Question

I have a list of rules for a given input file for my function. If any of them are violated in the file given, I want my program to return an error message and quit.

• Every gene in the file should be on the same chromosome

Thus for a lines such as:

NM_001003443 chr11 + 5997152 5927598 5921052 5926098 1 5928752,5925972, 5927204,5396098,
NM_001003444 chr11 + 5925152 5926098 5925152 5926098 2 5925152,5925652, 5925404,5926098,
NM_001003489 chr11 + 5925145 5926093 5925115 5926045 4 5925151,5925762, 5987404,5908098,
etc.

Each line in the file will be variations of this line

Thus, I want to make sure every line in the file is on chr11

Yet I may be given a file with a different list of chr(and any number of numbers). Thus I want to write a function that will make sure whatever number is found on chr in the line is the same for every line.

Should I use a regular expression for this, or what should I do? This is in python by the way.

Such as: chr\d+ ?
I am unsure how to make sure that whatever is matched is the same in every line though…

I currently have:

from re import *
for line in file:
    r = 'chr\d+'
    i = search(r, line)
    if i in line:

but I don’t know how to make sure it is the same in every line…

In reference to sajattack’s answer

fp = open(infile, 'r')
for line in fp:
        filestring = ''
        filestring +=line
        chrlist = search('chr\d+', filestring)
        chrlist = chrlist.group()
        for chr in chrlist:
            if chr != chrlist[0]:
                print('Every gene in file not on same chromosome')

Answer 1

Just read the file and have a while loop check each line to make sure it contains chr11. There are string functions to search for substrings in a string. As soon as you find a line that returns false (does not contain chr11) then break out of the loop and set a flag valid = false.

import re

fp = open(infile, 'r')
fp.readline()
tar = re.findall(r'chr\d+', fp.readline())[0]
for line in fp:
    if (line.find(tar) == -1):
        print("Not valid")
        break

This should search for a number in the line and check for validity.