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-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py164
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,
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 23:31:40 +0000