def parse(self):
self.curr_line = FileReader.nextLine(self)
while self.curr_line:
if not self.curr_line:
return
self.parseLine(self.curr_line)
self.curr_line = FileReader.nextLine(self)
def nextGene(self):
if not self.curr_line:
tmpgene = self.curr_gene
self.curr_gene = None
return tmpgene
while self.curr_line:
feat = self.parseLine(self.curr_line)
self.addFeature(feat)
#print "CCCC %s %s"%(self.curr_geneid,feat.hid)
tmpid = self.curr_geneid
self.curr_feat = feat
self.curr_geneid = feat.hitattr['gene_id']
self.curr_gene = self.genes[self.curr_geneid]
self.curr_line = FileReader.nextLine(self)
# print "Got feat %s [%s]"%(feat.hid,self.curr_geneid)
if tmpid and feat.hitattr['gene_id'] != tmpid:
return tmpid
def nextFeature(self):
if not self.curr_line:
return
while self.curr_line.startswith("#"):
self.curr_line = FileReader.nextLine(self)
line = self.curr_line
feat = self.parseLine(self.curr_line)
self.addFeature(feat)
self.curr_line = FileReader.nextLine(self)
return feat
def __init__(self, file):
super(FileReader, self).__init__()
self.filename = file
self.fh = open(file)
self.lnum = 0
self.queryhits = {}
self.targethits = {}
self.curr_line = FileReader.nextLine(self)
def nextFeature(self):
line = self.curr_line
if not self.curr_line:
return
feat = self.parseLine(self.curr_line)
self.addFeature(feat)
self.curr_line = FileReader.nextLine(self)
return feat
def __init__(self,file):
super(FileReader,self).__init__()
# Why? Just why?
self.filename = file
self.fh = open(file)
self.lnum = 0
self.genes = {}
self.curr_line = FileReader.nextLine(self)
self.curr_geneid = None
self.curr_feat = None
self.curr_gene = None
