def GetCounts(FileName):
global Bases, Counts
Bases = {}
Counts = {}
Bases["Constrained"] = 0
Counts["Constrained"] = 0
gff.GetRecs(FileName, DoRec)
return Counts, Bases
print >> sys.stderr, sys.argv[0], "***ERROR***", s
sys.exit(1)
def DoRec():
global GeneIndexes
AttrDict = gff.GetAttrDict()
CurrGeneIndex = gff.GetIntAttr("gene_index", -1)
if CurrGeneIndex == -1:
gff.WriteRec(sys.stdout)
return
Key = gff.Label + "." + str(CurrGeneIndex)
if Key in GeneIndexes.keys():
NewGeneIndex = GeneIndexes[Key]
else:
NewGeneIndex = len(GeneIndexes)
GeneIndexes[Key] = NewGeneIndex
AttrDict["gene_index"] = NewGeneIndex
gff.SetAttrsFromDict(AttrDict)
gff.WriteRec(sys.stdout)
FileName = sys.argv[1]
GeneIndexes = {}
gff.GetRecs(FileName, DoRec)
print >> sys.stderr, len(GeneIndexes), "genes found"