def OnSeq(Label, Seq):
global MissingRankCount
global EmptyTaxCount
global BadLevelCount
global SeqCount
SeqCount += 1
Acc = utax2.GetAccFromLabel(Label)
Acc = Acc.replace("_", "")
TaxStr = utax2.GetTaxFromLabel(Label)
Fields = TaxStr.split(',')
if len(Fields) != RequiredLevelCount:
BadLevelCount += 1
return
MotTaxStr = ""
LastRankIndex = -1
LastLevelChar = ""
for Field in Fields:
assert Field[1] == ':'
LevelChar = Field[0]
RankIndex = utax2.LevelCharToRankIndex(LevelChar)
if LastRankIndex != -1 and LastRankIndex > 1 and not RankIndex == LastRankIndex + 1:
MissingRankCount += 1
# print >> sys.stderr, "Missing rank: %c,%d %c,%d %s" % (LastLevelChar, LastRankIndex, LevelChar, RankIndex, TaxStr)
break
LastRankIndex = RankIndex
LastLevelChar = LevelChar
if MotTaxStr != "":
MotTaxStr += ';'
MotTaxStr += LevelChar + ":" + Field[2:]
if MotTaxStr == "":
EmptyTaxCount += 1
return
MotTaxStr += ";"
fasta.WriteSeq(fFa, Seq, Acc)
print >> fTax, Acc + "\t" + MotTaxStr
def OnSeq(Label, Seq):
global Missing
Acc = utax2.GetAccFromLabel(Label)
Family = utax2.GetNameFromLabel(Label, 'f')
Genus = utax2.GetNameFromLabel(Label, 'g')
Species = utax2.GetNameFromLabel(Label, 's')
if Genus == "" or Species == "":
Missing += 1
return
if Family == "":
Family = "NA"
Family = Family.replace("f:", "")
Genus = Genus.replace("g:", "")
Species = Species.replace("s:", "")
NewLabel = Acc + "\t" + Species + "\t" + Genus + "\t" + Family
fasta.WriteSeq(sys.stdout, Seq, NewLabel)