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
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