Quick basic loop

Question

I have the following lines in a file. Here is an example of one line:

NM_???? chr12 - 10 110 10 110 3 10,50,100, 20,60,110,

I have the following code to get the info out:

fp = open(infile, 'r')
for line in fp:
     tokens = line.split()
     exonstarts = tokens[8][:-1].split(',')
     exonends = tokens[9][:-1].split(',')

This will give me a list like these:

exonstarts = [10,50,100]
exonends = [20,60,110]

This has 3 exons (ALTHOUGH OTHER LINES IN THE FILE MAY HAVE MORE OR LESS THAN 3, so this must work for any number of exons), and they go from:

 10-20
 50-60
 100-110

So for each number in the start list there is one in the finish list. Which means that the first codon start at exonstarts[0] and ends at exonends[0]. The second starts at exonstarts[1] and ends at exonends[1]. And so on.

How do I write the rest of this code so it pairs up the elements as such?

Update:

From this:

tokens = line.split()
exonstarts = tokens[8][:-1].split(',')
exonends = tokens[9][:-1].split(',')
zipped = list(zip(exonstarts, exonends))

I have another problem, I have a sting that I want these pieces of. So for example, I would want chr_string[10:20]+chr_string[50:60]+chr_string[100:110] Is there a way I could easily say this??

Sorry for the noob programming question. I just really need some help for the time crunch I have found myself in — Peter Hanson
– Peter Hanson, Commented Apr 28, 2012 at 0:02
No need to apologize Patrick, that's what the site is here for :) — John Sheehan
– John Sheehan, Commented Apr 28, 2012 at 0:05
@PatrickCampbell: In general, it's preferred that you open a new question for followups like that. — Bill Lynch
– Bill Lynch, Commented Apr 28, 2012 at 0:36
About your second question: try running that code. It should work. — Blender
– Blender, Commented Apr 28, 2012 at 0:36
Oh, I know it will work, but considering I will have a variable list of numbers and length, I cannot simply write that. I need some kind of variable or something to include in them — Peter Hanson
– Peter Hanson, Commented Apr 28, 2012 at 0:38

garnertb · Accepted Answer · 2012-04-28 00:04:11Z

3

The zip built-in is what your looking for:

>>> exonstarts = [10,50,100]
>>> exonends = [20,60,110]
>>> zip(exonstarts,exonends)
[(10, 20), (50, 60), (100, 110)]

answered Apr 28, 2012 at 0:04

garnertb

9,62439 silver badges38 bronze badges

Sign up to request clarification or add additional context in comments.

Comments

Bill Lynch · Accepted Answer · 2012-04-28 00:03:45Z

2

I believe you want the zip function.

In [1]: exonstarts = [10,50,100]

In [2]: exonends = [20,60,110]

In [3]: zip(exonstarts, exonends)
Out[3]: [(10, 20), (50, 60), (100, 110)]

answered Apr 28, 2012 at 0:03

Bill Lynch

82.3k16 gold badges132 silver badges181 bronze badges

4 Comments

Peter Hanson Over a year ago

Is the zip function built in? Because when I try zip(exonstarts, exonends) all I get back is <zip object at 0x0290A8C8>

Bill Lynch Over a year ago

The zip function is builtin unless you overwrote it. It was added in version 2.0

Bill Lynch Over a year ago

In python3, I believe it returns an iterator. Try list(zip(exonstarts, exonends))

johnsyweb Over a year ago

zip() returns an object in Python 3. Try list(zip(exonstarts, exonends)) to see the contents.

johnsyweb · Accepted Answer · 2012-04-28 00:52:30Z

0

You can get these pairs using zip():

>>> for t in zip(exonstarts, exonends):
...     print('%d-%d' % t)
... 
10-20
50-60
100-110

To get a list by slicing chr_string (which I have fabricated) using these pairs:

>>> [chr_string[start:end] for start,end in zip(exonstarts, exonends)]
['0506070809', '2526272829', '5051525354']

To join these together:

>>> ''.join(chr_string[start:end] for start,end in zip(exonstarts, exonends))
'050607080925262728295051525354'

edited Apr 28, 2012 at 0:52

answered Apr 28, 2012 at 0:17

johnsyweb

143k26 gold badges197 silver badges253 bronze badges

2 Comments

Peter Hanson Over a year ago

So, another problem, I have a sting that I want these pieces of. So for example, I would want chr_string[10:20]+chr_string[50:60]+chr_string[100:110] Is there a way I could easily say this??

johnsyweb Over a year ago

@PatrickCampbell: It would help if you explained the actual problem that you are trying to solve. See also: meta.stackexchange.com/questions/66377/what-is-the-xy-problem

Collectives™ on Stack Overflow

Quick basic loop

3 Answers 3

Comments

4 Comments

2 Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

3 Answers 3

Comments

4 Comments

2 Comments

Your Answer

Sign up or log in

Post as a guest

Related