[Tutor] extract information from txtfile

[Anna Olofsson]

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.

Best,
Anna
 		 	   		  
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