Question

So i’m trying to write a script that reads a file and extracts 2 values once a certain word is found. In this case, when the string ‘exon’ is encountered it will save the two integers that follow it.

I started by creating empty strings:

exon_start = []
exon_end = []

Here is an example of the simplified data I am using:

for line in data:
    print data

>>>

 exon            1..35
                 /gene="CDKN1A"

 CDS             73..567
                 /translation="MSEPAGDVRQNPCGSKACRRLFGPVDSEQLSRDCDALMAGCIQE
                 ARERWNFDFVTETPLEGDFAWERVRGLGLPKLYLPTGPRRGRDELGGGRRPGTSPALL
                 QGTAEEDHVDLSLSCTLVPRSGEQAEGSPGGPGDSQGRKRRQTSMTDFYHSKRRLIFS
                 KRKP"

 misc_feature    76..78
                 /gene="CDKN1A"


 exon            518..2106
                 /gene="CDKN1A"

I tried importing regular expression module for the re.findall() function:

indx_exon = range(0,len(data))

# so this relates each line of the data to a specific number in the index

i’m having trouble recognizing the ‘exon’ phrase within each individual line
first i just tried to identify which line of the text had the exon sequence to see if the re.findall() was working and I put:

for p,line in zip(indx_line,data):

    if re.findall(r'exon',line) is True:
        print p

and I got None

when I put:

for p,line in zip(indx_line,data):

    exon_test = re.findall(r'exon',line)
    print exon_test

i got a bunch of [] for the lines that did not contain ‘exon’
and for the lines the did contain ‘exon’ they gave me ‘exon’ . so i know that i can use the re.findall() feature to find every occurence of ‘exon’ within each of the strings

i just need to find out exactly how i can say when it finds the ‘exon’ it needs to look in that line until it finds ‘..’ and then append the integers flanking it to their corresponding lists; i.e.

exon_start = [1,518]
exon_end = [35,2106]

Answer 1

The problem is in if re.findall(r'exon',line) is True: line. Because re.finall() will not return True or False. Example:

>>> mystr = '123 exon'
>>> import re
>>> re.findall(r'exon', mystr)
['exon']
>>> re.findall(r'exon', mystr) is True
False
>>> bool(re.findall(r'exon',mystr))
True
>>> if re.findall(r'exon', mystr):
...     print 'true'
... 
true

Change the original code to:

for p,line in zip(indx_line,data):

    if re.findall(r'exon',line):
        print p

should make it work.

---

Edit: As @TimPietzcker pointed out, you don’t need to use re at all for this case. And to address your second question of getting the number flanking .., here is the code that could be helpful:

>>> line = ' exon            1..35'
>>> if 'exon' in line:
...     ranges = line.split()[1].split('..')
...     print ranges
...
['1', '35']