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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 am trying to write a regex in Python to extract some information from a string.
Given:
"Only in Api_git/Api/folder A: new.txt"
I would like to print:
Folder Path: Api_git/Api/folder A
Filename: new.txt
After having a look at some examples on the re manual page, I'm still a bit stuck.
This is what I've tried so far
m = re.match(r"(Only in ?P<folder_path>\w+:?P<filename>\w+)","Only in Api_git/Api/folder A: new.txt")
print m.group('folder_path')
print m.group('filename')
Can anybody point me in the right direction??
Get the matched group from index 1 and 2 using capturing groups.
^Only in ([^:]*): (.*)$
Here is demo
sample code:
import re
p = re.compile(ur'^Only in ([^:]*): (.*)$')
test_str = u"Only in Api_git/Api/folder A: new.txt"
re.findall(p, test_str)
If you want to print in the below format then try with substitution.
Folder Path: Api_git/Api/folder A
Filename: new.txt
DEMO
sample code:
import re
p = re.compile(ur'^Only in ([^:]*): (.*)$')
test_str = u"Only in Api_git/Api/folder A: new.txt"
subst = u"Folder Path: $1\nFilename: $2"
result = re.sub(p, subst, test_str)
Your pattern: (Only in ?P<folder_path>\w+:?P<filename>\w+) has a few flaws in it.
The ?P construct is only valid as the first bit inside a parenthesized expression,
so we need this.
(Only in (?P<folder_path>\w+):(?P<filename>\w+))
The \w character class is only for letters and underscores. It won't match / or ., for example. We need to use a different character class that more closely aligns with requirements. In fact, we can just use ., the class of nearly all characters:
(Only in (?P<folder_path>.+):(?P<filename>.+))
The colon has a space after it in your example text. We need to match it:
(Only in (?P<folder_path>.+): (?P<filename>.+))
The outermost parentheses are not needed. They aren't wrong, just not needed:
Only in (?P<folder_path>.+): (?P<filename>.+)
It is often convenient to provide the regular expression separate from the call to the regular expression engine. This is easily accomplished by creating a new variable, for example:
regex = r'Only in (?P<folder_path>.+): (?P<filename>.+)'
... # several lines later
m = re.match(regex, "Only in Api_git/Api/folder A: new.txt")
The above is purely for the convenience of the programmer: it neither saves nor squanders time or memory space. There is, however, a technique that can save some of the time involved in regular expressions: compiling.
Consider this code segment:
regex = r'Only in (?P<folder_path>.+): (?P<filename>.+)'
for line in input_file:
m = re.match(regex, line)
...
For each iteration of the loop, the regular expression engine must interpret the regular expression and apply it to the line variable. The re module allows us to separate the interpretation from the application; we can interpret once but apply several times:
regex = re.compile(r'Only in (?P<folder_path>.+): (?P<filename>.+)')
for line in input_file:
m = re.match(regex, line)
...
Now, your original program should look like this:
regex = re.compile(r'Only in (?P<folder_path>.+): (?P<filename>.+)')
m = re.match(regex, "Only in Api_git/Api/folder A: new.txt")
print m.group('folder_path')
print m.group('filename')
However, I'm a fan of using comments to explain regular expressions. My version, including some general cleanup, looks like this:
import re
regex = re.compile(r'''(?x) # Verbose
Only\ in\ # Literal match
(?P<folder_path>.+) # match longest sequence of anything, and put in 'folder_path'
:\ # Literal match
(?P<filename>.+) # match longest sequence of anything and put in 'filename'
''')
with open('diff.out') as input_file:
for line in input_file:
m = re.match(regex, line)
if m:
print m.group('folder_path')
print m.group('filename')
It really depends on the limitation of the input, if this is the only input this will do the trick.
^Only in (?P<folder_path>[a-zA-Z_/ ]*): (?P<filename>[a-z]*.txt)$
I wrote a script to catch and correct commands before they are read by a parser. The parser requires equal, not equal, greater, etc, entries to be separated by commas, such as:
'test(a>=b)' is wrong
'test(a,>=,b)' is correct
The script i wrote works fine, but i would love to know if there's a more efficient way to do this.
Here's my script:
# Correction routine
def corrector(exp):
def rep(exp,a,b):
foo = ''
while(True):
foo = exp.replace(a,b)
if foo == exp:
return exp
exp = foo
# Replace all instances with a unique identifier. Do it in a specific order
# so for example we catch an instance of '>=' before we get to '='
items = ['>=','<=','!=','==','>','<','=']
for i in range(len(items)):
exp = rep(exp,items[i],'###%s###'%i)
# Re-add items with commas
for i in range(len(items)):
exp = exp.replace('###%s###'%i,',%s,'%items[i])
# Remove accidental double commas we may have added
return exp.replace(',,',',')
print corrector('wrong_syntax(b>=c) correct_syntax(b,>=,c)')
// RESULT: wrong_syntax(b,>=,c) correct_syntax(b,>=,c)
thanks!
As mentioned in the comments, one approach would be to use a regular expression. The following regex matches any of your operators when they are not surrounded by commas, and replaces them with the same string with the commas inserted:
inputstring = 'wrong_syntax(b>=c) correct_syntax(b,>=,c)'
regex = r"([^,])(>=|<=|!=|==|>|<|=)([^,])"
replace = r"\1,\2,\3"
result = re.sub(regex, replace, inputstring)
print(result)
Simple regexes are relatively easy, but they can get complicated quickly. Check out the docs for more info:
http://docs.python.org/2/library/re.html
Here is a regex that will do what you asked:
import re
regex = re.compile(r'''
(?<!,) # Negative lookbehind
(!=|[><=]=?)
(?!,) # Negative lookahead
''', re.VERBOSE)
print regex.sub(r',\1,', 'wrong_expression(b>=c) or right_expression(b,>=,c)')
outputs
wrong_expression(b,>=,c) or right_expression(b,>=,c)
I want to parse a string, such as:
package: name='jp.tjkapp.droid1lwp' versionCode='2' versionName='1.1'
uses-permission:'android.permission.WRITE_APN_SETTINGS'
uses-permission:'android.permission.RECEIVE_BOOT_COMPLETED'
uses-permission:'android.permission.ACCESS_NETWORK_STATE'
I want to get:
string1: jp.tjkapp.droidllwp`
string2: 1.1
Because there are multiple uses-permission, I want to get permission as a list, contains:
WRITE_APN_SETTINGS, RECEIVE_BOOT_COMPLETED and ACCESS_NETWORK_STATE.
Could you help me write the python regular expression to get the strings I want?
Thanks.
Assuming the code block you provided is one long string, here stored in a variable called input_string:
name = re.search(r"(?<=name\=\')[\w\.]+?(?=\')", input_string).group(0)
versionName = re.search(r"(?<=versionName\=\')\d+?\.\d+?(?=\')", input_string).group(0)
permissions = re.findall(r'(?<=android\.permission\.)[A-Z_]+(?=\')', input_string)
Explanation:
name
(?<=name\=\'): check ahead of the main string in order to return only strings that are preceded by name='. The \ in front of = and ' serve to escape them so that the regex knows we're talking about the = string and not a regex command. name=' is not also returned when we get the result, we just know that the results we get are all preceded by it.
[\w\.]+?: This is the main string we're searching for. \w means any alphanumeric character and underscore. \. is an escaped period, so the regex knows we mean . and not the regex command represented by an unescaped period. Putting these in [] means we're okay with anything we've stuck in brackets, so we're saying that we'll accept any alphanumeric character, _, or .. + afterwords means at least one of the previous thing, meaning at least one (but possibly more) of [\w\.]. Finally, the ? means don't be greedy--we're telling the regex to get the smallest possible group that meets these specifications, since + could go on for an unlimited number of repeats of anything matched by [\w\.].
(?=\'): check behind the main string in order to return only strings that are followed by '. The \ is also an escape, since otherwise regex or Python's string execution might misinterpret '. This final ' is not returned with our results, we just know that in the original string, it followed any result we do end up getting.
You can do this without regex by reading the file content line by line.
>>> def split_string(s):
... if s.startswith('package'):
... return [i.split('=')[1] for i in s.split() if "=" in i]
... elif s.startswith('uses-permission'):
... return s.split('.')[-1]
...
>>> split_string("package: name='jp.tjkapp.droid1lwp' versionCode='2' versionName='1.1'")
["'jp.tjkapp.droid1lwp'", "'2'", "'1.1'"]
>>> split_string("uses-permission:'android.permission.WRITE_APN_SETTINGS'")
"WRITE_APN_SETTINGS'"
>>> split_string("uses-permission:'android.permission.RECEIVE_BOOT_COMPLETED'")
"RECEIVE_BOOT_COMPLETED'"
>>> split_string("uses-permission:'android.permission.ACCESS_NETWORK_STATE'")
"ACCESS_NETWORK_STATE'"
>>>
Here is one example code
#!/usr/bin/env python
inputFile = open("test.txt", "r").readlines()
for line in inputFile:
if line.startswith("package"):
words = line.split()
string1 = words[1].split("=")[1].replace("'","")
string2 = words[3].split("=")[1].replace("'","")
test.txt file contains input data you mentioned earlier..