[Tutor] help with loops

[bob gailer]

On 3/25/2010 11:34 AM, kumar s wrote:
> Dear group:
>
> I need some tips/help from experts.
>
> I have two files tab-delimted.
> One file is 4K lines. The other files is 40K lines.
>
> I want to search contents of a file to other and print those lines that satisfy.
>
>
> File 1:
> chr         X           Y
> chr1    8337733 8337767 NM_001042682_cds_0_0_chr1_8337734_r     0       -       RERE
> chr1    8338065 8338246 NM_001042682_cds_1_0_chr1_8338066_r     0       -       RERE
> chr1    8338746 8338893 NM_001042682_cds_2_0_chr1_8338747_r     0       -       RERE
> chr1    8340842 8341563 NM_001042682_cds_3_0_chr1_8340843_r     0       -       RERE
> chr1    8342410 8342633 NM_001042682_cds_4_0_chr1_8342411_r     0       -       RERE
>
>
> File 2:
> Chr          X         Y
> chr1    871490  871491
> chr1    925085  925086
> chr1    980143  980144
> chr1    1548655 1548656
> chr1    1589675 1589676
> chr1    1977853 1977854
> chr1    3384899 3384900
> chr1    3406309 3406310
> chr1    3732274 3732275
>
>
> I want to search if file 2 X is greater or less then X and Y and print line of file 2 and last column of file 1:
>
>    

I don't understand your desired result. Could you post a very simplified 
example of file1 and 2 and the desired result.

> for j in file2:
>          col = j.split('\t')
>           for k in file1:
>    

Note that the first time this loop is executed it will leave file2 at 
eof. Subsequent executions of this loop will process no lines as file2 
is at eof.
>           cols = k.split('\t')
>            if col[1]>  cols[1]:
>    

Note that this compares 2 strings; which may not give the same result as 
integer comparison.

>                   if col[1]<  cols[2]:
>                   print j +'\t'+cols[6]
>
>
> This prints a lot of duplicate lines and is slow.  Is there any other way I can make it fast.
>
> In file 1, how a dictionary can be made. I mean unique keys that are common to file 1 and 2.
>
> thanks
> Kumar.
>
>
>
>
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>    


-- 
Bob Gailer
919-636-4239
Chapel Hill NC