Fgt the link
http://code.google.com/edu/languages/google-python-class/regular-expressions.html
2011/9/19 mahendra N <mahendra0...@gmail.com>
> 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
>> >
>> >
>> >
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>> >
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>
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