Have you thought of using regular expressions?. It might make ur job easier.
Checkout this link good explaination of reg exps. Thanks and Regards, Mahendra Naik 2011/9/18 Gopalakrishnan Subramani <gopalakrishnan.subram...@gmail.com> > Senthil and Gora Mohanty pointed out whats wrong on the code. > > This is alternative option, not its best since I feel always good to parse > the file B based on file spec instead of the following approach. > > > file_a_lines = open('FileA.txt').readlines() > file_b_content = open('FileB.txt').read() > > for line in file_a_lines: > start_pos = file_b_content.find(line) > > if start_pos >= 0: > end_pos = file_b_content.find(">", start_pos + 1) > > if end_pos > 0: > print file_b_content[start_pos:end_pos] > else: # to deal with end of the line > print file_b_content[start_pos:] > > > > On Sat, Sep 17, 2011 at 7:49 PM, Senthil Kumaran <sent...@uthcode.com > >wrote: > > > On Fri, Sep 16, 2011 at 11:26:34PM -0500, Ananya Sharma wrote: > > > > > > *File A-* > > > >PSUB.GBD61H402FPT34:0-372 > > > > > > *File B-* > > > >PSUB.GBD61H402FPT34:0-372 > > > XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX > > > XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX > > > XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX > > > XXXXXXXXNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN > > > NNNNCATTTCCTTGAGTATTAGGCCATTCATGCTGTCAATTTTCTTAACT > > > ATTTGGAAATCCTAGTTGTACAAGATGGCCTTTTTCCCACCTGTATTTGC > > > TTGGTCTGTGTACTGTAGTCTGCCTCTGCAAATGTTGTGGGAGGACTAAA > > > TGTGGCGGGGGTGGGCTGACAG > > > > Here is the simplest scenario of your case. In this what do you want > > to do Ignore XXX...CAG in File-B and print only the >PSUB.? > > > > If that is the case, you could iterate over file-b and look for lines > > starting with > and then put them to a list and then do your > > operations. > > > > In your code: > > > > > f1=open('fileA','r') > > > f2=open('fileB','r') > > > a="" > > > b="" > > > > > for n in f1: > > > while not b.startswith(n): > > > b=f2.readline() > > > > This loop will break when f2 has line starting with >PSUB. > > > > > if len(a)>0: > > > print a > > > > Won't have any effect. > > > > > b="" > > > > You are resetting b. > > > > > while not b.startswith(">"): > > > a=a+f2.readline()+"__" > > > > > Won't have any effect. > > > > > > > > Any help would be highly appreciated. Thanks. > > > > Do you see why your program is not working when reduced to the > > simplest case? > > > > If you are trying to find entities in B which are in A. > > Just recreate B so that you remove all the non > starting lines and > > then compare. > > > > -- > > Senthil > > > > > > > > _______________________________________________ > > BangPypers mailing list > > BangPypers@python.org > > http://mail.python.org/mailman/listinfo/bangpypers > > > _______________________________________________ > BangPypers mailing list > BangPypers@python.org > http://mail.python.org/mailman/listinfo/bangpypers > _______________________________________________ BangPypers mailing list BangPypers@python.org http://mail.python.org/mailman/listinfo/bangpypers