Re: [Tutor] how to unique the string
On Mon, Oct 24, 2011 at 3:24 PM, Peter Otten <__pete...@web.de> wrote:
> lina wrote:
>
>> But I am getting confused later:
>>
>> def translate_process(dictionary,tobetranslatedfile):
>> results=[]
>> unique={}
>> for line in open(tobetranslatedfile,"r"):
>> tobetranslatedparts=line.strip().split()
>> results.append(dictionary[tobetranslatedparts[2]])
>
>> unique=Counter(results)
>> with open(base+OUTPUTFILEEXT,"w") as f:
>> for residue, numbers in unique.items():
>> print(residue,numbers,file=f)
>
> As Dave says, the above four lines should run only once, outside the for-
> loop.
>
> Here's a way to avoid the intermediate results list. As a bonus I'm removing
> access to the `base` global variable:
>
> def change_ext(name, new_ext):
> """
> >>> change_ext("/deep/blue.eyes", ".c")
> '/deep/blue.c'
> """
> return os.path.splitext(name)[0] + new_ext
>
> def translate_process(dictionary, tobetranslatedfile):
> with open(tobetranslatedfile, "r") as f:
> results = (dictionary[line.split()[2]] for line in f)
> unique = Counter(results)
>
> with open(change_ext(tobetranslatedfile, OUTPUTFILEEXT), "w") as out:
> for residue, numbers in unique.items():
> print(residue, numbers, file=out)
Now work as expected. concise than before.
Thanks,
>
>
>> it still the same in the OUTPUTFILE as before,
>>
>> $ more atom-pair_6.txt
>> {'26SER': 2, '16LYS': 1, '83ILE': 2, '70LYS': 6, '55HIS': 5}
>
> Unlikely. Verify that you are running the correct script and looking into
> the right output file.
>
>
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Re: [Tutor] how to unique the string
>>
>> def translate_process(dictionary,tobetranslatedfile):
>> results=[]
>> unique={}
>> for line in open(tobetranslatedfile,"r"):
>> tobetranslatedparts=line.strip().split()
>> results.append(dictionary[tobetranslatedparts[2]])
>> unique=Counter(results)
>> with open(base+OUTPUTFILEEXT,"w") as f:
>
> Every time you do this, you're truncating the file. It'd be better to open
> the file outside the for-line loop, and just use the file object in the
> loop.
Before I did not understand well, until I read Peter's following post.
Thanks,
>
> --
>
> DaveA
>
>
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Re: [Tutor] how to unique the string
On Mon, Oct 24, 2011 at 3:24 PM, Peter Otten <__pete...@web.de> wrote:
> lina wrote:
>
>> But I am getting confused later:
>>
>> def translate_process(dictionary,tobetranslatedfile):
>> results=[]
>> unique={}
>> for line in open(tobetranslatedfile,"r"):
>> tobetranslatedparts=line.strip().split()
>> results.append(dictionary[tobetranslatedparts[2]])
>
>> unique=Counter(results)
>> with open(base+OUTPUTFILEEXT,"w") as f:
>> for residue, numbers in unique.items():
>> print(residue,numbers,file=f)
>
> As Dave says, the above four lines should run only once, outside the for-
> loop.
>
> Here's a way to avoid the intermediate results list. As a bonus I'm removing
> access to the `base` global variable:
>
> def change_ext(name, new_ext):
> """
> >>> change_ext("/deep/blue.eyes", ".c")
> '/deep/blue.c'
> """
> return os.path.splitext(name)[0] + new_ext
>
> def translate_process(dictionary, tobetranslatedfile):
> with open(tobetranslatedfile, "r") as f:
> results = (dictionary[line.split()[2]] for line in f)
> unique = Counter(results)
>
> with open(change_ext(tobetranslatedfile, OUTPUTFILEEXT), "w") as out:
> for residue, numbers in unique.items():
> print(residue, numbers, file=out)
>
>
>> it still the same in the OUTPUTFILE as before,
>>
>> $ more atom-pair_6.txt
>> {'26SER': 2, '16LYS': 1, '83ILE': 2, '70LYS': 6, '55HIS': 5}
>
> Unlikely. Verify that you are running the correct script and looking into
> the right output file.
Thanks,
print(residue,numbers,"\n",file=f)
achieve this.
62PHE 10
34LEU 37
43ASP 6
but seems the \n added one more line,
>
>
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Re: [Tutor] how to unique the string
lina wrote:
> But I am getting confused later:
>
> def translate_process(dictionary,tobetranslatedfile):
> results=[]
> unique={}
> for line in open(tobetranslatedfile,"r"):
> tobetranslatedparts=line.strip().split()
> results.append(dictionary[tobetranslatedparts[2]])
> unique=Counter(results)
> with open(base+OUTPUTFILEEXT,"w") as f:
> for residue, numbers in unique.items():
> print(residue,numbers,file=f)
As Dave says, the above four lines should run only once, outside the for-
loop.
Here's a way to avoid the intermediate results list. As a bonus I'm removing
access to the `base` global variable:
def change_ext(name, new_ext):
"""
>>> change_ext("/deep/blue.eyes", ".c")
'/deep/blue.c'
"""
return os.path.splitext(name)[0] + new_ext
def translate_process(dictionary, tobetranslatedfile):
with open(tobetranslatedfile, "r") as f:
results = (dictionary[line.split()[2]] for line in f)
unique = Counter(results)
with open(change_ext(tobetranslatedfile, OUTPUTFILEEXT), "w") as out:
for residue, numbers in unique.items():
print(residue, numbers, file=out)
> it still the same in the OUTPUTFILE as before,
>
> $ more atom-pair_6.txt
> {'26SER': 2, '16LYS': 1, '83ILE': 2, '70LYS': 6, '55HIS': 5}
Unlikely. Verify that you are running the correct script and looking into
the right output file.
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Re: [Tutor] how to unique the string
On 10/23/2011 08:01 AM, lina wrote:
On Sun, Oct 23, 2011 at 6:06 PM, Peter Otten<__pete...@web.de> wrote:
lina wrote:
tobetranslatedparts=line.strip().split()
strip() is superfluous here, split() will take care of the stripping:
" alpha \tbeta\n".split()
['alpha', 'beta']
for residue in results:
if residue not in unique:
unique[residue]=1
else:
unique[residue]+=1
There is a dedicated class to help you with that, collections.Counter:
from collections import Counter
results = ["alpha", "beta", "gamma", "alpha"]
unique = Counter(results)
unique
Counter({'alpha': 2, 'beta': 1, 'gamma': 1})
Counter is a subclass of dict, so the stuff you are doing with `unique`
elswhere should continue to work.
This part I just wish the output in file like:
{'26SER': 2, '16LYS': 1, '83ILE': 2, '70LYS': 6}
as
26SER 2
16LYS 1
83ILE 2
70LYS 6
You can redirect the output of print() to a file using the `file` keyword
argument:
unique = {'26SER': 2, '16LYS': 1, '83ILE': 2, '70LYS': 6}
with open("tmp.txt", "w") as f:
... for k, v in unique.items():
... print(k, v, file=f)
I tested it in idle3, it has no problem achieving this.
But I am getting confused later:
def translate_process(dictionary,tobetranslatedfile):
results=[]
unique={}
for line in open(tobetranslatedfile,"r"):
tobetranslatedparts=line.strip().split()
results.append(dictionary[tobetranslatedparts[2]])
unique=Counter(results)
with open(base+OUTPUTFILEEXT,"w") as f:
Every time you do this, you're truncating the file. It'd be better to
open the file outside the for-line loop, and just use the file object in
the loop.
for residue, numbers in unique.items():
print(residue,numbers,file=f)
it still the same in the OUTPUTFILE as before,
$ more atom-pair_6.txt
{'26SER': 2, '16LYS': 1, '83ILE': 2, '70LYS': 6, '55HIS': 5}
Thanks,
...
$ cat tmp.txt
26SER 2
83ILE 2
70LYS 6
16LYS 1
$
--
DaveA
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Re: [Tutor] how to unique the string
On Sun, Oct 23, 2011 at 6:06 PM, Peter Otten <__pete...@web.de> wrote:
> lina wrote:
>
tobetranslatedparts=line.strip().split()
>
> strip() is superfluous here, split() will take care of the stripping:
>
" alpha \tbeta\n".split()
> ['alpha', 'beta']
>
for residue in results:
if residue not in unique:
unique[residue]=1
else:
unique[residue]+=1
>
> There is a dedicated class to help you with that, collections.Counter:
>
from collections import Counter
results = ["alpha", "beta", "gamma", "alpha"]
unique = Counter(results)
unique
> Counter({'alpha': 2, 'beta': 1, 'gamma': 1})
>
> Counter is a subclass of dict, so the stuff you are doing with `unique`
> elswhere should continue to work.
>
>> This part I just wish the output in file like:
>>
>> {'26SER': 2, '16LYS': 1, '83ILE': 2, '70LYS': 6}
>>
>> as
>>
>> 26SER 2
>> 16LYS 1
>> 83ILE 2
>> 70LYS 6
>
> You can redirect the output of print() to a file using the `file` keyword
> argument:
>
unique = {'26SER': 2, '16LYS': 1, '83ILE': 2, '70LYS': 6}
with open("tmp.txt", "w") as f:
> ... for k, v in unique.items():
> ... print(k, v, file=f)
I tested it in idle3, it has no problem achieving this.
But I am getting confused later:
def translate_process(dictionary,tobetranslatedfile):
results=[]
unique={}
for line in open(tobetranslatedfile,"r"):
tobetranslatedparts=line.strip().split()
results.append(dictionary[tobetranslatedparts[2]])
unique=Counter(results)
with open(base+OUTPUTFILEEXT,"w") as f:
for residue, numbers in unique.items():
print(residue,numbers,file=f)
it still the same in the OUTPUTFILE as before,
$ more atom-pair_6.txt
{'26SER': 2, '16LYS': 1, '83ILE': 2, '70LYS': 6, '55HIS': 5}
Thanks,
> ...
> $ cat tmp.txt
> 26SER 2
> 83ILE 2
> 70LYS 6
> 16LYS 1
> $
>
>
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Re: [Tutor] how to unique the string
lina wrote:
>>> tobetranslatedparts=line.strip().split()
strip() is superfluous here, split() will take care of the stripping:
>>> " alpha \tbeta\n".split()
['alpha', 'beta']
>>> for residue in results:
>>> if residue not in unique:
>>> unique[residue]=1
>>> else:
>>> unique[residue]+=1
There is a dedicated class to help you with that, collections.Counter:
>>> from collections import Counter
>>> results = ["alpha", "beta", "gamma", "alpha"]
>>> unique = Counter(results)
>>> unique
Counter({'alpha': 2, 'beta': 1, 'gamma': 1})
Counter is a subclass of dict, so the stuff you are doing with `unique`
elswhere should continue to work.
> This part I just wish the output in file like:
>
> {'26SER': 2, '16LYS': 1, '83ILE': 2, '70LYS': 6}
>
> as
>
> 26SER 2
> 16LYS 1
> 83ILE 2
> 70LYS 6
You can redirect the output of print() to a file using the `file` keyword
argument:
>>> unique = {'26SER': 2, '16LYS': 1, '83ILE': 2, '70LYS': 6}
>>> with open("tmp.txt", "w") as f:
... for k, v in unique.items():
... print(k, v, file=f)
...
>>>
$ cat tmp.txt
26SER 2
83ILE 2
70LYS 6
16LYS 1
$
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Re: [Tutor] how to unique the string
The updated one -- following Alan's advice.
#!/usr/bin/python3
import os.path
mapping={}
DICTIONARYFILE="dictionary.pdb"
TOBETRANSLATEDFILEEXT=".out"
OUTPUTFILEEXT=".txt"
def generate_dict(dictionarysourcefile):
for line in open(dictionarysourcefile,"r"):
parts=line.strip().split()
mapping[parts[2]]=parts[0]
def translate_process(dictionary,tobetranslatedfile):
results=[]
unique={}
for line in open(tobetranslatedfile,"r"):
tobetranslatedparts=line.strip().split()
results.append(dictionary[tobetranslatedparts[2]])
for residue in results:
unique[residue]=unique.get(residue,0)+1
for residue, numbers in unique.items():
print(residue,numbers)
with open(base+OUTPUTFILEEXT,"w") as f:
f.write(str(unique))
if __name__=="__main__":
generate_dict(DICTIONARYFILE)
for infilename in os.listdir("."):
base, ext = os.path.splitext(infilename)
if ext == TOBETRANSLATEDFILEEXT:
translate_process(mapping, infilename)
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Re: [Tutor] how to unique the string
On Sun, Oct 23, 2011 at 5:08 PM, Alan Gauld wrote:
> On 23/10/11 09:33, lina wrote:
>
>> I have a further question:
>>
>
>> Welcome anyone help me transform the code to another form.
>
> What form would you like it transformed to?
> A flow chart? Another programming language? A different style of Python
> (Functional programming or OOP maybe?)
Just an updated version. Like the comments you gave.
BTW, thanks for the comments.
>
> I'm not sure what you want here?
> In the meantime I'll offer some general comments:
>
>> #!/usr/bin/python3
>> import os.path
>> mapping={}
>>
>>
>> DICTIONARYFILE="dictionary.pdb"
>> TOBETRANSLATEDFILEEXT=".out"
>> OUTPUTFILEEXT=".txt"
>>
>> def generate_dict(dictionarysourcefile):
>> for line in open(dictionarysourcefile,"r").readlines():
>
> You don't need the readlines(). Just
> use
>
> for line in open(dictionarysourcefile,"r"):
>
> That will work just as well.
>
>> parts=line.strip().split()
>> mapping[parts[2]]=parts[0]
>>
>>
>> def translate_process(dictionary,tobetranslatedfile):
>> results=[]
>> unique={}
>> for line in open(tobetranslatedfile,"r").readlines():
>> tobetranslatedparts=line.strip().split()
>> results.append(dictionary[tobetranslatedparts[2]])
>> for residue in results:
>> if residue not in unique:
>> unique[residue]=1
>> else:
>> unique[residue]+=1
>
> You can replace the if/else with the get() metjod of a dictionary:
>
> unique[residue] = unique.get(residue,0) + 1
>
> get returns the current value and if the value is not there it returns the
> second parameter(zero here)
>
>
>> for residue, numbers in unique.items():
>> print(residue,numbers)
>> with open(base+OUTPUTFILEEXT,"w") as f:
>> f.write(str(unique)) ### How can I output the
>> results the same as the print one. Thanks.
>
> create a string before you write it:
>
> mystr = str(residue) + str(numbers)
This part I just wish the output in file like:
{'26SER': 2, '16LYS': 1, '83ILE': 2, '70LYS': 6}
as
26SER 2
16LYS 1
83ILE 2
70LYS 6
still have problem in writing the dict.
Thanks again for your time,
Best regards,
>
> is the simplest way. However you may prefer to format the string in another
> way first. But thats your choice...
>
>> if __name__=="__main__":
>> generate_dict(DICTIONARYFILE)
>> for infilename in os.listdir("."):
>> base, ext = os.path.splitext(infilename)
>> if ext == TOBETRANSLATEDFILEEXT:
>> translate_process(mapping, infilename)
>
> --
> Alan G
> Author of the Learn to Program web site
> http://www.alan-g.me.uk/
>
> ___
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Re: [Tutor] how to unique the string
On 23/10/11 09:33, lina wrote:
I have a further question:
> Welcome anyone help me transform the code to another form.
What form would you like it transformed to?
A flow chart? Another programming language? A different style of Python
(Functional programming or OOP maybe?)
I'm not sure what you want here?
In the meantime I'll offer some general comments:
#!/usr/bin/python3
import os.path
mapping={}
DICTIONARYFILE="dictionary.pdb"
TOBETRANSLATEDFILEEXT=".out"
OUTPUTFILEEXT=".txt"
def generate_dict(dictionarysourcefile):
for line in open(dictionarysourcefile,"r").readlines():
You don't need the readlines(). Just
use
for line in open(dictionarysourcefile,"r"):
That will work just as well.
parts=line.strip().split()
mapping[parts[2]]=parts[0]
def translate_process(dictionary,tobetranslatedfile):
results=[]
unique={}
for line in open(tobetranslatedfile,"r").readlines():
tobetranslatedparts=line.strip().split()
results.append(dictionary[tobetranslatedparts[2]])
for residue in results:
if residue not in unique:
unique[residue]=1
else:
unique[residue]+=1
You can replace the if/else with the get() metjod of a dictionary:
unique[residue] = unique.get(residue,0) + 1
get returns the current value and if the value is not there it returns
the second parameter(zero here)
for residue, numbers in unique.items():
print(residue,numbers)
with open(base+OUTPUTFILEEXT,"w") as f:
f.write(str(unique)) ### How can I output the
results the same as the print one. Thanks.
create a string before you write it:
mystr = str(residue) + str(numbers)
is the simplest way. However you may prefer to format the string in
another way first. But thats your choice...
if __name__=="__main__":
generate_dict(DICTIONARYFILE)
for infilename in os.listdir("."):
base, ext = os.path.splitext(infilename)
if ext == TOBETRANSLATEDFILEEXT:
translate_process(mapping, infilename)
--
Alan G
Author of the Learn to Program web site
http://www.alan-g.me.uk/
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Re: [Tutor] how to unique the string
On Sun, Oct 23, 2011 at 12:50 AM, Steven D'Aprano wrote:
> lina wrote:
>>
>> Hi,
>>
>> I googled for a while, but failed to find the perfect answer,
>>
>> for a string
>>
>> ['85CUR', '85CUR']
>
>
> That's not a string, it is a list.
>
>
>> how can I unique it as:
>>
>> ['85CUR']
>
> Your question is unclear. If you have this:
>
> ['85CUR', '99bcd', '85CUR', '85CUR']
>
> what do you expect to get?
>
>
> # keep only the very first item
> ['85CUR']
> # keep the first copy of each string, in order
> ['85CUR', '99bcd']
> # keep the last copy of each string, in order
> ['99bcd', '85CUR']
> # ignore duplicates only when next to each other
> ['85CUR', '99bcd', '85CUR']
>
>
> Does the order of the result matter?
>
> If order matters, and you want to keep the first copy of each string:
>
> unique = []
> for item in items:
> if item not in unique:
> unique.append(item)
>
>
> If order doesn't matter, then use this:
>
> unique = list(set(items))
Thanks, this one unique=list(set(item)) works well.
I have a further question:
#!/usr/bin/python3
import os.path
mapping={}
DICTIONARYFILE="dictionary.pdb"
TOBETRANSLATEDFILEEXT=".out"
OUTPUTFILEEXT=".txt"
def generate_dict(dictionarysourcefile):
for line in open(dictionarysourcefile,"r").readlines():
parts=line.strip().split()
mapping[parts[2]]=parts[0]
def translate_process(dictionary,tobetranslatedfile):
results=[]
unique={}
for line in open(tobetranslatedfile,"r").readlines():
tobetranslatedparts=line.strip().split()
results.append(dictionary[tobetranslatedparts[2]])
for residue in results:
if residue not in unique:
unique[residue]=1
else:
unique[residue]+=1
for residue, numbers in unique.items():
print(residue,numbers)
with open(base+OUTPUTFILEEXT,"w") as f:
f.write(str(unique)) ### How can I output the
results the same as the print one. Thanks.
if __name__=="__main__":
generate_dict(DICTIONARYFILE)
for infilename in os.listdir("."):
base, ext = os.path.splitext(infilename)
if ext == TOBETRANSLATEDFILEEXT:
translate_process(mapping, infilename)
https://docs.google.com/leaf?id=0B93SVRfpVVg3ZTBiYjU1MzYtNTNkMS00ZjQ1LWI4MzEtNDEyZWUwYTFmNjU4&hl=en_GB
https://docs.google.com/leaf?id=0B93SVRfpVVg3ODU4MDlkMDQtOTJmMy00MDJiLTkwM2EtY2EyNTUyZmNhNTNm&hl=en_GB
Welcome anyone help me transform the code to another form.
>
>
>
> --
> Steven
>
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Re: [Tutor] how to unique the string
On 23 Oct, 2011, at 0:22, Devin Jeanpierre wrote: > You should be able to do this yourself, with the help of the following link: > > http://docs.python.org/library/stdtypes.html#set Thanks. > > Is this a homework question? No. > > Devin > > On Sat, Oct 22, 2011 at 12:09 PM, lina wrote: >> Hi, >> >> I googled for a while, but failed to find the perfect answer, >> >> for a string >> >> ['85CUR', '85CUR'] >> >> how can I unique it as: >> >> ['85CUR'] >> >> Thanks, >> ___ >> Tutor maillist - Tutor@python.org >> To unsubscribe or change subscription options: >> http://mail.python.org/mailman/listinfo/tutor >> ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] how to unique the string
lina wrote: Hi, I googled for a while, but failed to find the perfect answer, for a string ['85CUR', '85CUR'] That's not a string, it is a list. how can I unique it as: ['85CUR'] Your question is unclear. If you have this: ['85CUR', '99bcd', '85CUR', '85CUR'] what do you expect to get? # keep only the very first item ['85CUR'] # keep the first copy of each string, in order ['85CUR', '99bcd'] # keep the last copy of each string, in order ['99bcd', '85CUR'] # ignore duplicates only when next to each other ['85CUR', '99bcd', '85CUR'] Does the order of the result matter? If order matters, and you want to keep the first copy of each string: unique = [] for item in items: if item not in unique: unique.append(item) If order doesn't matter, then use this: unique = list(set(items)) -- Steven ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] how to unique the string
On 10/22/2011 12:09 PM, lina wrote: Hi, I googled for a while, but failed to find the perfect answer, for a string ['85CUR', '85CUR'] how can I unique it as: ['85CUR'] Try set(['85CUR', '85CUR'] -- Bob Gailer 919-636-4239 Chapel Hill NC ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] how to unique the string
You should be able to do this yourself, with the help of the following link: http://docs.python.org/library/stdtypes.html#set Is this a homework question? Devin On Sat, Oct 22, 2011 at 12:09 PM, lina wrote: > Hi, > > I googled for a while, but failed to find the perfect answer, > > for a string > > ['85CUR', '85CUR'] > > how can I unique it as: > > ['85CUR'] > > Thanks, > ___ > Tutor maillist - Tutor@python.org > To unsubscribe or change subscription options: > http://mail.python.org/mailman/listinfo/tutor > ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
