Ejemplo n.º 1
0
 def parseFrHitLine(self, line):
     cells=line.rstrip('\n\r').split('\t')
     self.read=cells[0]
     self.evalue=parseExp(cells[2])
     self.score=None
     self.mlen=cells[3]
     self.qstart=int(cells[4])
     self.qend=int(cells[5])
     self.pctid=float(cells[7])
     self.hit=cells[8]
     self.hstart=int(cells[9])
     self.hend=int(cells[10])
Ejemplo n.º 2
0
 def parseFrHitLine(self, line):
     cells = line.rstrip('\n\r').split('\t')
     self.read = cells[0]
     self.evalue = parseExp(cells[2])
     self.score = None
     self.mlen = cells[3]
     self.qstart = int(cells[4])
     self.qend = int(cells[5])
     self.pctid = float(cells[7])
     self.hit = cells[8]
     self.hstart = int(cells[9])
     self.hend = int(cells[10])
Ejemplo n.º 3
0
 def parseBlastPlusLine(self, line):
     cells=line.rstrip('\n\r').split('\t')
     self.read=cells[0]
     self.hit=cells[1]
     self.pctid=float(cells[2])
     self.mlen=int(cells[3])
     self.mismatch=int(cells[4])
     self.gaps=int(cells[5])
     self.qstart=int(cells[6])
     self.qend=int(cells[7])
     self.hstart=int(cells[8])
     self.hend=int(cells[9])
     self.evalue=parseExp(cells[10])
     self.score=float(cells[11])
Ejemplo n.º 4
0
 def parseGeneLine(self, line):
     cells=line.rstrip('\n\r').split('\t')
     self.read=cells[0]
     self.readDesc=cells[1]
     self.hit=cells[2]
     self.hitDesc=cells[3]
     self.pctid=float(cells[4])
     self.mlen=int(cells[5])
     self.qstart=int(cells[6])
     self.qend=int(cells[7])
     self.hstart=int(cells[8])
     self.hend=int(cells[9])
     self.score=float(cells[10])
     self.evalue=parseExp(cells[11])
     self.aln=float(cells[12])
Ejemplo n.º 5
0
 def parseYanmeiLine(self, line):
     cells = line.rstrip('\n\r').split('\t')
     self.read = cells[0]
     self.hit = cells[1]
     self.pctid = float(cells[2])
     self.mlen = int(cells[3])
     self.mismatch = int(cells[4])
     self.gaps = int(cells[5])
     self.qstart = int(cells[6])
     self.qend = int(cells[7])
     self.hstart = int(cells[8])
     self.hend = int(cells[9])
     self.evalue = parseExp(cells[10])
     self.score = float(cells[11])
     self.hitDesc = cells[12]
Ejemplo n.º 6
0
 def parseBlastPlusLine(self, line):
     if line[0] == '#':
         raise EmptyHitException("Comment line")
     cells = line.rstrip('\n\r').split('\t')
     self.read = cells[0]
     self.hit = cells[1]
     self.pctid = float(cells[2])
     self.mlen = int(cells[3])
     self.mismatch = int(cells[4])
     self.gaps = int(cells[5])
     self.qstart = int(cells[6])
     self.qend = int(cells[7])
     self.hstart = int(cells[8])
     self.hend = int(cells[9])
     self.evalue = parseExp(cells[10])
     self.score = float(cells[11])
Ejemplo n.º 7
0
 def parseBlastPlusLine(self, line):
     if line[0] == '#':
         raise EmptyHitException("Comment line")
     cells = line.rstrip('\n\r').split('\t')
     self.read = cells[0]
     self.hit = cells[1]
     self.pctid = float(cells[2])
     self.mlen = int(cells[3])
     self.mismatch = int(cells[4])
     self.gaps = int(cells[5])
     self.qstart = int(cells[6])
     self.qend = int(cells[7])
     self.hstart = int(cells[8])
     self.hend = int(cells[9])
     self.evalue = parseExp(cells[10])
     self.score = float(cells[11])
Ejemplo n.º 8
0
 def parseLizLine(self, line):
     cells = line.rstrip('\n\r').split('\t')
     self.read = cells[0]
     self.hit = cells[1]
     self.hitDesc = cells[2]
     try:
         self.pctid = float(cells[3])
     except ValueError:
         # leave unset if it's not a float
         pass
     self.mlen = int(cells[4])
     self.qstart = int(cells[5])
     self.qend = int(cells[6])
     self.hstart = int(cells[7])
     self.hend = int(cells[8])
     self.score = float(cells[9])
     self.evalue = parseExp(cells[10])
     self.aln = float(cells[11])
Ejemplo n.º 9
0
 def parseLizLine(self, line):
     cells = line.rstrip('\n\r').split('\t')
     self.read = cells[0]
     self.hit = cells[1]
     self.hitDesc = cells[2]
     try:
         self.pctid = float(cells[3])
     except:
         # leave unset if it's not a float
         pass
     self.mlen = int(cells[4])
     self.qstart = int(cells[5])
     self.qend = int(cells[6])
     self.hstart = int(cells[7])
     self.hend = int(cells[8])
     self.score = float(cells[9])
     self.evalue = parseExp(cells[10])
     self.aln = float(cells[11])