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())
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 print "Loading a file, manually adjust to a local BAM file or will fail " bamParser = uParser("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BAM/H2AZ.bam","BAM") bed6writer = uWriter("","BED6") someToken = uToken() print "Get first entry and write to standard output in bed6" someToken = bamParser.get_next_entry() bed6writer.write_token(someToken) bed6writer = uWriter("current.txt","BED6") bed6writer =bamParser.get_next_entry() #while (A.eof()==0): # C.write_token(A.get_next_entry())
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()
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("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BED/bedH2AZ.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 "BAM" A = uParser("/home/local/USHERBROOKE/nora2001/Work/class/NGS_testing/data/BAM/H2AZ.bam","BAM") B = uToken() B = A.get_next_entry() print A.eof()