Question

This code was established in a previous post. I’m trying to adapt it to fit our data. But it doesn’t work .. Here is an example of our file :

read:1424:2165 TGACCA/1:2165 TGACCA/2 
1..100  +chr1:3033296..3033395 #just this line
1..100  -chr1:3127494..3127395  
1..100  +chr1:3740372..3740471  

1 concordant    read:1483:2172 TGACCA/1:2172 TGACCA/2 
1..100  -chr7:94887644..94887545 #and just this line

This code should do the following :

1. search through each line
2. Recognize the string ‘read:’
3. Go to next line and extract what looks like ‘+chr:number..number’
   just once ! Then search for the next ‘read:’ etc…

So if I have “-chr : no..no” multiple times after “read:” that would only take the 1st one.

Unfortunately I cannot figure out how to get this to work…

    import re

    infile='myfile.txt'
    outfile='outfile.txt'

    pat1 = re.compile(r'read:')
    pat2 = re.compile(r'([+-])chr([^:]+):(\d+)\.\.(\d+)')

    with open(infile, mode='r') as in_f, open(outfile, mode='w') as out_f:
        for line in in_f.readlines():
            if '\t' not in line.rstrip():
                continue
            a = pat1.search(line)
            if a:
            m = pat2.search(line)
            out_f.write(' '.join(m.groups()) + '\n')
            if not a:
                continue

The output should look like that :

  1 3033293 3033395 
  7 94887644 94887545

Somebody throw me a bone please

Updated From Answer Below

Alright I’m uploading a slightly modified version from Tim McNamara that I use. It works well but the output doesn’t recognize number with two digit after “chr” and it prints a string after the last number

with open(infile, mode='r') as in_f, open(outfile, mode='w') as out_f:
    lines = [line for line in in_f.readlines()]
    for i, line in enumerate(lines):
       if 'read' in line:
            data = lines[i+1].replace(':', '..').split('..')
            try:
                out_f.write('{} {} {}\n'.format(data[1][-1], data[2], data[3])) #Here I tried to remove data[3] to avoid to have "start" in the output file.. didn't work .. 
            except IndexError:
                continue

Here is the output obtained with this code :

6 140302505 140302604 start  # 'start' is a string in our data after this number
5 46605561 46605462 start    # I don't understand why it grabs it thou...
5 46605423 46605522 start    # I tried to modify the code to avoid this, but ... didn't work out
6 29908310 29908409 start
6 29908462 29908363 start
4 12712132 12712231 start

How can I fix these two errors ?

Answer 1

Your big mistake is that you need to include readlines before you can iterate over ‘in_f’:

with open(infile, mode='r') as in_f, open(outfile, mode='w') as out_f:
    for line in in_f.readlines():
        ...

However, that whole section of code can probably be tidied up quite a bit.

with open(infile, mode='r') as in_f, open(outfile, mode='w') as out_f:
    lines = [line for line in in_f.readlines()]
    for i, line in enumerate(lines):
        if 'read' in line:
            data = lines[i+1].replace(':', '..').split('..')
            try:
                a = data[1].split('chr')[-1]
                b = data[2]
                c = data[3].split()[0]
                out_f.write('{} {} {}\n'.format(a, b, c))
            except IndexError:
                pass