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])
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])
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])
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])
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]
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])
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])
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])
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])