStart"])*1000.0 tenPercentLength = geneLength*0.0001 @@ -2765,41 +2825,77 @@ class DisplayMappingResults(object): this_row = [selectCheck.__str__(), str(tableIterationsCnt), - HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank").__str__(), - HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank").__str__(), - HT.Href("javascript:rangeView('%s', %f, %f)" % (str(chr_as_int), txStart-tenPercentLength, txEnd+tenPercentLength), "%0.3f" % geneLength).__str__(), + str(HtmlGenWrapper.create_link_tag( + geneIdString, + theGO["GeneSymbol"], + target="_blank") + ), + str(HtmlGenWrapper.create_link_tag( + mouseStartString, + "{:.6f}".format(txStart), + target="_blank") + ), + str(HtmlGenWrapper.create_link_tag( + "javascript:rangeView('{}', {:f}, {:f})".format( + str(chr_as_int), + txStart-tenPercentLength, + txEnd+tenPercentLength), + "{:.3f}".format(geneLength))), snpString, snpDensityStr, avgExpr, humanChr, - HT.Href(humanStartString, humanStartDisplay, target="_blank").__str__(), + str(HtmlGenWrapper.create_link_tag( + humanStartString, + humanStartDisplay, + target="_blank")), literatureCorrelationString, geneDescription] else: this_row = [selectCheck.__str__(), str(tableIterationsCnt), - HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank").__str__(), - HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank").__str__(), - HT.Href("javascript:rangeView('%s', %f, %f)" % (str(chr_as_int), txStart-tenPercentLength, txEnd+tenPercentLength), "%0.3f" % geneLength).__str__(), + str(HtmlGenWrapper.create_link_tag( + geneIdString, theGO["GeneSymbol"], + target="_blank")), + str(HtmlGenWrapper.create_link_tag( + mouseStartString, + "{:.6f}".format(txStart), + target="_blank")), + str(HtmlGenWrapper.create_link_tag( + "javascript:rangeView('{}', {:f}, {:f})".format( + str(chr_as_int), + txStart-tenPercentLength, + txEnd+tenPercentLength), + "{:.3f}".format(geneLength))), snpString, snpDensityStr, avgExpr, humanChr, - HT.Href(humanStartString, humanStartDisplay, target="_blank").__str__(), + str(HtmlGenWrapper.create_link_tag( + humanStartString, + humanStartDisplay, + target="_blank")), geneDescription] gene_table_body.append(this_row) elif self.dataset.group.species == 'rat': for gIndex, theGO in enumerate(geneCol): - this_row = [] #container for the cells of each row - selectCheck = HT.Input(type="checkbox", name="selectCheck", Class="checkbox trait_checkbox").__str__() #checkbox for each row + this_row = [] # container for the cells of each row + selectCheck = str(HtmlGenWrapper.create_input_tag( + type="checkbox", + name="selectCheck", + Class="checkbox trait_checkbox")) # checkbox for each row #ZS: May want to get this working again later #webqtlSearch = HT.Href(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], ">>", target="_blank").__str__() if theGO["GeneID"] != "": - geneSymbolNCBI = HT.Href("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % theGO["GeneID"], theGO["GeneSymbol"], Class="normalsize", target="_blank").__str__() + geneSymbolNCBI = str(HtmlGenWrapper.create_link_tag( + "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={}".format(theGO["GeneID"]), + theGO["GeneSymbol"], + Class="normalsize", + target="_blank")) else: geneSymbolNCBI = theGO["GeneSymbol"] @@ -2839,7 +2935,9 @@ class DisplayMappingResults(object): str(gIndex+1), geneSymbolNCBI, "%0.6f" % theGO["TxStart"], - HT.Href(geneLengthURL, "%0.3f" % (geneLength*1000.0)).__str__(), + str(HtmlGenWrapper.create_link_tag( + geneLengthURL, + "{:.3f}".format(geneLength*1000.0))), avgExprVal, mouseChr, mouseTxStart, |