def get_next_entry(self):
toReturn = uToken()
toReturn.obj = self.libNGS.getNextEntry_parser(self.obj)
return toReturn
toReturn = uToken()
toReturn.obj = self.libNGS.getNextEntry_parser(self.obj)
return toReturn
def get_previous_raw(self):
self.libNGS.getPreviousRaw_parser.restype = c_char_p
return self.libNGS.getPreviousRaw_parser(self.obj)
def get_unformated_header(self):
self.libNGS.getUnformatedHeader_parser.restype = c_char_p
return self.libNGS.getUnformatedHeader_parser(self.obj)
if __name__ == "__main__":
A = uParser("data/sample.bed", "BED")
B = uToken()
B = A.get_next_entry()
print A.eof()
while (A.eof() == 0):
B = A.get_next_entry()
print A.eof()
if (B.is_param_set("CHR", 0)):
print(B.get_param("CHR", 0))
print A.get_previous_raw()
print A.get_unformated_header()
print "SAM"
A = uParser("data/sample.sam", "SAM")
B = uToken()
B = A.get_next_entry()
print A.eof()
def get_next_entry(self):
toReturn =uToken()
toReturn.obj= self.libNGS.getNextEntry_parser(self.obj)
return toReturn
if (filename!=""):
self.obj = self.libNGS.new_Writer(filename,typename)
else:
self.obj = self.libNGS.new_cout_Writer(typename)
def __del__(self):
self.libNGS.delete_Writer(self.obj)
def write_token(self,token):
self.libNGS.writeToken_writer(self.obj,token.obj)
def write_string(self, text):
self.libNGS.printString_Writer(self.obj,text)
if __name__=="__main__":
from uParser_wrapper import uParser
samParser = uParser("data/sample.sam","SAM")
bed6writer = uWriter("","BED6")
someToken = uToken()
print "Get first entry and write to standard output in bed6 to current.txt"
someToken = samParser.get_next_entry()
bed6writer.write_token(someToken)
bed6writer = uWriter("current.txt","BED6")
bed6writer.write_token(samParser.get_next_entry())
toReturn =uToken()
toReturn.obj= self.libNGS.getNextEntry_parser(self.obj)
return toReturn
def get_previous_raw(self):
self.libNGS.getPreviousRaw_parser.restype=c_char_p
return self.libNGS.getPreviousRaw_parser(self.obj)
def get_unformated_header(self):
self.libNGS.getUnformatedHeader_parser.restype=c_char_p
return self.libNGS.getUnformatedHeader_parser(self.obj)
if __name__=="__main__":
A = uParser("data/sample.bed","BED")
B = uToken()
B = A.get_next_entry()
print A.eof()
while (A.eof()==0):
B = A.get_next_entry()
print A.eof()
if (B.is_param_set("CHR",0)):
print (B.get_param("CHR",0))
print A.get_previous_raw()
print A.get_unformated_header()
print "SAM"
A = uParser("data/sample.sam","SAM")
B = uToken()
B = A.get_next_entry()
print A.eof()
