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-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py255
-rw-r--r--wqflask/wqflask/templates/gsearch_gene.html25
-rw-r--r--wqflask/wqflask/templates/gsearch_pheno.html2
3 files changed, 146 insertions, 136 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 28831937..fa20e8ad 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -1158,22 +1158,24 @@ class DisplayMappingResults(object):
plotRight = xRightOffset
#### find out PlotRight
- for i, _locus in enumerate(self.genotype[0]):
- txStart = self.genotype[0][i].Mb
- txEnd = self.genotype[0][i].Mb
+ for i, _chr in enumerate(self.genotype):
+ if _chr.name == self.ChrList[self.selectedChr][0]:
+ for j, _locus in enumerate(_chr):
+ txStart = _chr[j].Mb
+ txEnd = _chr[j].Mb
- geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb) - 0
- geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) - 0
+ geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb) - 0
+ geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) - 0
- drawit = 1
- if (geneStartPix < xLeftOffset):
- drawit = 0;
- if (geneStartPix > xLeftOffset + plotWidth):
- drawit = 0;
+ drawit = 1
+ if (geneStartPix < xLeftOffset):
+ drawit = 0;
+ if (geneStartPix > xLeftOffset + plotWidth):
+ drawit = 0;
- if drawit == 1:
- if self.genotype[0][i].name != " - " :
- plotRight = geneEndPix + 4
+ if drawit == 1:
+ if _chr[j].name != " - " :
+ plotRight = geneEndPix + 4
#### end find out PlotRight
@@ -1185,139 +1187,142 @@ class DisplayMappingResults(object):
#Now there should always be some value set for "oldgeno" - Zach 12/14/2010
oldgeno = [None]*len(self.strainlist)
- for i, _locus in enumerate(self.genotype[0]):
- txStart = self.genotype[0][i].Mb
- txEnd = self.genotype[0][i].Mb
-
- geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb) - 0
- geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) + 0
+ for i, _chr in enumerate(self.genotype):
+ if _chr.name == self.ChrList[self.selectedChr][0]:
+ for j, _locus in enumerate(_chr):
+ txStart = _chr[j].Mb
+ txEnd = _chr[j].Mb
- if oldgeneEndPix >= xLeftOffset:
- drawStart = oldgeneEndPix + 4
- else:
- drawStart = xLeftOffset + 3
+ geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb) - 0
+ geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) + 0
- drawEnd = plotRight - 9
+ if oldgeneEndPix >= xLeftOffset:
+ drawStart = oldgeneEndPix + 4
+ else:
+ drawStart = xLeftOffset + 3
- drawit = 1
+ drawEnd = plotRight - 9
- if (geneStartPix < xLeftOffset):
- if firstGene == 1:
drawit = 1
- else:
- drawit = 0
- elif (geneStartPix > (xLeftOffset + plotWidth - 3)):
- if lastGene == 0:
- drawit = 1
- drawEnd = xLeftOffset + plotWidth - 6
- lastGene = 1
- else:
- break
-
- else:
- firstGene = 0
- drawit = 1
-
- if drawit == 1:
- myColor = pid.darkblue
- outlineColor = myColor
- fillColor = myColor
-
- maxind=0
+ if (geneStartPix < xLeftOffset):
+ if firstGene == 1:
+ drawit = 1
+ else:
+ drawit = 0
- #Draw Genes
+ elif (geneStartPix > (xLeftOffset + plotWidth - 3)):
+ if lastGene == 0:
+ drawit = 1
+ drawEnd = xLeftOffset + plotWidth - 6
+ lastGene = 1
+ else:
+ break
- geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * (self.EACH_GENE_HEIGHT)*zoom
- if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
- geneYLocation += 4*self.BAND_HEIGHT + 4*self.BAND_SPACING
- else:
- geneYLocation += 3*self.BAND_HEIGHT + 3*self.BAND_SPACING
+ else:
+ firstGene = 0
+ drawit = 1
- if self.genotype[0][i].name != " - " :
+ if drawit == 1:
+ myColor = pid.darkblue
+ outlineColor = myColor
+ fillColor = myColor
- if (firstGene == 1) and (lastGene != 1):
- oldgeneEndPix = drawStart = xLeftOffset
- oldgeno = self.genotype[0][i].genotype
- continue
+ maxind=0
- for j,_geno in enumerate (self.genotype[0][i].genotype):
+ #Draw Genes
- plotbxd=0
- for item in smd:
- if item.name == samplelist[j]:
- plotbxd=1
-
- if (plotbxd == 1):
- ind = 0
- counter = 0
- for item in smd:
- counter = counter + 1
- if item.name == samplelist[j]:
- ind = counter
- maxind=max(ind,maxind)
-
- # lines
- if (oldgeno[j] == -1 and _geno == -1):
- mylineColor = self.HAPLOTYPE_NEGATIVE
- elif (oldgeno[j] == 1 and _geno == 1):
- mylineColor = self.HAPLOTYPE_POSITIVE
- elif (oldgeno[j] == 0 and _geno == 0):
- mylineColor = self.HAPLOTYPE_HETEROZYGOUS
- else:
- mylineColor = self.HAPLOTYPE_RECOMBINATION # XZ: Unknown
+ geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * (self.EACH_GENE_HEIGHT)*zoom
+ if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
+ geneYLocation += 4*self.BAND_HEIGHT + 4*self.BAND_SPACING
+ else:
+ geneYLocation += 3*self.BAND_HEIGHT + 3*self.BAND_SPACING
+
+ if _chr[j].name != " - " :
+
+ if (firstGene == 1) and (lastGene != 1):
+ oldgeneEndPix = drawStart = xLeftOffset
+ oldgeno = _chr[j].genotype
+ continue
+
+ for k, _geno in enumerate (_chr[j].genotype):
+ plotbxd=0
+ for item in smd:
+ if item.name == samplelist[k]:
+ plotbxd=1
+
+ if (plotbxd == 1):
+ ind = 0
+ counter = 0
+ for item in smd:
+ counter = counter + 1
+ if item.name == samplelist[k]:
+ ind = counter
+ maxind=max(ind,maxind)
+
+ # lines
+ if (oldgeno[k] == -1 and _geno == -1):
+ mylineColor = self.HAPLOTYPE_NEGATIVE
+ elif (oldgeno[k] == 1 and _geno == 1):
+ mylineColor = self.HAPLOTYPE_POSITIVE
+ elif (oldgeno[k] == 0 and _geno == 0):
+ mylineColor = self.HAPLOTYPE_HETEROZYGOUS
+ else:
+ mylineColor = self.HAPLOTYPE_RECOMBINATION # XZ: Unknown
+
+ canvas.drawLine(drawStart, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, drawEnd, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, color = mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2))
+
+ fillColor=pid.black
+ outlineColor=pid.black
+ if lastGene == 0:
+ canvas.drawRect(geneStartPix, geneYLocation+2*ind*self.EACH_GENE_HEIGHT*zoom, geneEndPix, geneYLocation+2*ind*self.EACH_GENE_HEIGHT+ 2*self.EACH_GENE_HEIGHT*zoom, edgeColor = outlineColor, fillColor = fillColor)
+
+
+ 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))
+
+ # 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.
+ if (plotRight < (xLeftOffset + plotWidth - 3)) and (lastGene == 0):
+ drawEnd = xLeftOffset + plotWidth - 6
+ mylineColor = self.HAPLOTYPE_RECOMBINATION
+ canvas.drawLine(plotRight, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, drawEnd, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, color = mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2))
- canvas.drawLine(drawStart, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, drawEnd, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, color = mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2))
- fillColor=pid.black
- outlineColor=pid.black
if lastGene == 0:
- canvas.drawRect(geneStartPix, geneYLocation+2*ind*self.EACH_GENE_HEIGHT*zoom, geneEndPix, geneYLocation+2*ind*self.EACH_GENE_HEIGHT+ 2*self.EACH_GENE_HEIGHT*zoom, edgeColor = outlineColor, fillColor = fillColor)
-
+ canvas.drawString("%s" % (_chr[j].name), geneStartPix , geneYLocation+17+2*maxind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black, angle=-90)
- 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[j], self.genotype[0][i].name, float(txStart))
- HREF = ''
- gifmap.areas.append(HT.Area(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.
- if (plotRight < (xLeftOffset + plotWidth - 3)) and (lastGene == 0):
- drawEnd = xLeftOffset + plotWidth - 6
- mylineColor = self.HAPLOTYPE_RECOMBINATION
- canvas.drawLine(plotRight, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, drawEnd, geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom, color = mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2))
-
-
- if lastGene == 0:
- canvas.drawString("%s" % (self.genotype[0][i].name), geneStartPix , geneYLocation+17+2*maxind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black, angle=-90)
-
- oldgeneEndPix = geneEndPix;
- oldgeno = self.genotype[0][i].genotype
- firstGene = 0
- else:
- lastGene = 0
+ oldgeneEndPix = geneEndPix;
+ oldgeno = _chr[j].genotype
+ firstGene = 0
+ else:
+ lastGene = 0
- for j, _geno in enumerate (self.genotype[0][1].genotype):
+ for i, _chr in enumerate(self.genotype):
+ if _chr.name == self.ChrList[self.selectedChr][0]:
+ for j, _geno in enumerate(_chr[1]):
- plotbxd=0
- for item in smd:
- if item.name == samplelist[j]:
- plotbxd=1
+ plotbxd=0
+ for item in smd:
+ if item.name == samplelist[j]:
+ plotbxd=1
- if (plotbxd == 1):
+ if (plotbxd == 1):
- ind = 0
- counter = 0
- expr = 0
- for item in smd:
- counter = counter + 1
- if item.name == samplelist[j]:
- ind = counter
- expr = item.value
+ ind = 0
+ counter = 0
+ expr = 0
+ for item in smd:
+ counter = counter + 1
+ if item.name == samplelist[j]:
+ ind = counter
+ expr = item.value
- # Place where font is hardcoded
- canvas.drawString("%s" % (samplelist[j]), (xLeftOffset + plotWidth + 10) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
- canvas.drawString("%2.2f" % (expr), (xLeftOffset + plotWidth + 60) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
+ # Place where font is hardcoded
+ canvas.drawString("%s" % (samplelist[j]), (xLeftOffset + plotWidth + 10) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
+ canvas.drawString("%2.2f" % (expr), (xLeftOffset + plotWidth + 60) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
## END HaplotypeAnalyst
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 5433f2c5..71e290f3 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -43,8 +43,7 @@
{% endblock %}
{% block js %}
- <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
-
+ <script language="javascript" type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
<script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.12/js/jquery.dataTables.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
@@ -76,15 +75,14 @@
'createdRow': function ( row, data, index ) {
$('td', row).eq(0).attr("style", "text-align: center; padding: 4px 10px 2px 10px;");
$('td', row).eq(1).attr("align", "right");
- $('td', row).slice(10,14).attr("align", "right");
- $('td', row).eq(8).attr('title', $('td', row).eq(8).text());
- if ($('td', row).eq(8).text().length > 45) {
- $('td', row).eq(8).text($('td', row).eq(8).text().substring(0, 45));
- $('td', row).eq(8).text($('td', row).eq(8).text() + '...')
+ $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
+ if ($('td', row).eq(4).text().length > 20) {
+ $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 20));
+ $('td', row).eq(4).text($('td', row).eq(4).text() + '...')
}
$('td', row).eq(5).attr('title', $('td', row).eq(5).text());
- if ($('td', row).eq(5).text().length > 25) {
- $('td', row).eq(5).text($('td', row).eq(5).text().substring(0, 25));
+ if ($('td', row).eq(5).text().length > 20) {
+ $('td', row).eq(5).text($('td', row).eq(5).text().substring(0, 20));
$('td', row).eq(5).text($('td', row).eq(5).text() + '...')
}
$('td', row).eq(6).attr('title', $('td', row).eq(6).text());
@@ -92,6 +90,12 @@
$('td', row).eq(6).text($('td', row).eq(6).text().substring(0, 35));
$('td', row).eq(6).text($('td', row).eq(6).text() + '...')
}
+ $('td', row).eq(8).attr('title', $('td', row).eq(8).text());
+ if ($('td', row).eq(8).text().length > 45) {
+ $('td', row).eq(8).text($('td', row).eq(8).text().substring(0, 45));
+ $('td', row).eq(8).text($('td', row).eq(8).text() + '...')
+ }
+ $('td', row).slice(10,14).attr("align", "right");
},
'data': the_rows,
'columns': [
@@ -99,7 +103,7 @@
'data': null,
'orderDataType': "dom-checkbox",
'render': function(data, type, row, meta) {
- return '<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + data.hmac + '">'
+ return '<input type="checkbox" name="searchResult" class="trait_checkbox checkbox" value="' + data.hmac + '">'
}
},
{
@@ -210,4 +214,5 @@
});
</script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
{% endblock %}
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index 01b2403e..941bf39d 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -84,8 +84,8 @@
{% endblock %}
{% block js %}
+ <script language="javascript" type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
-
<script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.12/js/jquery.dataTables.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 11:55:54 +0000