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I'm trying to remove specific characters from a string using Python. This is the code I'm using right now. Unfortunately it appears to do nothing to the string.
for char in line:
if char in " ?.!/;:":
line.replace(char,'')
How do I do this properly?
Strings in Python are immutable (can't be changed). Because of this, the effect of line.replace(...) is just to create a new string, rather than changing the old one. You need to rebind (assign) it to line in order to have that variable take the new value, with those characters removed.
Also, the way you are doing it is going to be kind of slow, relatively. It's also likely to be a bit confusing to experienced pythonators, who will see a doubly-nested structure and think for a moment that something more complicated is going on.
Starting in Python 2.6 and newer Python 2.x versions *, you can instead use str.translate, (see Python 3 answer below):
line = line.translate(None, '!##$')
or regular expression replacement with re.sub
import re
line = re.sub('[!##$]', '', line)
The characters enclosed in brackets constitute a character class. Any characters in line which are in that class are replaced with the second parameter to sub: an empty string.
Python 3 answer
In Python 3, strings are Unicode. You'll have to translate a little differently. kevpie mentions this in a comment on one of the answers, and it's noted in the documentation for str.translate.
When calling the translate method of a Unicode string, you cannot pass the second parameter that we used above. You also can't pass None as the first parameter. Instead, you pass a translation table (usually a dictionary) as the only parameter. This table maps the ordinal values of characters (i.e. the result of calling ord on them) to the ordinal values of the characters which should replace them, or—usefully to us—None to indicate that they should be deleted.
So to do the above dance with a Unicode string you would call something like
translation_table = dict.fromkeys(map(ord, '!##$'), None)
unicode_line = unicode_line.translate(translation_table)
Here dict.fromkeys and map are used to succinctly generate a dictionary containing
{ord('!'): None, ord('#'): None, ...}
Even simpler, as another answer puts it, create the translation table in place:
unicode_line = unicode_line.translate({ord(c): None for c in '!##$'})
Or, as brought up by Joseph Lee, create the same translation table with str.maketrans:
unicode_line = unicode_line.translate(str.maketrans('', '', '!##$'))
* for compatibility with earlier Pythons, you can create a "null" translation table to pass in place of None:
import string
line = line.translate(string.maketrans('', ''), '!##$')
Here string.maketrans is used to create a translation table, which is just a string containing the characters with ordinal values 0 to 255.
Am I missing the point here, or is it just the following:
string = "ab1cd1ef"
string = string.replace("1", "")
print(string)
# result: "abcdef"
Put it in a loop:
a = "a!b#c#d$"
b = "!##$"
for char in b:
a = a.replace(char, "")
print(a)
# result: "abcd"
>>> line = "abc##!?efg12;:?"
>>> ''.join( c for c in line if c not in '?:!/;' )
'abc##efg12'
With re.sub regular expression
Since Python 3.5, substitution using regular expressions re.sub became available:
import re
re.sub('\ |\?|\.|\!|\/|\;|\:', '', line)
Example
import re
line = 'Q: Do I write ;/.??? No!!!'
re.sub('\ |\?|\.|\!|\/|\;|\:', '', line)
'QDoIwriteNo'
Explanation
In regular expressions (regex), | is a logical OR and \ escapes spaces and special characters that might be actual regex commands. Whereas sub stands for substitution, in this case with the empty string ''.
The asker almost had it. Like most things in Python, the answer is simpler than you think.
>>> line = "H E?.LL!/;O:: "
>>> for char in ' ?.!/;:':
... line = line.replace(char,'')
...
>>> print line
HELLO
You don't have to do the nested if/for loop thing, but you DO need to check each character individually.
For the inverse requirement of only allowing certain characters in a string, you can use regular expressions with a set complement operator [^ABCabc]. For example, to remove everything except ascii letters, digits, and the hyphen:
>>> import string
>>> import re
>>>
>>> phrase = ' There were "nine" (9) chick-peas in my pocket!!! '
>>> allow = string.letters + string.digits + '-'
>>> re.sub('[^%s]' % allow, '', phrase)
'Therewerenine9chick-peasinmypocket'
From the python regular expression documentation:
Characters that are not within a range can be matched by complementing
the set. If the first character of the set is '^', all the characters
that are not in the set will be matched. For example, [^5] will match
any character except '5', and [^^] will match any character except
'^'. ^ has no special meaning if it’s not the first character in the
set.
line = line.translate(None, " ?.!/;:")
>>> s = 'a1b2c3'
>>> ''.join(c for c in s if c not in '123')
'abc'
Strings are immutable in Python. The replace method returns a new string after the replacement. Try:
for char in line:
if char in " ?.!/;:":
line = line.replace(char,'')
This is identical to your original code, with the addition of an assignment to line inside the loop.
Note that the string replace() method replaces all of the occurrences of the character in the string, so you can do better by using replace() for each character you want to remove, instead of looping over each character in your string.
I was surprised that no one had yet recommended using the builtin filter function.
import operator
import string # only for the example you could use a custom string
s = "1212edjaq"
Say we want to filter out everything that isn't a number. Using the filter builtin method "...is equivalent to the generator expression (item for item in iterable if function(item))" [Python 3 Builtins: Filter]
sList = list(s)
intsList = list(string.digits)
obj = filter(lambda x: operator.contains(intsList, x), sList)))
In Python 3 this returns
>> <filter object # hex>
To get a printed string,
nums = "".join(list(obj))
print(nums)
>> "1212"
I am not sure how filter ranks in terms of efficiency but it is a good thing to know how to use when doing list comprehensions and such.
UPDATE
Logically, since filter works you could also use list comprehension and from what I have read it is supposed to be more efficient because lambdas are the wall street hedge fund managers of the programming function world. Another plus is that it is a one-liner that doesnt require any imports. For example, using the same string 's' defined above,
num = "".join([i for i in s if i.isdigit()])
That's it. The return will be a string of all the characters that are digits in the original string.
If you have a specific list of acceptable/unacceptable characters you need only adjust the 'if' part of the list comprehension.
target_chars = "".join([i for i in s if i in some_list])
or alternatively,
target_chars = "".join([i for i in s if i not in some_list])
Using filter, you'd just need one line
line = filter(lambda char: char not in " ?.!/;:", line)
This treats the string as an iterable and checks every character if the lambda returns True:
>>> help(filter)
Help on built-in function filter in module __builtin__:
filter(...)
filter(function or None, sequence) -> list, tuple, or string
Return those items of sequence for which function(item) is true. If
function is None, return the items that are true. If sequence is a tuple
or string, return the same type, else return a list.
Try this one:
def rm_char(original_str, need2rm):
''' Remove charecters in "need2rm" from "original_str" '''
return original_str.translate(str.maketrans('','',need2rm))
This method works well in Python 3
Here's some possible ways to achieve this task:
def attempt1(string):
return "".join([v for v in string if v not in ("a", "e", "i", "o", "u")])
def attempt2(string):
for v in ("a", "e", "i", "o", "u"):
string = string.replace(v, "")
return string
def attempt3(string):
import re
for v in ("a", "e", "i", "o", "u"):
string = re.sub(v, "", string)
return string
def attempt4(string):
return string.replace("a", "").replace("e", "").replace("i", "").replace("o", "").replace("u", "")
for attempt in [attempt1, attempt2, attempt3, attempt4]:
print(attempt("murcielago"))
PS: Instead using " ?.!/;:" the examples use the vowels... and yeah, "murcielago" is the Spanish word to say bat... funny word as it contains all the vowels :)
PS2: If you're interested on performance you could measure these attempts with a simple code like:
import timeit
K = 1000000
for i in range(1,5):
t = timeit.Timer(
f"attempt{i}('murcielago')",
setup=f"from __main__ import attempt{i}"
).repeat(1, K)
print(f"attempt{i}",min(t))
In my box you'd get:
attempt1 2.2334518376057244
attempt2 1.8806643818474513
attempt3 7.214925774955572
attempt4 1.7271184513757465
So it seems attempt4 is the fastest one for this particular input.
Here's my Python 2/3 compatible version. Since the translate api has changed.
def remove(str_, chars):
"""Removes each char in `chars` from `str_`.
Args:
str_: String to remove characters from
chars: String of to-be removed characters
Returns:
A copy of str_ with `chars` removed
Example:
remove("What?!?: darn;", " ?.!:;") => 'Whatdarn'
"""
try:
# Python2.x
return str_.translate(None, chars)
except TypeError:
# Python 3.x
table = {ord(char): None for char in chars}
return str_.translate(table)
#!/usr/bin/python
import re
strs = "how^ much for{} the maple syrup? $20.99? That's[] ricidulous!!!"
print strs
nstr = re.sub(r'[?|$|.|!|a|b]',r' ',strs)#i have taken special character to remove but any #character can be added here
print nstr
nestr = re.sub(r'[^a-zA-Z0-9 ]',r'',nstr)#for removing special character
print nestr
You can also use a function in order to substitute different kind of regular expression or other pattern with the use of a list. With that, you can mixed regular expression, character class, and really basic text pattern. It's really useful when you need to substitute a lot of elements like HTML ones.
*NB: works with Python 3.x
import re # Regular expression library
def string_cleanup(x, notwanted):
for item in notwanted:
x = re.sub(item, '', x)
return x
line = "<title>My example: <strong>A text %very% $clean!!</strong></title>"
print("Uncleaned: ", line)
# Get rid of html elements
html_elements = ["<title>", "</title>", "<strong>", "</strong>"]
line = string_cleanup(line, html_elements)
print("1st clean: ", line)
# Get rid of special characters
special_chars = ["[!##$]", "%"]
line = string_cleanup(line, special_chars)
print("2nd clean: ", line)
In the function string_cleanup, it takes your string x and your list notwanted as arguments. For each item in that list of elements or pattern, if a substitute is needed it will be done.
The output:
Uncleaned: <title>My example: <strong>A text %very% $clean!!</strong></title>
1st clean: My example: A text %very% $clean!!
2nd clean: My example: A text very clean
My method I'd use probably wouldn't work as efficiently, but it is massively simple. I can remove multiple characters at different positions all at once, using slicing and formatting.
Here's an example:
words = "things"
removed = "%s%s" % (words[:3], words[-1:])
This will result in 'removed' holding the word 'this'.
Formatting can be very helpful for printing variables midway through a print string. It can insert any data type using a % followed by the variable's data type; all data types can use %s, and floats (aka decimals) and integers can use %d.
Slicing can be used for intricate control over strings. When I put words[:3], it allows me to select all the characters in the string from the beginning (the colon is before the number, this will mean 'from the beginning to') to the 4th character (it includes the 4th character). The reason 3 equals till the 4th position is because Python starts at 0. Then, when I put word[-1:], it means the 2nd last character to the end (the colon is behind the number). Putting -1 will make Python count from the last character, rather than the first. Again, Python will start at 0. So, word[-1:] basically means 'from the second last character to the end of the string.
So, by cutting off the characters before the character I want to remove and the characters after and sandwiching them together, I can remove the unwanted character. Think of it like a sausage. In the middle it's dirty, so I want to get rid of it. I simply cut off the two ends I want then put them together without the unwanted part in the middle.
If I want to remove multiple consecutive characters, I simply shift the numbers around in the [] (slicing part). Or if I want to remove multiple characters from different positions, I can simply sandwich together multiple slices at once.
Examples:
words = "control"
removed = "%s%s" % (words[:2], words[-2:])
removed equals 'cool'.
words = "impacts"
removed = "%s%s%s" % (words[1], words[3:5], words[-1])
removed equals 'macs'.
In this case, [3:5] means character at position 3 through character at position 5 (excluding the character at the final position).
Remember, Python starts counting at 0, so you will need to as well.
In Python 3.5
e.g.,
os.rename(file_name, file_name.translate({ord(c): None for c in '0123456789'}))
To remove all the number from the string
How about this:
def text_cleanup(text):
new = ""
for i in text:
if i not in " ?.!/;:":
new += i
return new
Below one.. with out using regular expression concept..
ipstring ="text with symbols!##$^&*( ends here"
opstring=''
for i in ipstring:
if i.isalnum()==1 or i==' ':
opstring+=i
pass
print opstring
Recursive split:
s=string ; chars=chars to remove
def strip(s,chars):
if len(s)==1:
return "" if s in chars else s
return strip(s[0:int(len(s)/2)],chars) + strip(s[int(len(s)/2):len(s)],chars)
example:
print(strip("Hello!","lo")) #He!
You could use the re module's regular expression replacement. Using the ^ expression allows you to pick exactly what you want from your string.
import re
text = "This is absurd!"
text = re.sub("[^a-zA-Z]","",text) # Keeps only Alphabets
print(text)
Output to this would be "Thisisabsurd". Only things specified after the ^ symbol will appear.
# for each file on a directory, rename filename
file_list = os.listdir (r"D:\Dev\Python")
for file_name in file_list:
os.rename(file_name, re.sub(r'\d+','',file_name))
Even the below approach works
line = "a,b,c,d,e"
alpha = list(line)
while ',' in alpha:
alpha.remove(',')
finalString = ''.join(alpha)
print(finalString)
output: abcde
The string method replace does not modify the original string. It leaves the original alone and returns a modified copy.
What you want is something like: line = line.replace(char,'')
def replace_all(line, )for char in line:
if char in " ?.!/;:":
line = line.replace(char,'')
return line
However, creating a new string each and every time that a character is removed is very inefficient. I recommend the following instead:
def replace_all(line, baddies, *):
"""
The following is documentation on how to use the class,
without reference to the implementation details:
For implementation notes, please see comments begining with `#`
in the source file.
[*crickets chirp*]
"""
is_bad = lambda ch, baddies=baddies: return ch in baddies
filter_baddies = lambda ch, *, is_bad=is_bad: "" if is_bad(ch) else ch
mahp = replace_all.map(filter_baddies, line)
return replace_all.join('', join(mahp))
# -------------------------------------------------
# WHY `baddies=baddies`?!?
# `is_bad=is_bad`
# -------------------------------------------------
# Default arguments to a lambda function are evaluated
# at the same time as when a lambda function is
# **defined**.
#
# global variables of a lambda function
# are evaluated when the lambda function is
# **called**
#
# The following prints "as yellow as snow"
#
# fleece_color = "white"
# little_lamb = lambda end: return "as " + fleece_color + end
#
# # sometime later...
#
# fleece_color = "yellow"
# print(little_lamb(" as snow"))
# --------------------------------------------------
replace_all.map = map
replace_all.join = str.join
If you want your string to be just allowed characters by using ASCII codes, you can use this piece of code:
for char in s:
if ord(char) < 96 or ord(char) > 123:
s = s.replace(char, "")
It will remove all the characters beyond a....z even upper cases.
I have a long string that is a phylogenetic tree and I want to do a very specific filtering.
(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;
Basically every x#y is a species#gene_id information. What I am trying to do is trimming this down so that I will only have x instead of x#y.
(Esy, Aar,(Spa,Cpl))...
I tried splitting the string first but the problem is string has different 'split points' for what I want to achieve i.e. some parts x#y is ending with a , and others with a ). I searched for a solution and saw regular expression operations, but I am new to Python and I couldn't be sure if that is what I should be focusing on. I also thought about strip() but it seems like I need to specify the characters to be stripped for this.
Main problem is there is no 'pattern' for me to tell Python to follow. Only thing is that all species ids are 3 letters and they are before an # character.
Is there a method that can do what I want? I will be really glad if you can help me out with my problem. Thanks in advance.
Give this a try:
import re:
pat = re.compile(r'(\w{3})#')
txt = "(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;"
pat.findall(t)
Result:
['Esy', 'Aar', 'Spa', 'Cpl', 'Bst', 'Aly', 'Ath', 'Chi', 'Cru', 'Hco', 'Hlo', 'Hla', 'Hse', 'Esa', 'Aal']
If you need the structure intact, we can try to remove the unnecessary parts instead:
pat = re.compile(r'(#|:)[^/),]*')
pat.sub('',t).replace(',', ', ')
Result:
'(Esy, Aar, ((Spa, Cpl), (((Bst, ((Aly, Ath), (Chi, Cru))), (((Hco, Hlo), Hla), Hse)), (Esa, Aal))))'
Regex demo
How about this kind of function:
def parse_string(string):
new_string = ''
skip = False
for char in string:
if char == '#':
skip = True
if char == ',':
skip = False
if not skip or char in ['(', ')']:
new_string += char
return new_string
Calling it on your string:
string = '(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;'
parse_string(string)
> '(Esy,Aar,((Spa,Cpl),(((Bst,((Aly,Ath),(Chi,Cru))),(((Hco,Hlo),Hla),Hse)),(Esa,Aal))))'
you can use regex:
import re
s = "(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;"
p = "...?(?=#)|\(|\)"
result = re.findall(p, s)
and you have your result as a list, so you can make it string or do anything with it
for explaining what is happening :
p is regular expression pattern
so in this pattern:
. means matching any word
...?(?=#) means match any word until I get to a word ? wich ? is #, so this whole pattern means that you get any three words before #
| is or statement, I used it here to find another pattern
and the rest of them is to find ) and (
Try this regex if you need the brackets in the output:
import re
regex = r"#[A-Za-z0-9_\.:]+|[0-9:\.;e-]+"
phylogenetic_tree = "(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;"
print(re.sub(regex,"",phylogenetic_tree))
Output:
(Esy,Aar,((Spa,Cpl),(((Bst,((Aly,Ath),(Chi,Cru))),(((Hco,Hlo),Hla),Hs)),(Esa,Aal))))
Because you are trying to parse a phylogenetic tree, I highly suggest to let BioPython do the heavy lifting for you.
You can easily parse and display a phylogenetic with Bio.Phylo. Then it is just iterating over all tree elements and splitting the names at the 'at'-sign.
Because Phylo expects the input to be in a file, we create an in-memory file-like object with io.StringIO. Getting the complete tree is then as easy as
Phylo.read(io.StringIO(s), 'newick')
In order to check if the parsed tree looks sane, I print it once with print(tree).
Now we want to change all node names that contain a '#'. With tree.find_elements we get access to all nodes. Some nodes don't have a name and some might not contain a '#'. So to be extra careful, we first check if n.name and '#' in n.name. Only then do we split each node's name at the '#' and take just the first part (index 0) of it:
n.name = n.name.split('#')[0]
In order to recreate the initial string representation, we use Phylo.write:
out = io.StringIO()
Phylo.write(tree, out, "newick")
print(out.getvalue())
Again, write wants to get a file argument - if we just want to get a string, we can use a StringIO object again.
Full code:
import io
from Bio import Phylo
if __name__ == '__main__':
s = '(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;'
tree = Phylo.read(io.StringIO(s), 'newick')
print(' before '.center(20, '='))
print(tree)
for n in tree.find_elements():
if n.name and '#' in n.name:
n.name = n.name.split('#')[0]
print(' result '.center(20, '='))
out = io.StringIO()
Phylo.write(tree, out, "newick")
print(out.getvalue())
Output:
====== before ======
Tree(rooted=False, weight=1.0)
Clade(branch_length=0.0129090235079)
Clade(branch_length=0.0726396855636, name='Esy#ESY15_g64743_DN3_SP7_c0')
Clade(branch_length=0.137507902808, name='Aar#AA_maker7399_1')
Clade(branch_length=0.0129090235079)
Clade(branch_length=9.05326020871e-05)
Clade(branch_length=0.0318934795022, name='Spa#Tp2g18720')
Clade(branch_length=0.0273465005242, name='Cpl#CP2_g48793_DN3_SP8_c')
Clade(branch_length=0.00328120860999)
Clade(branch_length=0.00859075940423)
Clade(branch_length=0.0340484449097)
Clade(branch_length=0.0332592496158, name='Bst#Bostr_13083s0053_1')
Clade(branch_length=0.0150356382287)
Clade(branch_length=0.0205924636564)
Clade(branch_length=0.0328569260951, name='Aly#AL8G21130_t1')
Clade(branch_length=0.0391706378372, name='Ath#AT5G48370_1')
Clade(branch_length=0.00998579652059)
Clade(branch_length=0.0954469923893, name='Chi#CARHR183840_1')
Clade(branch_length=0.0570981548016, name='Cru#Carubv10026342m')
Clade(branch_length=0.0372829371381)
Clade(branch_length=0.0206478928557)
Clade(branch_length=0.0144626717872)
Clade(branch_length=0.00823215335663, name='Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100')
Clade(branch_length=0.0085462978729, name='Hlo#DN13684_c0_g1_i1_p1')
Clade(branch_length=0.0225079453622, name='Hla#DN22821_c0_g1_i1_p1')
Clade(branch_length=0.048590776459, name='Hse#DN23412_c0_g1_i3_p1')
Clade(branch_length=1.00000050003e-06)
Clade(branch_length=0.0378509854703, name='Esa#Thhalv10004228m')
Clade(branch_length=0.0712272454125, name='Aal#Aa_G102140_t1')
==== result =====
(Esy:0.07264,Aar:0.13751,((Spa:0.03189,Cpl:0.02735):0.00009,(((Bst:0.03326,((Aly:0.03286,Ath:0.03917):0.02059,(Chi:0.09545,Cru:0.05710):0.00999):0.01504):0.03405,(((Hco:0.00823,Hlo:0.00855):0.01446,Hla:0.02251):0.02065,Hse:0.04859):0.03728):0.00859,(Esa:0.03785,Aal:0.07123):0.00000):0.00328):0.01291):0.01291;
The default format of Phylo uses less digits than in your original tree. In order to keep the numbers unchanged, just override the branch length format string with a '%s':
Phylo.write(tree, out, "newick", format_branch_length="%s")
Parsing code can be hard to follow. Tatsu lets you write readable parsing code by combining grammars and python:
text = "(Esy#ESY15_g64743_DN3_SP7_c0:0.0726396855636,Aar#AA_maker7399_1:0.137507902808,((Spa#Tp2g18720:0.0318934795022,Cpl#CP2_g48793_DN3_SP8_c:0.0273465005242):9.05326020871e-05,(((Bst#Bostr_13083s0053_1:0.0332592496158,((Aly#AL8G21130_t1:0.0328569260951,Ath#AT5G48370_1:0.0391706378372):0.0205924636564,(Chi#CARHR183840_1:0.0954469923893,Cru#Carubv10026342m:0.0570981548016):0.00998579652059):0.0150356382287):0.0340484449097,(((Hco#scaff1034_g23864_DN3_SP8_c_TE35_CDS100:0.00823215335663,Hlo#DN13684_c0_g1_i1_p1:0.0085462978729):0.0144626717872,Hla#DN22821_c0_g1_i1_p1:0.0225079453622):0.0206478928557,Hse#DN23412_c0_g1_i3_p1:0.048590776459):0.0372829371381):0.00859075940423,(Esa#Thhalv10004228m:0.0378509854703,Aal#Aa_G102140_t1:0.0712272454125):1.00000050003e-06):0.00328120860999):0.0129090235079):0.0129090235079;"
import sys
import tatsu
grammar = """
start = things ';'
;
things = thing [ ',' things ]
;
thing = x '#' y ':' number
| '(' things ')' ':' number
;
x = /\w+/
;
y = /\w+/
;
number = /[+-]?\d+\.?\d*(e?[+-]?\d*)/
;
"""
class Semantics:
def x(self, ast):
# the method name matches the rule name
print('X =', ast)
parser = tatsu.compile(grammar, semantics=Semantics())
parser.parse(text)
I can use this code below to create a new file with the substitution of a with aa using regular expressions.
import re
with open("notes.txt") as text:
new_text = re.sub("a", "aa", text.read())
with open("notes2.txt", "w") as result:
result.write(new_text)
I was wondering do I have to use this line, new_text = re.sub("a", "aa", text.read()), multiple times but substitute the string for others letters that I want to change in order to change more than one letter in my text?
That is, so a-->aa,b--> bb and c--> cc.
So I have to write that line for all the letters I want to change or is there an easier way. Perhaps to create a "dictionary" of translations. Should I put those letters into an array? I'm not sure how to call on them if I do.
The answer proposed by #nhahtdh is valid, but I would argue less pythonic than the canonical example, which uses code less opaque than his regex manipulations and takes advantage of python's built-in data structures and anonymous function feature.
A dictionary of translations makes sense in this context. In fact, that's how the Python Cookbook does it, as shown in this example (copied from ActiveState http://code.activestate.com/recipes/81330-single-pass-multiple-replace/ )
import re
def multiple_replace(dict, text):
# Create a regular expression from the dictionary keys
regex = re.compile("(%s)" % "|".join(map(re.escape, dict.keys())))
# For each match, look-up corresponding value in dictionary
return regex.sub(lambda mo: dict[mo.string[mo.start():mo.end()]], text)
if __name__ == "__main__":
text = "Larry Wall is the creator of Perl"
dict = {
"Larry Wall" : "Guido van Rossum",
"creator" : "Benevolent Dictator for Life",
"Perl" : "Python",
}
print multiple_replace(dict, text)
So in your case, you could make a dict trans = {"a": "aa", "b": "bb"} and then pass it into multiple_replace along with the text you want translated. Basically all that function is doing is creating one huge regex containing all of your regexes to translate, then when one is found, passing a lambda function to regex.sub to perform the translation dictionary lookup.
You could use this function while reading from your file, for example:
with open("notes.txt") as text:
new_text = multiple_replace(replacements, text.read())
with open("notes2.txt", "w") as result:
result.write(new_text)
I've actually used this exact method in production, in a case where I needed to translate the months of the year from Czech into English for a web scraping task.
As #nhahtdh pointed out, one downside to this approach is that it is not prefix-free: dictionary keys that are prefixes of other dictionary keys will cause the method to break.
You can use capturing group and backreference:
re.sub(r"([characters])", r"\1\1", text.read())
Put characters that you want to double up in between []. For the case of lower case a, b, c:
re.sub(r"([abc])", r"\1\1", text.read())
In the replacement string, you can refer to whatever matched by a capturing group () with \n notation where n is some positive integer (0 excluded). \1 refers to the first capturing group. There is another notation \g<n> where n can be any non-negative integer (0 allowed); \g<0> will refer to the whole text matched by the expression.
If you want to double up all characters except new line:
re.sub(r"(.)", r"\1\1", text.read())
If you want to double up all characters (new line included):
re.sub(r"(.)", r"\1\1", text.read(), 0, re.S)
You can use the pandas library and the replace function. I represent one example with five replacements:
df = pd.DataFrame({'text': ['Billy is going to visit Rome in November', 'I was born in 10/10/2010', 'I will be there at 20:00']})
to_replace=['Billy','Rome','January|February|March|April|May|June|July|August|September|October|November|December', '\d{2}:\d{2}', '\d{2}/\d{2}/\d{4}']
replace_with=['name','city','month','time', 'date']
print(df.text.replace(to_replace, replace_with, regex=True))
And the modified text is:
0 name is going to visit city in month
1 I was born in date
2 I will be there at time
You can find the example here
None of the other solutions work if your patterns are themselves regexes.
For that, you need:
def multi_sub(pairs, s):
def repl_func(m):
# only one group will be present, use the corresponding match
return next(
repl
for (patt, repl), group in zip(pairs, m.groups())
if group is not None
)
pattern = '|'.join("({})".format(patt) for patt, _ in pairs)
return re.sub(pattern, repl_func, s)
Which can be used as:
>>> multi_sub([
... ('a+b', 'Ab'),
... ('b', 'B'),
... ('a+', 'A.'),
... ], "aabbaa") # matches as (aab)(b)(aa)
'AbBA.'
Note that this solution does not allow you to put capturing groups in your regexes, or use them in replacements.
Using tips from how to make a 'stringy' class, we can make an object identical to a string but for an extra sub method:
import re
class Substitutable(str):
def __new__(cls, *args, **kwargs):
newobj = str.__new__(cls, *args, **kwargs)
newobj.sub = lambda fro,to: Substitutable(re.sub(fro, to, newobj))
return newobj
This allows to use the builder pattern, which looks nicer, but works only for a pre-determined number of substitutions. If you use it in a loop, there is no point creating an extra class anymore. E.g.
>>> h = Substitutable('horse')
>>> h
'horse'
>>> h.sub('h', 'f')
'forse'
>>> h.sub('h', 'f').sub('f','h')
'horse'
I found I had to modify Emmett J. Butler's code by changing the lambda function to use myDict.get(mo.group(1),mo.group(1)). The original code wasn't working for me; using myDict.get() also provides the benefit of a default value if a key is not found.
OIDNameContraction = {
'Fucntion':'Func',
'operated':'Operated',
'Asist':'Assist',
'Detection':'Det',
'Control':'Ctrl',
'Function':'Func'
}
replacementDictRegex = re.compile("(%s)" % "|".join(map(re.escape, OIDNameContraction.keys())))
oidDescriptionStr = replacementDictRegex.sub(lambda mo:OIDNameContraction.get(mo.group(1),mo.group(1)), oidDescriptionStr)
If you dealing with files, I have a simple python code about this problem.
More info here.
import re
def multiple_replace(dictionary, text):
# Create a regular expression from the dictionaryary keys
regex = re.compile("(%s)" % "|".join(map(re.escape, dictionary.keys())))
# For each match, look-up corresponding value in dictionaryary
String = lambda mo: dictionary[mo.string[mo.start():mo.end()]]
return regex.sub(String , text)
if __name__ == "__main__":
dictionary = {
"Wiley Online Library" : "Wiley",
"Chemical Society Reviews" : "Chem. Soc. Rev.",
}
with open ('LightBib.bib', 'r') as Bib_read:
with open ('Abbreviated.bib', 'w') as Bib_write:
read_lines = Bib_read.readlines()
for rows in read_lines:
#print(rows)
text = rows
new_text = multiple_replace(dictionary, text)
#print(new_text)
Bib_write.write(new_text)
Based on Eric's great answer, I came up with a more general solution that is capable of handling capturing groups and backreferences:
import re
from itertools import islice
def multiple_replace(s, repl_dict):
groups_no = [re.compile(pattern).groups for pattern in repl_dict]
def repl_func(m):
all_groups = m.groups()
# Use 'i' as the index within 'all_groups' and 'j' as the main
# group index.
i, j = 0, 0
while i < len(all_groups) and all_groups[i] is None:
# Skip the inner groups and move on to the next group.
i += (groups_no[j] + 1)
# Advance the main group index.
j += 1
# Extract the pattern and replacement at the j-th position.
pattern, repl = next(islice(repl_dict.items(), j, j + 1))
return re.sub(pattern, repl, all_groups[i])
# Create the full pattern using the keys of 'repl_dict'.
full_pattern = '|'.join(f'({pattern})' for pattern in repl_dict)
return re.sub(full_pattern, repl_func, s)
Example. Calling the above with
s = 'This is a sample string. Which is getting replaced. 1234-5678.'
REPL_DICT = {
r'(.*?)is(.*?)ing(.*?)ch': r'\3-\2-\1',
r'replaced': 'REPLACED',
r'\d\d((\d)(\d)-(\d)(\d))\d\d': r'__\5\4__\3\2__',
r'get|ing': '!##'
}
gives:
>>> multiple_replace(s, REPL_DICT)
'. Whi- is a sample str-Th is !##t!## REPLACED. __65__43__.'
For a more efficient solution, one can create a simple wrapper to precompute groups_no and full_pattern, e.g.
import re
from itertools import islice
class ReplWrapper:
def __init__(self, repl_dict):
self.repl_dict = repl_dict
self.groups_no = [re.compile(pattern).groups for pattern in repl_dict]
self.full_pattern = '|'.join(f'({pattern})' for pattern in repl_dict)
def get_pattern_repl(self, pos):
return next(islice(self.repl_dict.items(), pos, pos + 1))
def multiple_replace(self, s):
def repl_func(m):
all_groups = m.groups()
# Use 'i' as the index within 'all_groups' and 'j' as the main
# group index.
i, j = 0, 0
while i < len(all_groups) and all_groups[i] is None:
# Skip the inner groups and move on to the next group.
i += (self.groups_no[j] + 1)
# Advance the main group index.
j += 1
return re.sub(*self.get_pattern_repl(j), all_groups[i])
return re.sub(self.full_pattern, repl_func, s)
Use it as follows:
>>> ReplWrapper(REPL_DICT).multiple_replace(s)
'. Whi- is a sample str-Th is !##t!## REPLACED. __65__43__.'
I dont know why most of the solutions try to compose a single regex pattern instead of replacing multiple times. This answer is just for the sake of completeness.
That being said, the output of this approach is different than the output of the combined regex approach. Namely, repeated substitutions may evolve the text over time. However, the following function returns the same output as a call to unix sed would:
def multi_replace(rules, data: str) -> str:
ret = data
for pattern, repl in rules:
ret = re.sub(pattern, repl, ret)
return ret
usage:
RULES = [
(r'a', r'b'),
(r'b', r'c'),
(r'c', r'd'),
]
multi_replace(RULES, 'ab') # output: dd
With the same input and rules, the other solutions will output "bc". Depending on your use case you may or may not want to replace strings consecutively. In my case I wanted to rebuild the sed behavior. Also, note that the order of rules matters. If you reverse the rule order, this example would also return "bc".
This solution is faster than combining the patterns into a single regex (by a factor of 100). So, if your use-case allows it, you should prefer the repeated substitution method.
Of course, you can compile the regex patterns:
class Sed:
def __init__(self, rules) -> None:
self._rules = [(re.compile(pattern), sub) for pattern, sub in rules]
def replace(self, data: str) -> str:
ret = data
for regx, repl in self._rules:
ret = regx.sub(repl, ret)
return ret
This question already has answers here:
Match a whole word in a string using dynamic regex
(1 answer)
Word boundary with words starting or ending with special characters gives unexpected results
(2 answers)
Closed 4 years ago.
I have a script that runs into my text and search and replace all the sentences I write based in a database.
The script:
with open('C:/Users/User/Desktop/Portuguesetranslator.txt') as f:
for l in f:
s = l.split('*')
editor.replace(s[0],s[1])
And the Database example:
Event*Evento*
result*resultado*
And so on...
Now what is happening is that I need the "whole word only" in that script, because I'm finding myself with problems.
For example with Result and Event, because when I replace for Resultado and Evento, and I run the script one more time in the text the script replace again the Resultado and Evento.
And the result after I run the script stays like this Resultadoado and Eventoo.
Just so you guys know.. Its not only for Event and Result, there is more then 1000+ sentences that I already set for the search and replace to work..
I don't need a simples search and replace for two words.. because I'm going to be editing the database over and over for different sentences..
You want a regular expression. You can use the token \b to match a word boundary: i.e., \bresult\b would match only the exact word "result."
import re
with open('C:/Users/User/Desktop/Portuguesetranslator.txt') as f:
for l in f:
s = l.split('*')
editor = re.sub(r"\b%s\b" % s[0] , s[1], editor)
Use re.sub:
replacements = {'the':'a',
'this':'that'}
def replace(match):
return replacements[match.group(0)]
# notice that the 'this' in 'thistle' is not matched
print re.sub('|'.join(r'\b%s\b' % re.escape(s) for s in replacements),
replace, 'the cat has this thistle.')
Prints
a cat has that thistle.
Notes:
All the strings to be replaced are joined into a single pattern so
that the string needs to be looped over just once.
The source strings are passed to re.escape to make avoid
interpreting them as regular expressions.
The words are surrounded by r'\b' to make sure matches are for
whole words only.
A replacement function is used so that any match can be replaced.
Use re.sub instead of normal string replace to replace only whole words.So your script,even if it runs again will not replace the already replaced words.
>>> import re
>>> editor = "This is result of the match"
>>> new_editor = re.sub(r"\bresult\b","resultado",editor)
>>> new_editor
'This is resultado of the match'
>>> newest_editor = re.sub(r"\bresult\b","resultado",new_editor)
>>> newest_editor
'This is resultado of the match'
It is very simple. use re.sub, don't use replace.
import re
replacements = {r'\bthe\b':'a',
r'\bthis\b':'that'}
def replace_all(text, dic):
for i, j in dic.iteritems():
text = re.sub(i,j,text)
return text
replace_all("the cat has this thistle.", replacements)
It will print
a cat has that thistle.
import re
match = {} # create a dictionary of words-to-replace and words-to-replace-with
f = open("filename", "r")
data = f.read() # string of all file content
def replace_all(text, dic):
for i, j in dic.items():
text = re.sub(r"\b%s\b" % i, j, text)
# r"\b%s\b"% enables replacing by whole word matches only
return text
data = replace_all(data, match)
print(data) # you can copy and paste the result to whatever file you like
Suppose I have a string like this:
"key1=value1;key2=value2;key3=(key3.1=value3.1;key3.2=value3.2)"
I would like to get a dictionary corresponding to the above, where the value for key3 is the string
"(key3.1=value3.1;key3.2=value3.2)"
and eventually the corresponding sub-dictionary.
I know how to split the string at the semicolons, but how can I tell the parser to ignore the semicolon between parentheses?
This includes potentially nested parentheses.
Currently I am using an ad-hoc routine that looks for pairs of matching parentheses, "clears" its content, gets split positions and applies them to the original string, but this does not appear very elegant, there must be some prepackaged pythonic way to do this.
If anyone is interested, here is the code I am currently using:
def pparams(parameters, sep=';', defs='=', brc='()'):
'''
unpackages parameter string to struct
for example, pippo(a=21;b=35;c=pluto(h=zzz;y=mmm);d=2d3f) becomes:
a: '21'
b: '35'
c.fn: 'pluto'
c.h='zzz'
d: '2d3f'
fn_: 'pippo'
'''
ob=strfind(parameters,brc[0])
dp=strfind(parameters,defs)
out={}
if len(ob)>0:
if ob[0]<dp[0]:
#opening function
out['fn_']=parameters[:ob[0]]
parameters=parameters[(ob[0]+1):-1]
if len(dp)>0:
temp=smart_tokenize(parameters,sep,brc);
for v in temp:
defp=strfind(v,defs)
pname=v[:defp[0]]
pval=v[1+defp[0]:]
if len(strfind(pval,brc[0]))>0:
out[pname]=pparams(pval,sep,defs,brc);
else:
out[pname]=pval
else:
out['fn_']=parameters
return out
def smart_tokenize( instr, sep=';', brc='()' ):
'''
tokenize string ignoring separators contained within brc
'''
tstr=instr;
ob=strfind(instr,brc[0])
while len(ob)>0:
cb=findclsbrc(tstr,ob[0])
tstr=tstr[:ob[0]]+'?'*(cb-ob[0]+1)+tstr[cb+1:]
ob=strfind(tstr,brc[1])
sepp=[-1]+strfind(tstr,sep)+[len(instr)+1]
out=[]
for i in range(1,len(sepp)):
out.append(instr[(sepp[i-1]+1):(sepp[i])])
return out
def findclsbrc(instr, brc_pos, brc='()'):
'''
given a string containing an opening bracket, finds the
corresponding closing bracket
'''
tstr=instr[brc_pos:]
o=strfind(tstr,brc[0])
c=strfind(tstr,brc[1])
p=o+c
p.sort()
s1=[1 if v in o else 0 for v in p]
s2=[-1 if v in c else 0 for v in p]
s=[s1v+s2v for s1v,s2v in zip(s1,s2)]
s=[sum(s[:i+1]) for i in range(len(s))] #cumsum
return p[s.index(0)]+brc_pos
def strfind(instr, substr):
'''
returns starting position of each occurrence of substr within instr
'''
i=0
out=[]
while i<=len(instr):
try:
p=instr[i:].index(substr)
out.append(i+p)
i+=p+1
except:
i=len(instr)+1
return out
If you want to build a real parser, use one of the Python parsing libraries, like PLY or PyParsing. If you figure such a full-fledged library is overkill for the task at hand, go for some hack like the one you already have. I'm pretty sure there is no clean few-line solution without an external library.
Expanding on Sven Marnach's answer, here's an example of a pyparsing grammar that should work for you:
from pyparsing import (ZeroOrMore, Word, printables, Forward,
Group, Suppress, Dict)
collection = Forward()
simple_value = Word(printables, excludeChars='()=;')
key = simple_value
inner_collection = Suppress('(') + collection + Suppress(')')
value = simple_value ^ inner_collection
key_and_value = Group(key + Suppress('=') + value)
collection << Dict(key_and_value + ZeroOrMore(Suppress(';') + key_and_value))
coll = collection.parseString(
"key1=value1;key2=value2;key3=(key3.1=value3.1;key3.2=value3.2)")
print coll['key1'] # value1
print coll['key2'] # value2
print coll['key3']['key3.1'] # value3.1
You could use a regex to capture the groups:
>>> import re
>>> s = "key1=value1;key2=value2;key3=(key3.1=value3.1;key3.2=value3.2)"
>>> r = re.compile('(\w+)=(\w+|\([^)]+\));?')
>>> dict(r.findall(s))
This regex says:
(\w)+ # Find and capture a group with 1 or more word characters (letters, digits, underscores)
= # Followed by the literal character '='
(\w+ # Followed by a group with 1 or more word characters
|\([^)]+\) # or a group that starts with an open paren (parens escaped with '\(' or \')'), followed by anything up until a closed paren, which terminates the alternate grouping
);? # optionally this grouping might be followed by a semicolon.
Gotta say, kind of a strange grammar. You should consider using a more standard format. If you need guidance choosing one maybe ask another question. Good luck!