onkeyup='my_search(0, "inp1", "myTable")',
placeholder="Search for a genesymbol..")
with table(id="myTable") as _table:
_tr = tr()
_tr.add([th(x) for x in header])
for d in data:
newd, gene = annotate(d, gene2annotation)
with tr():
td(
raw('<a href=%s target="_blank">%s</a>' % (os.path.join(
args.genes_dir, newd[0] + ".html"), newd[0])))
td(newd[1])
td(newd[2])
td(
raw('<a href=%s target="_blank">link</a>' %
add_ucsc(gene, args.ucsc, chr_dict=chrom_dict)))
for el in newd[3:]:
a = el.split(",")
if (len(a) == 1):
td(el)
else:
with td():
for aa in a:
p(aa)
_script = script(raw(plain_script), type='text/javascript')
with open(os.path.join(args.outdir, args.name + ".html"), 'w') as f:
#print(doc.render())
f.write(doc.render())
onkeyup='my_filter_greater(13, "inp4", "myTable")',
placeholder="Filter top coverage content greater than..")
input(type="number",
id="inp5",
onkeyup='my_filter_lesser_abs(9, "inp5", "myTable")',
placeholder="Filter distance to TSS closer than..")
with table(id="myTable") as _table:
_tr = tr()
_tr.add([
th(x[1][0], onclick='sortTable(%d, %d)' % (x[0], x[1][1]))
for x in enumerate(zip(header, dtypes))
])
for peak in peaks:
with tr():
td(
raw('<a href=%s target="_blank">ucsc_link</a>' % add_ucsc(
peak, args.ucsc, flank=25, chr_dict=chr_dict)))
for entry in flatten_peak(peak):
td(entry)
_script = script(raw(plain_script), type='text/javascript')
with open(os.path.join(args.outdir, 'peaks.html'), 'w') as f:
#print(doc.render())
f.write(doc.render())
with open(os.path.join(args.outdir, 'peaks.tsv'), 'w') as f:
f.write("%s\n" % "\t".join(header[1:]))
for peak in peaks:
f.write("%s\n" % "\t".join([str(x) for x in flatten_peak(peak)]))
id="inp1",
onkeyup='my_search(1, "inp1", "myTable")',
placeholder="Search for a genesymbol..")
with table(id="myTable") as _table:
_tr = tr()
_tr.add([th(x) for x in header])
for d in data:
newd, gene = annotate(d, gene2annotation)
with tr():
td(
raw('<a href=%s target="_blank">%s</a>' %
(os.path.join(args.genes_dir,
gene.name + ".html"), newd[0])))
td(
raw('<a href=%s target="_blank">link</a>' %
add_ucsc(gene, args.ucsc)))
for el in newd[1:]:
a = el.split(",")
if (len(a) == 1):
td(el)
else:
with td():
for aa in a:
p(aa)
_script = script(raw(plain_script), type='text/javascript')
path = os.path.join(args.outdir, "cluster_%d" % cl)
with open(path + ".html", 'w') as f:
f.write(doc.render())
onkeyup='my_filter_greater(13, "inp4", "myTable")',
placeholder="Filter top coverage content greater than..")
input(type="number",
id="inp5",
onkeyup='my_filter_lesser_abs(9, "inp5", "myTable")',
placeholder="Filter distance to TSS closer than..")
with table(id="myTable") as _table:
_tr = tr()
_tr.add([
th(x[1][0], onclick='sortTable(%d, %d)' % (x[0], x[1][1]))
for x in enumerate(zip(header, dtypes))
])
for peak in peaks:
with tr():
td(
raw('<a href=%s target="_blank">ucsc_link</a>' %
add_ucsc(peak, args.ucsc, flank=25, chr_dict=chrdict)))
for entry in flatten_peak(peak):
td(entry)
_script = script(raw(plain_script), type='text/javascript')
with open(os.path.join(args.outdir, 'peaks.html'), 'w') as f:
#print(doc.render())
f.write(doc.render())
with open(os.path.join(args.outdir, 'peaks.tsv'), 'w') as f:
f.write("%s\n" % "\t".join(header[1:]))
for peak in peaks:
f.write("%s\n" % "\t".join([str(x) for x in flatten_peak(peak)]))
style(_style)
with doc:
p(strong(_title))
input(type="text", id="myInput", onkeyup="my_search(5)", placeholder="Search for a gene ...")
#input(type="number", id="myInputGreater", onkeyup="my_filter_greater(6)", placeholder="Filter AT content greater than..")
with table(id = "myTable") as _table:
_tr = tr()
_tr.add([ th(x[1][0], onclick='sortTable(%d, %d)' % (x[0], x[1][1])) for x in enumerate(zip(headers, dtypes)) ])
for interval in peaks:
center = int(interval.name)
sense, antisense, tip = split_sequence(interval, genome, args.flank)
#print(sense)
with tr():
td(raw('<a href=%s target="_blank">ucsc_link</a>' % add_ucsc(interval, args.ucsc)) )
td(center-args.flank)
td(center+args.flank)
td(center)
td(interval.strand)
td(interval.attrs['gene'])
td(interval.attrs['tss'])
td(interval.score)
td(interval.attrs['pam_min'])
td(interval.attrs['pam_score'])
#print(sense)
with td(__pretty=False, style= 'font-family:monospace; font-size: 12pt'):
for seq, color in zip(sense, sense_colors):
span(seq, style="color:%s" % color)
for seq, color in zip(tip, tip_colors):
span(seq, style="color:%s" % color)
for gene in genes:
########### HTML SECTION ###########
with open(os.path.join(args.outdir, "%s.html" % gene.name), 'w') as f:
doc = dominate.document(title="%s: gene overview" % gene.name)
with doc.head:
style(_style)
with doc:
p(strong(gene.name))
br()
with p():
b("Gene Symbol:")
raw("\t%s" % gene.attrs['genesymbol'])
with p():
b("CDS:")
raw('<a href=%s target="_blank">\t%s(%s) %d-%d</a>' %
(add_ucsc(gene, args.ucsc), gene.chrom, gene.strand,
gene.start, gene.stop))
#raw("\t%s(%s) %d-%d " % (gene.chrom, gene.strand, gene.start, gene.stop))
with p():
b("Alternative TSS:")
raw("\t%s" % gene.attrs["alt_tss"].replace(",", ", "))
with p():
b("Annotation:")
raw("\t%s" % gene.attrs['annotation'])
with p():
b("Function:")
raw("\t%s" % gene.attrs.get('function',
gene.attrs.get('product', 'None')))
with p():
b("Phage:")
raw("\t%s" % PHAGE[gene.attrs.get('phage')])