Re: [Tutor] map one file and print it out following the sequence
On 2011-10-12 05:31, lina wrote:
I tried to write one (not working one) as below, so many problems here.
Just some quick remarks:
#!/usr/bin/python3
import os.path
LINESTOSKIP=0
CHAINID="CDEFGHI"
INFILENAME="pdbone.pdb"
DICTIONARYFILE="itpone.itp"
mapping={}
valuefromdict={}
def sortfile():
for chainid in CHAINID:
sortoneblock(chainid)
def generatedictionary(dictfilename):
You define the function with the parameter "dictfilename" but you'll
never use it.
text=fetchonefiledata(DICTIONARYFILE)
for line in text:
parts=line.strip().split()
if len(parts)==8:
mapping[parts[4]]=parts[0]
print(mapping)
The if-branch is probably wrongly indented (should be inside the for-loop).
def sortoneblock(cID)
text=fetchonefiledata(INFILENAME)
for line in text:
blocks=line.strip().split()
if len(blocks)== 11 and blocks[3] == "CUR" and blocks[4] == "cID":
"cID" is a string-variable but you compare block 4 to the literal string
"cID". In "pdbone.pdb" you will never find "cID" so this function will
do nothing. You probably mean "blocks[4] == cID".
valuefromdict[blocks[2]]=mapping[block[2]]
You never fill up "mapping" because you never call your
"generatedictionary"-function. Therefore "mapping" is still an empty
dictionary and this line will raise an exception.
return
Firstly, the indentation is wrong because you would leave "sortoneblock"
after the first processed line. Secondly, as you return nothing, you
don't need this line because you will leave the function anyway.
def fetchonefiledata(infilename):
text=open("infilename").readlines()
Again, "infilename" is a variable, so no need for the quotes.
if os.path.splitext(infilename)[1]=".itp"
return text
if os.path.splitext(infilename)[1]=".pdb"
return text[LINESTOSKIP:]
if __name__=="__main__":
sortfiles()
There is no "sortfiles()" in your script. The function you probably mean
is called "sortfile()"
Bye, Andreas
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Re: [Tutor] Keyboard Module
On 12/10/11 02:32, Ryan Strunk wrote: The keyboard module I currently have access to is a wrapper for the wx keyboard handler, which is fine, but it prevents me from holding one key and pressing another. So use raw wx key events. They include key down,up and press events. I thought of using Pygame to pull this off, but I gather from my research that I can't just use certain pieces of Pygame; in order to get the functionality I want out of the keyboard module, I'll need other modules as well. I don't want to work specifically in Pygame, because I've heard Pygame is quite bloated and requires a good deal of overhead. (I wouldn't mind being proven wrong on this) Bloated carries the connotation of unnecessary code, but pygame provides a lot of functionality. You may not need it all, and using pygame may require you to import more than you need. But thats not quite the same as saying pygame is bloated. And its not that huge that it should stop you using it. If it works, why not? All of which leads me to my question. Can anyone recommend a keyboard module which will allow me to work with various facets of the keyboard to execute functions. Since you mentioned wx I assume thats the GUI you are using. If not you can also investigate Tkinter which likewise traps keyboard events and might be considered slightly easier to use. HTH, -- Alan G Author of the Learn to Program web site http://www.alan-g.me.uk/ ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] map one file and print it out following the sequence
On Wed, Oct 12, 2011 at 3:29 PM, Andreas Perstinger <
andreas.perstin...@gmx.net> wrote:
> On 2011-10-12 05:31, lina wrote:
>
>> I tried to write one (not working one) as below, so many problems here.
>>
>
> Just some quick remarks:
Thanks,
Now the newly-improved one as following: but still the "sort" parts did not
work.
#!/usr/bin/python3
import os.path
LINESTOSKIP=0
CHAINID="CDEFGHI"
INFILENAME="pdbone.pdb"
DICTIONARYFILE="itpone.itp"
mapping={}
valuefromdict={}
def sortfile():
for chainid in CHAINID:
sortoneblock(chainid)
def generatedictionary(dictfilename):
text=fetchonefiledata(DICTIONARYFILE)
for line in text:
parts=line.strip().split()
if len(parts)==8:
mapping[parts[4]]=parts[0]
print(mapping)
def sortoneblock(cID):
text=fetchonefiledata(INFILENAME)
for line in text:
blocks=line.strip().split()
if len(blocks)== 11 and blocks[3] == "CUR" and blocks[4] == cID and
blocks[2] in mapping.keys():
valuefromdict[cID]=mapping[blocks[2]]
print(valuefromdict)
def fetchonefiledata(infilename):
text=open(infilename).readlines()
if os.path.splitext(infilename)[1]==".itp":
return text
if os.path.splitext(infilename)[1]==".pdb":
return text[LINESTOSKIP:]
if __name__=="__main__":
generatedictionary(DICTIONARYFILE)
sortfile()
The result is:
$ python3 map-to-itp.py
{'O4': '2', 'C19': '3', 'C21': '1'}
{'C': '3'}
{'C': '2'}
{'C': '1'}
for print(mapping) part, {'O4': '2', 'C19': '3', 'C21': '1'} the value
doesn't keep the 1, 2, 3 order any more.
Thanks for further suggestions.
The relevant files I put it here:
https://docs.google.com/leaf?id=0B93SVRfpVVg3NzkyOGU2ZTUtZTFjNC00ZjE4LThhNmQtOWY1YWFkOWI0NWEw&hl=en_GB
https://docs.google.com/leaf?id=0B93SVRfpVVg3YTEwZjhiOTItN2I2Yi00NTEyLTljODAtYTc2ODI4Njk1YzZl&hl=en_GB
https://docs.google.com/leaf?id=0B93SVRfpVVg3M2Y1MWZiMmEtOTE2Mi00M2VjLTljNjAtYWNlMjhiNzEyODY1&hl=en_GB
>
> #!/usr/bin/python3
>>
>> import os.path
>>
>> LINESTOSKIP=0
>> CHAINID="CDEFGHI"
>> INFILENAME="pdbone.pdb"
>> DICTIONARYFILE="itpone.itp"
>> mapping={}
>> valuefromdict={}
>>
>> def sortfile():
>> for chainid in CHAINID:
>> sortoneblock(chainid)
>>
>>
>> def generatedictionary(**dictfilename):
>>
>
> You define the function with the parameter "dictfilename" but you'll never
> use it.
>
>
> text=fetchonefiledata(**DICTIONARYFILE)
>> for line in text:
>> parts=line.strip().split()
>> if len(parts)==8:
>> mapping[parts[4]]=parts[0]
>> print(mapping)
>>
>
> The if-branch is probably wrongly indented (should be inside the for-loop).
>
>
> def sortoneblock(cID)
>> text=fetchonefiledata(**INFILENAME)
>> for line in text:
>> blocks=line.strip().split()
>> if len(blocks)== 11 and blocks[3] == "CUR" and blocks[4] ==
>> "cID":
>>
>
>
> "cID" is a string-variable but you compare block 4 to the literal string
> "cID". In "pdbone.pdb" you will never find "cID" so this function will do
> nothing. You probably mean "blocks[4] == cID".
>
>
> valuefromdict[blocks[2]]=**mapping[block[2]]
>>
>
> You never fill up "mapping" because you never call your
> "generatedictionary"-function. Therefore "mapping" is still an empty
> dictionary and this line will raise an exception.
>
> return
>>
>
> Firstly, the indentation is wrong because you would leave "sortoneblock"
> after the first processed line. Secondly, as you return nothing, you don't
> need this line because you will leave the function anyway.
>
>
>
>>
>> def fetchonefiledata(infilename):
>> text=open("infilename").**readlines()
>>
>
> Again, "infilename" is a variable, so no need for the quotes.
>
>
> if os.path.splitext(infilename)[**1]=".itp"
>> return text
>> if os.path.splitext(infilename)[**1]=".pdb"
>> return text[LINESTOSKIP:]
>>
>>
>> if __name__=="__main__":
>> sortfiles()
>>
>
> There is no "sortfiles()" in your script. The function you probably mean is
> called "sortfile()"
>
> Bye, Andreas
>
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Re: [Tutor] map one file and print it out following the sequence
On 2011-10-12 10:27, lina wrote:
$ python3 map-to-itp.py
{'O4': '2', 'C19': '3', 'C21': '1'}
{'C': '3'}
{'C': '2'}
{'C': '1'}
for print(mapping) part, {'O4': '2', 'C19': '3', 'C21': '1'} the value
doesn't keep the 1, 2, 3 order any more.
That's fine, because "mapping" is a dictionary which has no order. From
the tutorial
(http://docs.python.org/py3k/tutorial/datastructures.html#dictionaries):
"It is best to think of a dictionary as an unordered set of key: value
pairs, with the requirement that the keys are unique (within one
dictionary)."
What you want (as far as I understand it) is sorting the lines in
"pdbone.pdb" based on the positions in file "itpone.itp". The connection
between both files is the column with the values "O4", "C19", "C21", ...
(= your keys). You've already succesfully built a dictionary in which
you saved the position for every key.
For the sorting you could now build a list of tuples of all lines in
"pdbone.pdb" you want to sort where the first element in the tuple is
the position and the second the line itself. Then you can easily sort
this temporary list and write the new ordered lines back to the file:
def sortoneblock(cID):
text = fetchonefiledata(INFILENAME)
temp = []# create an empty temporary list
for line in text:
blocks = line.strip().split()
if len(blocks) == 11 and blocks[3] == "CUR" and blocks[4] ==
cID and blocks[2] in mapping.keys():
temp.append((mapping[blocks[2]], line)) # add a tuple to
the list which has the following format: (position from the dictionary,
complete line)
# the following line just shows you, what we have done so far. You
can delete it without consequences.
for line in temp: print(line)
temp.sort() # this sorts the list based on the position
# the following line prints the sorted list (just the original line
without the position elements). If you want to write the result back to
the file you have to exchange "print()"
for line in temp: print(line[1])
Bye, Andreas
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[Tutor] Parsing /etc/passwd
Hi
I wrote the following code:
f = open('/etc/passwd', 'r')
users = f.read()
userelements = re.findall(r'(\w+):(\w+):(\w+):(\w+):(\w+):(\w+):(\w+)',
users)
print userelements
for user in userelements:
(username, encrypwd, uid, gid, gecos, homedir, usershell) = user #
unpack the tuple into 7 vars
print username
but I get no results so my parsing must be wrong but I am not sure why.
Incidentally while googling I found the module
http://docs.python.org/library/pwd.html which I will eventually use but I am
first curious to fix and understand the problem before I throw away this
code.
Regards
--
Gerhardus Geldenhuis
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Re: [Tutor] Parsing /etc/passwd
On Wed, Oct 12, 2011 at 3:41 PM, Gerhardus Geldenhuis
wrote:
> Hi
> I wrote the following code:
> f = open('/etc/passwd', 'r')
> users = f.read()
> userelements = re.findall(r'(\w+):(\w+):(\w+):(\w+):(\w+):(\w+):(\w+)',
> users)
> print userelements
> for user in userelements:
> (username, encrypwd, uid, gid, gecos, homedir, usershell) = user #
> unpack the tuple into 7 vars
> print username
>
> but I get no results so my parsing must be wrong but I am not sure why.
> Incidentally while googling I found the
> module http://docs.python.org/library/pwd.html which I will eventually use
> but I am first curious to fix and understand the problem before I throw away
> this code.
> Regards
>
the homedir and usershell parts are paths. Paths will contain slashes.
The \w character class captures only [A-Za-z0-9_], that is, letters,
numbers, and the underscore. That means slashes will not match, and so
the entire match fails.
On another note, the structure of the /etc/passwd file is pretty
simple, I don't think you need regexes. Simply use split:
users = f.readlines()
for user in users:
(username, encrypwd, uid, gid, gecos, homedir, usershell) = user.split(':')
HTH,
Hugo
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Re: [Tutor] Parsing /etc/passwd
Fantastic,
Thanks Hugo that makes 100% sense now! Testing both regex for including /
and doing split and when done throwing both away and using the default
module.
Regards
On Wed, Oct 12, 2011 at 2:49 PM, Hugo Arts wrote:
> On Wed, Oct 12, 2011 at 3:41 PM, Gerhardus Geldenhuis
> wrote:
> > Hi
> > I wrote the following code:
> > f = open('/etc/passwd', 'r')
> > users = f.read()
> > userelements = re.findall(r'(\w+):(\w+):(\w+):(\w+):(\w+):(\w+):(\w+)',
> > users)
> > print userelements
> > for user in userelements:
> > (username, encrypwd, uid, gid, gecos, homedir, usershell) = user #
> > unpack the tuple into 7 vars
> > print username
> >
> > but I get no results so my parsing must be wrong but I am not sure why.
> > Incidentally while googling I found the
> > module http://docs.python.org/library/pwd.html which I will eventually
> use
> > but I am first curious to fix and understand the problem before I throw
> away
> > this code.
> > Regards
> >
>
> the homedir and usershell parts are paths. Paths will contain slashes.
> The \w character class captures only [A-Za-z0-9_], that is, letters,
> numbers, and the underscore. That means slashes will not match, and so
> the entire match fails.
>
> On another note, the structure of the /etc/passwd file is pretty
> simple, I don't think you need regexes. Simply use split:
>
> users = f.readlines()
> for user in users:
>(username, encrypwd, uid, gid, gecos, homedir, usershell) =
> user.split(':')
>
> HTH,
> Hugo
>
--
Gerhardus Geldenhuis
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Re: [Tutor] map one file and print it out following the sequence
On Wed, Oct 12, 2011 at 8:50 PM, Andreas Perstinger <
andreas.perstin...@gmx.net> wrote:
> On 2011-10-12 10:27, lina wrote:
>
>> $ python3 map-to-itp.py
>> {'O4': '2', 'C19': '3', 'C21': '1'}
>> {'C': '3'}
>> {'C': '2'}
>> {'C': '1'}
>>
>> for print(mapping) part, {'O4': '2', 'C19': '3', 'C21': '1'} the value
>> doesn't keep the 1, 2, 3 order any more.
>>
>
> That's fine, because "mapping" is a dictionary which has no order. From the
> tutorial (http://docs.python.org/py3k/**tutorial/datastructures.html#**
> dictionaries
> ):
> "It is best to think of a dictionary as an unordered set of key: value
> pairs, with the requirement that the keys are unique (within one
> dictionary)."
>
> What you want (as far as I understand it) is sorting the lines in
> "pdbone.pdb" based on the positions in file "itpone.itp". The connection
> between both files is the column with the values "O4", "C19", "C21", ... (=
> your keys). You've already succesfully built a dictionary in which you saved
> the position for every key.
>
> For the sorting you could now build a list of tuples of all lines in
> "pdbone.pdb" you want to sort where the first element in the tuple is the
> position and the second the line itself. Then you can easily sort this
> temporary list and write the new ordered lines back to the file:
>
> def sortoneblock(cID):
>text = fetchonefiledata(INFILENAME)
>temp = []# create an empty temporary list
>
>for line in text:
>blocks = line.strip().split()
>if len(blocks) == 11 and blocks[3] == "CUR" and blocks[4] == cID and
> blocks[2] in mapping.keys():
>
>temp.append((mapping[blocks[2]**], line)) # add a tuple to the
> list which has the following format: (position from the dictionary, complete
> line)
>
># the following line just shows you, what we have done so far. You can
> delete it without consequences.
>
>for line in temp: print(line)
>
>temp.sort() # this sorts the list based on the position
>
># the following line prints the sorted list (just the original line
> without the position elements). If you want to write the result back to the
> file you have to exchange "print()"
>
I do have problems to write each blocks (differentiated by chainID) back
one by one, but this will leave it at the end. at present I still have
following problems
Q1: why the D E F G H I stopped being processed.
>
>for line in temp: print(line[1])
Thanks.
$ python3 map-to-itp.py
{'O4': '2', 'C19': '3', 'C21': '1'}
C
ATOM832 C21 CUR C 85 32.823 27.366 0.801 1.00
0.00
ATOM831 O4 CUR C 85 31.865 28.248 0.183 1.00
0.00
ATOM827 C19 CUR C 85 31.891 29.624 0.280 1.00
0.00
D
E
F
G
H
I
#!/usr/bin/python3
import os.path
LINESTOSKIP=0
CHAINID="CDEFGHI"
INFILENAME="pdbone.pdb"
DICTIONARYFILE="itpone.itp"
mapping={}
valuefromdict={}
def sortfile():
for chainid in CHAINID:
print(chainid)
sortoneblock(chainid)
def sortoneblock(cID):
text=fetchonefiledata(INFILENAME) ## Q2: How to avoid read this file
every time. actually it only need read once.
temp = []
for line in text:
blocks=line.strip().split()
if len(blocks)== 11 and blocks[3] == "CUR" and blocks[4] == cID and
blocks[2] in mapping.keys():
temp.append((mapping[blocks[2]],line))
temp.sort()
for line in temp:
print(line[1].strip())
def generatedictionary(dictfilename):
text=fetchonefiledata(DICTIONARYFILE)
for line in text:
parts=line.strip().split()
if len(parts)==8:
mapping[parts[4]]=parts[0]
print(mapping)
def fetchonefiledata(infilename):
text=open(infilename).readlines()
if os.path.splitext(infilename)[1]==".itp":
return text
if os.path.splitext(infilename)[1]==".pdb":
return text[LINESTOSKIP:]
if __name__=="__main__":
generatedictionary(DICTIONARYFILE)
sortfile()
Thanks.
>
>
> Bye, Andreas
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Re: [Tutor] Parsing /etc/passwd
Hugo Arts wrote:
>> f = open('/etc/passwd', 'r')
> users = f.readlines()
> for user in users:
...
You can iterate over the file directly:
for user in f:
...
The version using readlines() reads the whole file into a list of lines
where the alternative just has to remember the current line.
While it doesn't matter much for small files iterating over the file
directly will save a lot of memory if the input file is large.
Therefore avoiding readlines() is a good habit to get into.
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Re: [Tutor] map one file and print it out following the sequence
On 10/12/2011 09:57 AM, lina wrote:
I do have problems to write each blocks (differentiated by chainID) back
one by one, but this will leave it at the end. at present I still have
following problems
Q1: why the D E F G H I stopped being processed.
In what sense do you mean stopped? There are no records in pdbone.pdb
that have column 4 equal to any of the remaining CID values, D, E, F, etc.
So they don't print anything. You can see that 3 of them matched cID of "C"
for line in temp: print(line[1])
Thanks.
$ python3 map-to-itp.py
{'O4': '2', 'C19': '3', 'C21': '1'}
C
ATOM832 C21 CUR C 85 32.823 27.366 0.801 1.00
0.00
ATOM831 O4 CUR C 85 31.865 28.248 0.183 1.00
0.00
ATOM827 C19 CUR C 85 31.891 29.624 0.280 1.00
0.00
D
E
F
G
H
I
#!/usr/bin/python3
import os.path
LINESTOSKIP=0
CHAINID="CDEFGHI"
INFILENAME="pdbone.pdb"
DICTIONARYFILE="itpone.itp"
mapping={}
valuefromdict={}
def sortfile():
for chainid in CHAINID:
print(chainid)
sortoneblock(chainid)
def sortoneblock(cID):
text=fetchonefiledata(INFILENAME) ## Q2: How to avoid read this file
every time. actually it only need read once.
Simple. Move this line into sortfile (before the for loop), and pass
text as an argument when it calls sortoneblock(cID, text)
Naturally, you'd then add the parameter to sortoneblock(cID, text).
Once you try to create the output file, you'll also be adding the open()
call for that into sortfile(), and passing its file object into
sortoneblock(cID, text, outfile)
temp = []
for line in text:
blocks=line.strip().split()
if len(blocks)== 11 and blocks[3] == "CUR" and blocks[4] == cID and
blocks[2] in mapping.keys():
temp.append((mapping[blocks[2]],line))
temp.sort()
for line in temp:
print(line[1].strip())
def generatedictionary(dictfilename):
text=fetchonefiledata(DICTIONARYFILE)
for line in text:
parts=line.strip().split()
if len(parts)==8:
mapping[parts[4]]=parts[0]
print(mapping)
def fetchonefiledata(infilename):
text=open(infilename).readlines()
if os.path.splitext(infilename)[1]==".itp":
return text
if os.path.splitext(infilename)[1]==".pdb":
return text[LINESTOSKIP:]
if __name__=="__main__":
generatedictionary(DICTIONARYFILE)
sortfile()
Thanks.
I think your final version of sortfile() might look something like:
def sortfile(infilename=INFILENAME, outfilename=OUTFILENAME):
infile = open(infilename, "r")
intext = infile.readlines()
outfile = open(OUTFILENAME, "w")
for chainid in CHAINID:
print("chain id = ",chainid)
sortoneblock(chainid, intext, outfile)
infile.close()
outfile.close()
--
DaveA
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Re: [Tutor] I am trying to print list elements but i am getting 'none'
>for item in list: >print item Or you could do this inline with: print ' '.join( myList ) # Change ' ' to be the separator you desire if you want something other than a space between elements? Ramit Ramit Prasad | JPMorgan Chase Investment Bank | Currencies Technology 712 Main Street | Houston, TX 77002 work phone: 713 - 216 - 5423 This email is confidential and subject to important disclaimers and conditions including on offers for the purchase or sale of securities, accuracy and completeness of information, viruses, confidentiality, legal privilege, and legal entity disclaimers, available at http://www.jpmorgan.com/pages/disclosures/email. ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
[Tutor] extract specific column
Hi, I'm a beginner at python and I'm trying to extract a specific column from a txt file ( see attached file). In the attached file I want to extract the entire column pph2_prob (i.e. column 16). But I want to get all the values from that column without the headline pph2_prob. How do I accomplish that? Best, Anna #o_snp_id o_acc o_pos o_aa1 o_aa2 snp_id acc pos aa1 aa2 nt1 nt2 prediction based_oneffect pph2_class pph2_probpph2_FPRpph2_TPRpph2_FDR site regionPHATdScore Score1 Score2Nobs Nstruct Nfilt PDB_id PDB_pos PDB_ch ident length NormAcc SecStr MapRegdVol dProp B-fact H-bonds AveNHet MinDHet AveNInt MinDInt AveNSit MinDSitTransv CodPos CpG MinDJnc PfamHit IdPmax IdPSNP IdQmin Comments BSND_M1I Q8WZ551 M I BSND_M1I Q8WZ551 M I G T probably damaging alignment deleterious 0.999 0.00692 0.111 0.0222 2.055 2.148 0.093 10 0 1 2 0 0 17.5 BSND_M1K Q8WZ551 M K BSND_M1K Q8WZ551 M K T A probably damaging alignment deleterious 0.999 0.00692 0.111 0.0222 2.505 2.148 -0.357 10 0 1 1 0 0 17.5 BSND_M1L Q8WZ551 M L BSND_M1L Q8WZ551 M L A T probably damaging alignment deleterious 0.997 0.0208 0.332 0.0665 1.832.148 0.318 10 0 1 0 0 0 17.5 BSND_M1R Q8WZ551 M R BSND_M1R Q8WZ551 M R T G probably damaging alignment deleterious 0.999 0.00692 0.111 0.0222 2.505 2.148 -0.357 10 0 1 1 0 0 17.5 BSND_M1T Q8WZ551 M T BSND_M1T Q8WZ551 M T T C probably damaging alignment deleterious 0.999 0.00692 0.111 0.0222 2.505 2.148 -0.357 10 0 0 1 2 0 17.5 ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
[Tutor] extract specific column
Hi, I'm a beginner at python and I'm trying to extract a specific column from a txt file ( see attached file). In the attached file I want to extract the entire column pph2_prob (i.e. column 16). But I want to get all the values from that column without the headline pph2_prob. How do I accomplish that? Best, Anna ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] extract specific column
On Wed, Oct 12, 2011 at 12:21 PM, Anna Olofsson < olofsson_anna...@hotmail.com> wrote: > Hi, > > I'm a beginner at python and I'm trying to extract a specific column from a > txt file ( see attached file). > > In the attached file I want to extract the entire column* pph2_prob *(i.e. > column 16). But I want to get all the values from that column without the > headline * pph2_prob. > > *How do I accomplish that? > Hi Anna, We're more than happy to help, but we also would love to see what you've done so far. What have you tried so far? Can you get the entire column *with* the headline? When you show the effort that you've taken, you'll find people are much more inclined to help - very few people here will do your work for you, but most of us are perfectly willing to point you in the right direction! HTH, Wayne ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] extract specific column
On 12/10/2011 18:21, Anna Olofsson wrote:
Hi,
I'm a beginner at python and I'm trying to extract a specific column
from a txt file ( see attached file).
In the attached file I want to extract the entire column/pph2_prob
/(i.e. column 16). But I want to get all the values from that column
without the headline /pph2_prob.
/How do I accomplish that?
Best,
Anna
Dear Anna,
Using the CSV module should work.
Something along the lines of (untested):
inLines = CSV.DictReader("/path/to/myfile.csv")
data = []
for a in inLines:
data.append(a)
for line in data:
print line["/pph2_prob/"]
Once you've got that working you just need to put the results in a file,
instead of printing them.
On a practical note (and there may be many reasons why not to), it might
be easier to open in a spreadsheet and take the data from there
HTH,
Matt
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[Tutor] extract specific column
From: olofsson_anna...@hotmail.com To: tutor@python.org Subject: FW: [Tutor] extract specific column Date: Wed, 12 Oct 2011 21:59:34 +0200 The thing is, I don't know where to start. I know how to open the attached file, but I don't know how to work inside the file. Is this a csv file? Do I need to use a split function? In what way should I look at the file? As a string? As lines? Best, Anna From: waynejwer...@gmail.com Date: Wed, 12 Oct 2011 14:54:42 -0500 Subject: Re: [Tutor] extract specific column To: olofsson_anna...@hotmail.com CC: tutor@python.org On Wed, Oct 12, 2011 at 12:21 PM, Anna Olofsson wrote: Hi, I'm a beginner at python and I'm trying to extract a specific column from a txt file ( see attached file). In the attached file I want to extract the entire column pph2_prob (i.e. column 16). But I want to get all the values from that column without the headline pph2_prob. How do I accomplish that? Hi Anna, We're more than happy to help, but we also would love to see what you've done so far. What have you tried so far? Can you get the entire column *with* the headline? When you show the effort that you've taken, you'll find people are much more inclined to help - very few people here will do your work for you, but most of us are perfectly willing to point you in the right direction! HTH,Wayne #o_snp_id o_acc o_pos o_aa1 o_aa2 snp_id acc pos aa1 aa2 nt1 nt2 prediction based_oneffect pph2_class pph2_probpph2_FPRpph2_TPRpph2_FDR site regionPHATdScore Score1 Score2Nobs Nstruct Nfilt PDB_id PDB_pos PDB_ch ident length NormAcc SecStr MapRegdVol dProp B-fact H-bonds AveNHet MinDHet AveNInt MinDInt AveNSit MinDSitTransv CodPos CpG MinDJnc PfamHit IdPmax IdPSNP IdQmin Comments BSND_M1I Q8WZ551 M I BSND_M1I Q8WZ551 M I G T probably damaging alignment deleterious 0.999 0.00692 0.111 0.0222 2.055 2.148 0.093 10 0 1 2 0 0 17.5 BSND_M1K Q8WZ551 M K BSND_M1K Q8WZ551 M K T A probably damaging alignment deleterious 0.999 0.00692 0.111 0.0222 2.505 2.148 -0.357 10 0 1 1 0 0 17.5 BSND_M1L Q8WZ551 M L BSND_M1L Q8WZ551 M L A T probably damaging alignment deleterious 0.997 0.0208 0.332 0.0665 1.832.148 0.318 10 0 1 0 0 0 17.5 BSND_M1R Q8WZ551 M R BSND_M1R Q8WZ551 M R T G probably damaging alignment deleterious 0.999 0.00692 0.111 0.0222 2.505 2.148 -0.357 10 0 1 1 0 0 17.5 BSND_M1T Q8WZ551 M
[Tutor] FW: extract specific column
The thing is, I don't know where to start. I know how to open the attached file, but I don't know how to work inside the file. Is this a csv file? Do I need to use a split function? In what way should I look at the file? As a string? As lines? Best, Anna From: waynejwer...@gmail.com Date: Wed, 12 Oct 2011 14:54:42 -0500 Subject: Re: [Tutor] extract specific column To: olofsson_anna...@hotmail.com CC: tutor@python.org On Wed, Oct 12, 2011 at 12:21 PM, Anna Olofsson wrote: Hi, I'm a beginner at python and I'm trying to extract a specific column from a txt file ( see attached file). In the attached file I want to extract the entire column pph2_prob (i.e. column 16). But I want to get all the values from that column without the headline pph2_prob. How do I accomplish that? Hi Anna, We're more than happy to help, but we also would love to see what you've done so far. What have you tried so far? Can you get the entire column *with* the headline? When you show the effort that you've taken, you'll find people are much more inclined to help - very few people here will do your work for you, but most of us are perfectly willing to point you in the right direction! HTH,Wayne ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] extract specific column
On 10/12/2011 03:59 PM, Anna Olofsson wrote: (PLEASE don't top-post. And don't start multiple similar threads a couple of hours apart. Send your message as text without tons of blank lines, and don't assume the attachments will make it. In my case, I haven't a clue to what the file looks like.) From: olofsson_anna...@hotmail.com To: tutor@python.org Subject: FW: [Tutor] extract specific column Date: Wed, 12 Oct 2011 21:59:34 +0200 The thing is, I don't know where to start. I know how to open the attached file, but I don't know how to work inside the file. Is this a csv file? Do I need to use a split function? In what way should I look at the file? As a string? As lines? If you included about 5 lines of the file in your message, we might have a clue. When I saw the original message, I was going to respond with a message about using [col, col+1], which would give you one character from each line. -- DaveA ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] FW: extract specific column
Anna Olofsson wrote: The thing is, I don't know where to start. I know how to open the attached file, but I don't know how to work inside the file. Is this a csv file? Do I need to use a split function? In what way should I look at the file? As a string? As lines? It looks like a CSV file. Try opening it in Excel or OpenOffice spreadsheet and check that they are happy opening it as CSV. You'll probably need to play with the settings when you do, e.g. change the separator to tab instead of comma, etc. If you can open the file in Excel and get sensible results, you should be able to do the same thing with Python and the csv module. You can learn more about the csv module here: http://effbot.org/librarybook/csv.htm http://www.doughellmann.com/PyMOTW/csv/ After taking a quick glance at the file you provided, it looks to me like fixed width fields (padded with spaces) in a tab-separated format. So you might have to do some post-processing to get rid of the spaces. That's pretty easy: any time you extract a value, just call value.strip() to remove the spaces before doing anything else with it. -- Steven ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
[Tutor] Retrieve data from log file
Hi there, I'm sorry to ask this, I tried and example that was posted in 2009 but I couldn't make it work. I'm trying to parse a log file and retrieve what I just need. Hope you can help me with this, this is part of the log file: [2011-10-11 20:43:54:307] INFO [QuoteCompareDaoWSImpl: 24] Se va a invocar el ws de qualitas para comparar cotizaciones [2011-10-11 20:43:55:899] DEBUG [BaseQualitasDaoWS: 79] [http-80-3] wscall - hours:0.0 minutes:0.0 seconds:1.0 [2011-10-11 21:09:42:604] DEBUG [QuoteCompareDaoWSImpl: 25] [http-80-3]Se va a invocar el ws de qualitas para comparar cotizaciones [2011-10-11 21:09:42:708] DEBUG [BaseQualitasDaoWS: 71] [http-80-3] -request: 3519 [2011-10-12 21:02:43:380] DEBUG [BaseQualitasDaoWS: 78] [http-80-1][clientThread-Thread-3] -response: 3519 0 0 7650 2002 VOLKSWAGEN DERBY STD., 05 OCUP. 1 1 4 125 2 1091.24 20 2 0 279.26 50 2 0 310.0 8560 2 0 260.0 120 2 0 0.0 0 N 2011-10-12 2011-10-06 2011-10-09 0 17065 S 1109 1109 1109 14 0.0 1 0 0 14 12 1100.0 0 X01109 69 79 0 0 62 2 0.0 0 1940.5 400 46.57 262.58 2649.65 15 2011-10-06 2011-10-09 1940.5 400 46.57 262.58 2649.65 291.07 & [2011-10-12 21:02:43:383] DEBUG [BaseQualitasDaoWS: 86] [http-80-1][clientThread-Thread-3] -wscall - hours:0.0 minutes:0.0 seconds:3.0 & [2011-10-12 21:02:43:462] DEBUG [RestController : 81] [http-80-1][clientThread-Thread-3] - hours:0.0 minutes:0.0 seconds:16.0& It repeats itself for every transaction and I need to extract from this lines: [2011-10-12 21:02:43:383] DEBUG [BaseQualitasDaoWS: 86] [http-80-1][clientThread-Thread-3] -wscall - hours:0.0 minutes:0.0 seconds:3.0 & [2011-10-12 21:02:43:462] DEBUG [RestController : 81] [http-80-1][clientThread-Thread-3] - hours:0.0 minutes:0.0 seconds:16.0& this information: 2011-10-12 21:02:43:383 clientThread-Thread-3 hours:0.0 minutes:0.0 seconds:3.0 2011-10-12 21:02:43:462 clientThread-Thread-3 hours:0.0 minutes:0.0 seconds:16.0 Can this be done? Thanks! Abe ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor
[Tutor] Generic For Loop
I've been doing some research into C++, and I've noticed the for loops. Is
there a way to use the C++ version of the loops instead of the Python one?
For example, I believe that the Python syntax would be:
for a=1, a < 11, a += 1:
print(a)
print("Loop ended.")
if the 'for' keyword did it's function as in C++, Actionscript, or most
other programming languages. Is there a way to do this?
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Re: [Tutor] Generic For Loop
On 10/12/2011 8:41 PM, Max S. wrote:
I've been doing some research into C++, and I've noticed the for
loops. Is there a way to use the C++ version of the loops instead of
the Python one? For example, I believe that the Python syntax would be:
for a=1, a < 11, a += 1:
print(a)
print("Loop ended.")
if the 'for' keyword did it's function as in C++, Actionscript, or
most other programming languages. Is there a way to do this?
for i in range(1, 11, 1): # the final 1 can be omitted, as it is the
default value.
loop body
OR
i = 1
while i < 11:
i += 1
loop body
Your choice - that's all know of - and the for is easier to read and
write than the while.
--
Bob Gailer
919-636-4239
Chapel Hill NC
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Re: [Tutor] Generic For Loop
Thanks!
On Wed, Oct 12, 2011 at 8:56 PM, bob gailer wrote:
> On 10/12/2011 8:41 PM, Max S. wrote:
>
>> I've been doing some research into C++, and I've noticed the for loops.
>> Is there a way to use the C++ version of the loops instead of the Python
>> one? For example, I believe that the Python syntax would be:
>> for a=1, a < 11, a += 1:
>>print(a)
>> print("Loop ended.")
>> if the 'for' keyword did it's function as in C++, Actionscript, or most
>> other programming languages. Is there a way to do this?
>>
>
> for i in range(1, 11, 1): # the final 1 can be omitted, as it is the
> default value.
> loop body
>
> OR
>
> i = 1
> while i < 11:
> i += 1
> loop body
>
> Your choice - that's all know of - and the for is easier to read and write
> than the while.
>
> --
> Bob Gailer
> 919-636-4239
> Chapel Hill NC
>
>
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Re: [Tutor] Generic For Loop
On 13/10/11 01:41, Max S. wrote:
I've been doing some research into C++, and I've noticed the for loops.
If you are trying to program in Python you should probably research
Python rather than C++. Any tutorial will provide information about for
loops...
Is there a way to use the C++ version of the loops instead of the Python
one? For example, I believe that the Python syntax would be:
for a=1, a < 11, a += 1:
print(a)
print("Loop ended.")
for a in range(1,11): print( a )
if the 'for' keyword did it's function as in C++, Actionscript, or most
other programming languages. Is there a way to do this?
Of course, however...
Its generally better to think of the Python for lop as being a foreach
loop. It iterates over a collection.
The C style for loop is a much more primitive loop and is really just a
piece of syntactic sugar to implement a while loop:
a = 1
while a < 11:
a += 1
# loop body here
Because it is just a loosely disguised while loop you can put
arbitrarily complex expressions into it and to replicate those in Python
you need to use the while loop. But generally that kind of obfuscation
in C++ is better avoided anyway.
The Python style loop is much more powerful than C's in its ability to
iterate over lists, dictionaries, strings, files and any other iterable
object. C++ introduces iterators as a library class to address this and
enable foreach style processing, but at the expense of loop speed.
--
Alan G
Author of the Learn to Program web site
http://www.alan-g.me.uk/
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