def build(self):
BaseScene.build(self)
self.ui.spats.run.allow_negative_values = True
self.profiles = self.ui.spats.compute_profiles()
self.maxes = {
dt: (4 if dt == "rho" else self.profiles.data_range(dt)[1])
for dt in self.data_types
}
self.data_type_views = [
self.makeDataTypeView(data_type) for data_type in self.data_types
]
self.targetButtons([
self.togglePlotType, self.toggleCounts, self.toggleNull,
self.totalCounts
])
self.buttonWithKey('togglePlotType').text = "Plot Type: Row"
self.buttonWithKey('toggleCounts').text = "Show f+/f-: On"
self.buttonWithKey('toggleNull').text = "Flags: Off"
self.type_label = self.addView(
cjb.uif.views.Label("Query: {}".format(self.data_type),
fontSize=16))
if self.ui.has_tags:
sitemap = {
"{}:{}:{}:{}".format(self.target_id, s[0], s[2], s[1]): s[3]
for s in self.ui.db.result_sites(self.ui.result_set_id,
self.target_id)
}
else:
sitemap = self.ui.spats.counters.registered_dict()
self.matrix = cjb.uif.views.CustomView('SpatsMatrix')
self.matrix.properties["d"] = self.profiles.cotrans_data()
self.matrix.properties["plot"] = self.data_type
self.matrix.properties["max"] = self.profiles.data_range(
self.data_type)[1]
self.addView(self.matrix)
def build(self):
BaseScene.build(self)
counts = self.ui.db.tag_counts(self.ui.result_set_id,
self.incl_excl_tags[0],
self.incl_excl_tags[1])
counts = sorted([(key, counts[key]) for key in counts.keys()],
key=lambda x: x[1],
reverse=True)
total = float(
self.ui.db.count_matches(self.ui.result_set_id,
self.incl_excl_tags[0],
self.incl_excl_tags[1]))
tags = [
Tag(tc[0], "{:.1f}%".format(float(tc[1]) * 100.0 / total))
for tc in counts
]
query_tags = self.incl_excl_tags[0] + self.incl_excl_tags[1]
self.tagViews = [
self.addTagView(t, COLOR_BG) for t in tags
if t.tag not in query_tags
]
self.targetButtons([self.showMatches])
self.query_label = self.addView(
cjb.uif.views.Label("Query: {} matches.".format(int(total)),
fontSize=14))
self.queryTagViews = [self.addQueryTag(t) for t in query_tags]
def build(self):
BaseScene.build(self)
counts = self.ui.db.tag_counts(self.ui.result_set_id, self.incl_excl_tags[0], self.incl_excl_tags[1])
counts = sorted([ (key, counts[key]) for key in counts.keys() ], key = lambda x : x[1], reverse = True)
total = float(self.ui.db.count_matches(self.ui.result_set_id, self.incl_excl_tags[0], self.incl_excl_tags[1]))
tags = [ Tag(tc[0], "{:.1f}%".format(float(tc[1]) * 100.0 / total)) for tc in counts ]
query_tags = self.incl_excl_tags[0] + self.incl_excl_tags[1]
self.tagViews = [ self.addTagView(t, COLOR_BG) for t in tags if t.tag not in query_tags ]
self.targetButtons([self.showMatches])
self.query_label = self.addView(cjb.uif.views.Label("Query: {} matches.".format(int(total)), fontSize = 14))
self.queryTagViews = [ self.addQueryTag(t) for t in query_tags ]
def build(self):
BaseScene.build(self)
if self.site:
pairs = self.ui.db.results_matching_site(self.ui.result_set_id, self.site.target_id, self.site.end, self.site.site, limit = 50)
self.total_matches = self.site.total
else:
pairs = self.ui.db.results_matching(self.ui.result_set_id, self.include_tags, self.exclude_tags, limit = 50)
self.total_matches = self.ui.db.count_matches(self.ui.result_set_id, self.include_tags, self.exclude_tags)
matches = [ MatchedPair(p[2], p[3], p[4], p[0], p[1]) for p in pairs ]
self.matchViews = [ self.addMatchView(m) for m in matches ]
self.filter_label = self.addView(cjb.uif.views.Label("Filter: <None>", fontSize = 11))
def build(self):
BaseScene.build(self)
self.ui.spats.run.allow_negative_values = True
self.profiles = self.ui.spats.compute_profiles()
self.maxes = { dt : (4 if dt == "rho" else self.profiles.data_range(dt)[1]) for dt in self.data_types }
self.data_type_views = [ self.makeDataTypeView(data_type) for data_type in self.data_types ]
self.targetButtons([self.togglePlotType, self.toggleCounts, self.toggleNull, self.totalCounts])
self.buttonWithKey('togglePlotType').text = "Plot Type: Row"
self.buttonWithKey('toggleCounts').text = "Show f+/f-: On"
self.buttonWithKey('toggleNull').text = "Flags: Off"
self.type_label = self.addView(cjb.uif.views.Label("Query: {}".format(self.data_type), fontSize = 16))
if self.ui.has_tags:
sitemap = { "{}:{}:{}:{}".format(self.target_id, s[0], s[2], s[1]) : s[3] for s in self.ui.db.result_sites(self.ui.result_set_id, self.target_id) }
else:
sitemap = self.ui.spats.counters.registered_dict()
self.matrix = cjb.uif.views.CustomView('SpatsMatrix')
self.matrix.properties["d"] = self.profiles.cotrans_data()
self.matrix.properties["plot"] = self.data_type
self.matrix.properties["max"] = self.profiles.data_range(self.data_type)[1]
self.addView(self.matrix)
def build(self):
BaseScene.build(self)
self.targetButton(self.dump)
processor = self.ui.processor
seqs = {
"RRRY" : "RRRY",
"YYYR" : "YYYR",
}
for target in processor._tag_targets.targets:
seqs[target.name] = target.seq
self.tag_seqs = seqs
colors = self.ui.colors
color_idx = 1
for part_name in ( "r1", "r2" ):
part = getattr(self.pair, part_name)
seq = part.original_seq
self.parts[part_name] = map(lambda x: self.addNucView(x, TAG_COLORS[0]), [ Nuc(seq[idx], (part_name, idx, None)) for idx in range(len(seq)) ])
self.labels[part_name] = self.addView(Label(part_name.upper()))
for tindex in range(len(part.tags)):
tag = part.tags[tindex]
tkey = tag[0].rstrip("_rc_")
tcol = colors.color(tkey)
tseq = self.tag_seqs[tag[0]]
match_index = tag[3]
views = []
for idx in range(max(0,match_index - 4), min(len(tseq), match_index + tag[2] + 4)):
v = self.addNucView(Nuc(tseq[idx], (part_name, idx, tag)), tcol)
if idx < match_index or idx >= match_index + tag[2]:
v.alpha = 0.5
#print(" set a=0.5, bg: {}".format(v.bg))
views.append(v)
self.parts[part_name + str(tindex)] = views
label = Label(tag[0])
label.bg = tcol
self.labels[part_name + str(tindex)] = self.addView(label)
def build(self):
BaseScene.build(self)
targets = sorted(self.ui.db.targets(), key = lambda x : x[0])
self.targetViews = [ self.addTargetView(t, [ 1.0, 0.85, 0.7 ]) for t in targets ]
def build(self):
BaseScene.build(self)
targets = sorted(self.ui.db.targets(), key=lambda x: x[0])
self.targetViews = [
self.addTargetView(t, [1.0, 0.85, 0.7]) for t in targets
]
def build(self):
BaseScene.build(self)
processor = self.ui.processor
seqs = {
"adapter_t_rc" : reverse_complement(processor._run.adapter_t),
"adapter_b" : processor._run.adapter_b,
"RRRY" : "RRRY",
"YYYR" : "YYYR",
}
for target in processor._tag_targets.targets:
seqs[target.name] = target.seq
seqs[target.name + "_rc"] = reverse_complement(target.seq)
self.tag_seqs = seqs
colors = self.ui.colors
target = self.pair.target
colors._colors[target.name] = colors.color("target")
tcol = colors.color("target")
nomatch_col = colors.color("grey")
error_col = colors.color("error")
skips = self._skips()
tseq = target.seq
tlen = target.n
def should_skip(idx):
for skip in skips:
if idx >= skip[0] and idx < skip[0] + skip[1]:
return True
return False
self.parts[target.name] = [ None if should_skip(i) else self.addNucView(Nuc(tseq[i], (target.name, i, None)), tcol) for i in range(tlen) ]
self.labels[target.name] = self.addLabel(target.name, bg = tcol)
for part_name in ( "r1", "r2" ):
parts = []
part = getattr(self.pair, part_name)
seq = part.original_seq
idx = 0
for tag in sorted(part.tags, key = lambda t : t[1]):
tkey = tag[0].rstrip("_rc_")
while idx < tag[1] + tag[2]:
ntcol = nomatch_col if idx < tag[1] else colors.color(tkey)
if idx in part.match_errors or idx in part.adapter_errors:
ntcol = error_col
parts.append(self.addNucView(Nuc(seq[idx], (part_name, idx, None if idx < tag[1] else tag[0])), ntcol))
idx += 1
if self.expanded:
if tag[0] == target.name + "_rc":
rc = reverse_complement(seq[tag[1]:tag[1] + tag[2]])
self.parts[part_name + tag[0]] = [ self.addNucView(Nuc(rc[j], (tag[0], j, None)), tcol) for j in range(0, tag[2]) ]
self.labels[part_name + tag[0]] = self.addLabel("R1_rc")
elif tkey.startswith("adapter"):
tagseq = self.tag_seqs[tag[0]]
aparts = []
for j in range(max(tag[3] - 4, 0), min(tag[2] + 4, len(tagseq))):
v = self.addNucView(Nuc(tagseq[j], (tag[0], j, None)), colors.color(tkey))
if j < tag[3] or j >= tag[3] + tag[2]:
v.alpha = 0.5
aparts.append(v)
self.parts[part_name + tag[0]] = aparts
self.labels[part_name + tag[0]] = self.addLabel(tag[0], bg = colors.color(tkey))
elif part_name == "r1" and (tag[0] == 'YYYR' or tag[0] == 'RRRY'):
hcol = colors.color(tag[0])
self.parts[part_name + tag[0]] = [ self.addNucView(Nuc(tag[0][j], (tag[0], j, None)), hcol) for j in range(len(tag[0])) ]
self.labels[part_name + tag[0]] = self.addLabel(tag[0], bg = hcol)
while idx < len(seq):
parts.append(self.addNucView(Nuc(seq[idx], (part_name, idx, None)), nomatch_col))
idx += 1
self.parts[part_name] = parts
self.labels[part_name] = self.addLabel(part_name.upper())