Question

I just started learning python scripting yesterday and I’ve already gotten stuck. 🙁

So I have a data file with a lot of different information in various fields.

Formatted basically like…

Name (tab) Start# (tab) End# (tab) A bunch of fields I need but do not do anything with
Repeat

I need to write a script that takes the start and end numbers, and add/subtract a number accordingly depending on whether another field says + or -.

I know that I can replace words with something like this:

x = open("infile")
y = open("outfile","a")
while 1:
  line = f.readline()
  if not line: break
  line = line.replace("blah","blahblahblah")
  y.write(line + "\n")
y.close()

But I’ve looked at all sorts of different places and I can’t figure out how to extract specific fields from each line, read one field, and change other fields. I read that you can read the lines into arrays, but can’t seem to find out how to do it.

Any help would be great!

EDIT:

Example of a line from the data here: (Each | represents a tab character)

            |          |
            V          V
chr21 | 33025905 | 33031813 | ENST00000449339.1 | 0 | **-** | 33031813 | 33031813 | 0 | 3 | 1835,294,104, | 0,4341,5804,
chr21 | 33036618 | 33036795 | ENST00000458922.1 | 0 | **+** | 33036795 | 33036795 | 0 | 1 | 177,          | 0,

The second and third columns (indicated by arrows) would be the ones that I’d need to read/change.

Answer 1

You can use csv to do the splitting, although for these sorts of problems, I usually just use str.split:

with open(infile) as fin,open('outfile','w') as fout:
   for line in fin:
       #use line.split('\t'3) if the name of the field can contain spaces
       name,start,end,rest = line.split(None,3)  
       #do something to change start and end here.
       #Note that `start` and `end` are strings, but they can easily be changed
       #using `int` or `float` builtins.
       fout.write('\t'.join((name,start,end,rest)))

---

csv is nice if you want to split lines like this:

this is a "single argument"

into:

['this','is','a','single argument']

but it doesn’t seem like you need that here.