[Tutor] extract information from txtfile

[bob gailer]

On 10/4/2011 4:00 PM, Anna Olofsson wrote:
> Hi,
> I'm a beginner at Python and I'm trying to extract some information 
> from a textfile where I have a lot of data.
>
> The table looks something like this, but with many more columns and rows:
>
> # chr      Pos       ID       REF        ALT  . . . . . . . . . . .
>       1     13645      -           C             T
>       .           .          .            .              .
>       .           .          .            .              .
>
> I want to extract certain data from this table above and make it to a 
> sentence looking something like this:   chr1:13645 C/T
>
> I have created a pseudo code, just to get an overview of want I want 
> to do, looking like this:
>
> import OS
> open vcf_file.vcf
> for each line
>       words = 
> split(line)                                                                                                 
> # words[0] = 1 , words[1]=Pos , words[3]=REF , words[4]=ALT
>        if(words[0] not 
> "#"):                                                                                              
> #Sometimes the word starts with a hash and I don't want that to be 
> included.
>            str="chr" + words[0] + ":" + words[1] + "\t" + words[3] + 
> "/" + words[4]
>        score = OS.system(str)
> vcf_file.close()
>
> print result
>
> return score
>
>
> I'm not exactly sure how to proceed from here.

I suggest you convert the pseudo-code into a Pythin program, then run it.

If that gives you grief then tackle it one task at a time. For example, 
open, read, print, close a file. Then add another level of complication, 
for example open, read, split, print, close a file.

The part that makes no sense to me is score = OS.system(str). What will 
str be and what do you want system to return?

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

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