[Tutor] Using Regular Expression to extracting string in brackets on a list
Hello, I am trying to rewrite some contents on a long list that contains words within brackets and outside brackets and I'm having trouble extracting the words within brackets, especially since I have to add the append function for list as well. Does anyone have any suggestions? Thank you! *An example of list*: ['hypothetical protein BRAFLDRAFT_208408 [Branchiostoma floridae]\n', 'hypoxia-inducible factor 1-alpha [Mus musculus]\n', 'hypoxia-inducible factor 1-alpha [Gallus gallus]\n' ] *What I'm trying to extract out of this*: ['Branchiostoma floridae', 'Mus musculus', 'Gallus gallus'] ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Using Regular Expression to extracting string in brackets on a list
On Sun, Dec 29, 2013 at 4:02 PM, Jing Ai jai...@g.rwu.edu wrote: Hello, I am trying to rewrite some contents on a long list that contains words within brackets and outside brackets and I'm having trouble extracting the words within brackets, especially since I have to add the append function for list as well. Does anyone have any suggestions? Thank you! *An example of list*: ['hypothetical protein BRAFLDRAFT_208408 [Branchiostoma floridae]\n', 'hypoxia-inducible factor 1-alpha [Mus musculus]\n', 'hypoxia-inducible factor 1-alpha [Gallus gallus]\n' ] Is the above line a python list, or is it what you get when you read a line of a data file. The reason I ask, is if it is a list you can split the list by looping of each list item. Then just maybe try some of these ideas: http://stackoverflow.com/questions/10017147/python-replace-characters-in-string *What I'm trying to extract out of this*: ['Branchiostoma floridae', 'Mus musculus', 'Gallus gallus'] ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor -- Joel Goldstick http://joelgoldstick.com ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Using Regular Expression to extracting string in brackets on a list
On Sun, Dec 29, 2013 at 04:02:01PM -0500, Jing Ai wrote:
Hello,
I am trying to rewrite some contents on a long list that contains words
within brackets and outside brackets and I'm having trouble extracting the
words within brackets, especially since I have to add the append function
for list as well. Does anyone have any suggestions? Thank you!
*An example of list*:
['hypothetical protein BRAFLDRAFT_208408 [Branchiostoma floridae]\n',
'hypoxia-inducible factor 1-alpha [Mus musculus]\n', 'hypoxia-inducible
factor 1-alpha [Gallus gallus]\n' ]
*What I'm trying to extract out of this*:
['Branchiostoma floridae', 'Mus musculus', 'Gallus gallus']
You have a list of strings. Each string has exactly one pair of square
brackets []. You want the content of the square brackets.
Start with a function that extracts the content of the square brackets
from a single string.
def extract(s):
start = s.find('[')
if start == -1:
# No opening bracket found. Should this be an error?
return ''
start += 1 # skip the bracket, move to the next character
end = s.find(']', start)
if end == -1:
# No closing bracket found after the opening bracket.
# Should this be an error instead?
return s[start:]
else:
return s[start:end]
Let's test it and see if it works:
py s = 'hypothetical protein BRAFLDRAFT_208408 [Branchiostoma floridae]\n'
py extract(s)
'Branchiostoma floridae'
So far so good. Now let's write a loop:
names = []
for line in list_of_strings:
names.append(extract(line))
where list_of_strings is your big list like the example above.
We can simplify the loop by using a list comprehension:
names = [extract(line) for line in list_of_strings]
If you prefer to use a regular expression, that's simple enough. Here's
a new version of the extract function:
import re
def extract(s):
mo = re.search(r'\[(.*)\]', s)
if mo:
return mo.group(1)
return ''
The list comprehension remains the same.
--
Steven
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Re: [Tutor] Using Regular Expression to extracting string in brackets on a list
On Sun, Dec 29, 2013 at 9:00 PM, Jing Ai jai...@g.rwu.edu wrote: Thanks, but I don't think I can get out the string in the brackets by only replacing other items...(there's too many things to replace and may interfere with the items within the string). I am not sure what you mean by your previous sentence. Check out Steven's excellent answer. Also, remember to reply to the list, or no one will see your question. Good luck On Sun, Dec 29, 2013 at 7:08 PM, Joel Goldstick joel.goldst...@gmail.comwrote: On Sun, Dec 29, 2013 at 4:02 PM, Jing Ai jai...@g.rwu.edu wrote: Hello, I am trying to rewrite some contents on a long list that contains words within brackets and outside brackets and I'm having trouble extracting the words within brackets, especially since I have to add the append function for list as well. Does anyone have any suggestions? Thank you! *An example of list*: ['hypothetical protein BRAFLDRAFT_208408 [Branchiostoma floridae]\n', 'hypoxia-inducible factor 1-alpha [Mus musculus]\n', 'hypoxia-inducible factor 1-alpha [Gallus gallus]\n' ] Is the above line a python list, or is it what you get when you read a line of a data file. The reason I ask, is if it is a list you can split the list by looping of each list item. Then just maybe try some of these ideas: http://stackoverflow.com/questions/10017147/python-replace-characters-in-string *What I'm trying to extract out of this*: ['Branchiostoma floridae', 'Mus musculus', 'Gallus gallus'] ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor -- Joel Goldstick http://joelgoldstick.com -- Joel Goldstick http://joelgoldstick.com ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Using Regular Expression to extracting string in brackets on a list
Thank you all for the suggestions! I decided to use Steven's re loop in the end. Joel, what i meant earlier was that the link you sent seems to suggest me to replace some characters in the list and I'm not sure how it would work... On Sun, Dec 29, 2013 at 9:24 PM, Joel Goldstick joel.goldst...@gmail.comwrote: On Sun, Dec 29, 2013 at 9:00 PM, Jing Ai jai...@g.rwu.edu wrote: Thanks, but I don't think I can get out the string in the brackets by only replacing other items...(there's too many things to replace and may interfere with the items within the string). I am not sure what you mean by your previous sentence. Check out Steven's excellent answer. Also, remember to reply to the list, or no one will see your question. Good luck On Sun, Dec 29, 2013 at 7:08 PM, Joel Goldstick joel.goldst...@gmail.com wrote: On Sun, Dec 29, 2013 at 4:02 PM, Jing Ai jai...@g.rwu.edu wrote: Hello, I am trying to rewrite some contents on a long list that contains words within brackets and outside brackets and I'm having trouble extracting the words within brackets, especially since I have to add the append function for list as well. Does anyone have any suggestions? Thank you! *An example of list*: ['hypothetical protein BRAFLDRAFT_208408 [Branchiostoma floridae]\n', 'hypoxia-inducible factor 1-alpha [Mus musculus]\n', 'hypoxia-inducible factor 1-alpha [Gallus gallus]\n' ] Is the above line a python list, or is it what you get when you read a line of a data file. The reason I ask, is if it is a list you can split the list by looping of each list item. Then just maybe try some of these ideas: http://stackoverflow.com/questions/10017147/python-replace-characters-in-string *What I'm trying to extract out of this*: ['Branchiostoma floridae', 'Mus musculus', 'Gallus gallus'] ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor -- Joel Goldstick http://joelgoldstick.com -- Joel Goldstick http://joelgoldstick.com ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Using Regular Expression to extracting string in brackets on a list
Steven's answer is probably a lot more robust, but I would use a simple split. mylist = ['hypothetical protein BRAFLDRAFT_208408 [Branchiostoma floridae]\n', 'hypoxia-inducible factor 1-alpha [Mus musculus]\n', 'hypoxia-inducible factor 1-alpha [Gallus gallus]\n' ] for item in mylist: item.split([)[1].split(])[0] -- Bodsda On 30 December 2013 03:28, Jing Ai jai...@g.rwu.edu wrote: Thank you all for the suggestions! I decided to use Steven's re loop in the end. Joel, what i meant earlier was that the link you sent seems to suggest me to replace some characters in the list and I'm not sure how it would work... On Sun, Dec 29, 2013 at 9:24 PM, Joel Goldstick joel.goldst...@gmail.comwrote: On Sun, Dec 29, 2013 at 9:00 PM, Jing Ai jai...@g.rwu.edu wrote: Thanks, but I don't think I can get out the string in the brackets by only replacing other items...(there's too many things to replace and may interfere with the items within the string). I am not sure what you mean by your previous sentence. Check out Steven's excellent answer. Also, remember to reply to the list, or no one will see your question. Good luck On Sun, Dec 29, 2013 at 7:08 PM, Joel Goldstick joel.goldst...@gmail.com wrote: On Sun, Dec 29, 2013 at 4:02 PM, Jing Ai jai...@g.rwu.edu wrote: Hello, I am trying to rewrite some contents on a long list that contains words within brackets and outside brackets and I'm having trouble extracting the words within brackets, especially since I have to add the append function for list as well. Does anyone have any suggestions? Thank you! *An example of list*: ['hypothetical protein BRAFLDRAFT_208408 [Branchiostoma floridae]\n', 'hypoxia-inducible factor 1-alpha [Mus musculus]\n', 'hypoxia-inducible factor 1-alpha [Gallus gallus]\n' ] Is the above line a python list, or is it what you get when you read a line of a data file. The reason I ask, is if it is a list you can split the list by looping of each list item. Then just maybe try some of these ideas: http://stackoverflow.com/questions/10017147/python-replace-characters-in-string *What I'm trying to extract out of this*: ['Branchiostoma floridae', 'Mus musculus', 'Gallus gallus'] ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor -- Joel Goldstick http://joelgoldstick.com -- Joel Goldstick http://joelgoldstick.com ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
