def print_gffline(self, fw, f, seqid, parent=None):
score = phase = "."
type = f.type
if type == "source":
type = "contig"
attr = "ID=tmp"
source = self.source
start = get_number(f.location.start) + 1
end = get_number(f.location.end)
strand = '-' if f.strand < 0 else '+'
g = "\t".join(str(x) for x in \
(seqid, source, type, start, end, score, strand, phase, attr))
g = GffLine(g)
qual = f.qualifiers
id = "tmp"
if MT in qual:
id = seqid
elif LT in qual:
id, = qual[LT]
else:
qual[LT] = [self.current_id]
id, = qual[LT]
id = id.split()[0]
if parent:
id, = parent.qualifiers[LT]
id = id.split()[0]
assert id != "tmp", f
oid = id
self.counter[(oid, type)].append((start, end))
count = len(self.counter[(oid, type)])
if type in ("mRNA", "gene"):
if type == "gene" and count > 1:
return
self.start = min(a for a, b in self.counter[(id, type)])
self.end = max(a for a, b in self.counter[(id, type)])
self.set_attribute("gene", "Alias", qual, g)
self.set_attribute("product", "Note", qual, g)
else:
suffix = ".{0}.{1}".format(type.lower(), count)
id = id + suffix
g.attributes["Parent"] = [oid]
self.set_attribute("product", "Note", qual, g)
g.attributes["ID"] = [id]
g.update_attributes()
print >> fw, g
self.current_id = oid
def print_gffline(self, fw, f, seqid, parent=None):
score = phase = "."
type = f.type
if type == "source":
type = "contig"
attr = "ID=tmp"
source = self.source
start = get_number(f.location.start) + 1
end = get_number(f.location.end)
strand = '-' if f.strand < 0 else '+'
g = "\t".join(str(x) for x in \
(seqid, source, type, start, end, score, strand, phase, attr))
g = GffLine(g)
qual = f.qualifiers
id = "tmp"
if MT in qual:
id = seqid
elif LT in qual:
id, = qual[LT]
else:
qual[LT] = [self.current_id]
id, = qual[LT]
id = id.split()[0]
if parent:
id, = parent.qualifiers[LT]
id = id.split()[0]
if type == 'CDS':
parent_id = id
self.counter[id] += 1
suffix = ".cds.{0}".format(self.counter[id])
id = parent_id + suffix
g.attributes["Parent"] = [parent_id]
assert id != "tmp", f
g.attributes["ID"] = [id]
if type == "mRNA":
g.attributes["Name"] = g.attributes["ID"]
if "product" in qual:
note, = qual["product"]
g.attributes["Note"] = [note]
if "pseudo" in qual:
note = "Pseudogene"
g.attributes["Note"] = [note]
g.update_attributes()
print >> fw, g
self.current_id = id
def print_gffline(self, fw, f, seqid, parent=None):
score = phase = "."
type = f.type
if type == "source":
type = "contig"
attr = "ID=tmp"
source = self.source
start = get_number(f.location.start) + 1
end = get_number(f.location.end)
strand = '-' if f.strand < 0 else '+'
g = "\t".join(str(x) for x in \
(seqid, source, type, start, end, score, strand, phase, attr))
g = GffLine(g)
qual = f.qualifiers
id = "tmp"
if MT in qual:
id = seqid
elif LT in qual:
id, = qual[LT]
else:
qual[LT] = [self.current_id]
id, = qual[LT]
id = id.split()[0]
if parent:
id, = parent.qualifiers[LT]
id = id.split()[0]
if type == 'CDS':
parent_id = id
self.counter[id] += 1
suffix = ".cds.{0}".format(self.counter[id])
id = parent_id + suffix
g.attributes["Parent"] = [parent_id]
assert id != "tmp", f
g.attributes["ID"] = [id]
if type == "mRNA":
g.attributes["Name"] = g.attributes["ID"]
if "product" in qual:
note, = qual["product"]
g.attributes["Note"] = [note]
if "pseudo" in qual:
note = "Pseudogene"
g.attributes["Note"] = [note]
g.update_attributes()
print >> fw, g
self.current_id = id
def print_gffline(self, fw, f, seqid, parent=None):
score = phase = "."
type = f.type
if type == "source":
type = "contig"
attr = "ID=tmp"
source = self.source
start = get_number(f.location.start) + 1
end = get_number(f.location.end)
strand = '-' if f.strand < 0 else '+'
g = "\t".join(str(x) for x in \
(seqid, source, type, start, end, score, strand, phase, attr))
g = GffLine(g)
qual = f.qualifiers
id = "tmp"
if MT in qual:
id = seqid
elif LT in qual:
id, = qual[LT]
else:
qual[LT] = [self.current_id]
id, = qual[LT]
id = id.split()[0]
if parent:
id, = parent.qualifiers[LT]
id = id.split()[0]
assert id != "tmp", f
oid = id
self.counter[(oid, type)].append((start, end))
count = len(self.counter[(oid, type)])
if type in ("mRNA", "gene"):
if type == "gene" and count > 1:
return
self.start = min(a for a, b in self.counter[(id, type)])
self.end = max(a for a, b in self.counter[(id, type)])
self.set_attribute("gene", "Alias", qual, g)
self.set_attribute("product", "Note", qual, g)
else:
suffix = ".{0}.{1}".format(type.lower(), count)
id = id + suffix
g.attributes["Parent"] = [oid]
self.set_attribute("product", "Note", qual, g)
g.attributes["ID"] = [id]
g.update_attributes()
print(g, file=fw)
self.current_id = oid
