Integrating awk in Python
Hello, I'm developing a software package using python. I've programmed all necessary tools but I have to use other stuff from other people. Most of these external scripts are developed using awk. At the beggining I thought to "translate" them and program them in python but I prefer to avoid it because it means a lot of work and I should do it after each new version of this external stuff. I would like to integrate them into my python code. I know I can call them using the system environment but it is slower than if I call them inside the package. I know it is possible with C, do you have experience on integrate awk into python calling these awk scripts from python? Thanks in advance! Regards, Alfons. -- ---- Alfons Nonell-Canals, PhD Chemogenomics Lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Barcelona Biomedical Research Park (PRBB) C/ Doctor Aiguader, 88 - 08003 Barcelona alfons.non...@upf.edu - http://cgl.imim.es Tel. +34933160528 http://alfons.elmeuportal.cat http://www.selenocisteina.info -- http://mail.python.org/mailman/listinfo/python-list
Install modules with no root privilegies
Hello, Install python modules in a linux computer is really easy, it is because the module is a package of the distribution or because the python installation is really easy. But, in both situations, you need root privilegies. I would like to know how to install modules only for one user, with no root privilegies. Do you know if it is possible and easy. I would like to add that i need some modules only for my user and incly for one progam. Thanks in advance! Alfons. -- Alfons Nonell-Canals, PhD Chemogenomics Lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Barcelona Biomedical Research Park (PRBB) C/ Doctor Aiguader, 88 - 08003 Barcelona [EMAIL PROTECTED] - http://cgl.imim.es Tel. +34933160528 http://alfons.elmeuportal.cat http://www.selenocisteina.info -- http://mail.python.org/mailman/listinfo/python-list
Idenfity numbers in variables
Hello, I have a trouble and I don't know how to solve it. I am working with molecules and each molecule has a number of atoms. I obtain each atom spliting the molecule. Ok. It is fine and I have no problem with it. The problem is when I have to work with these atoms. These atoms usually are only a letter but, sometimes it can also contain one o more numbers. If they contein a number I have to manipulate them separately. If the number was allways the same I know how to identify them, for example, 1: atom = 'C1' if '1' in atom: print 'kk' But, how can I do to identify in '1' all possibilities from 1-9, I tried: if '[1-9]', \d,... Any comments, please? Regards, Alfons. -- Alfons Nonell-Canals, PhD Chemogenomics Lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Parc de Recerca Biomèdica de Barcelona (PRBB) C/ Doctor Aiguader, 88 - 08003 Barcelona [EMAIL PROTECTED] - http://cgl.imim.es http://alfons.elmeuportal.cat http://www.selenocisteina.info -- http://mail.python.org/mailman/listinfo/python-list
mySQL problems
Hello, I've developed a program using python that have to connect to a mysql server several times. In a local machine (running the program in the same machine where the mysql server is) I have no problems. I can run several instances of the program at the same time with no problem. Them problem arrives when I try to distribute the tasks to different machines, for example, in a cluster. In this situation, the machine that runs the python program is different than the machine that hosts the database. If I run the python program only an other machine, only one run of the program, there is no problem. But, If I run the program in different machines, all of them connecting to the same database server, randomly, it crash. Crash all running programs! at the same time. The output is clear: File "/cgl/programs/ChemBang/config.py", line 67, in mysql db = MySQLdb.connect(host=HOST, user="USER", passwd="PASSWD",db="DATABASE") File "/usr/local/lib/python2.5/site-packages/PIL/__init__.py", line 74, in Connect File "build/bdist.linux-x86_64/egg/MySQLdb/connections.py", line 170, in __init__ _mysql_exceptions.OperationalError: (2003, "Can't connect to MySQL server on 'HOST' (110)") It is clearly related with the connection to the mySQL server. As I said, it only happens when there are more than one programs running in different machines (or in the same) but conecting to a mysql server that is in an other machine. And... it is random, sometimes happens and sometimes no... Any idea? Thanks! Regards, Alfons. -- Alfons Nonell-Canals, PhD Chemogenomics Lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Barcelona Biomedical Research Park (PRBB) C/ Doctor Aiguader, 88 - 08003 Barcelona [EMAIL PROTECTED] - http://cgl.imim.es Tel. +34933160528 http://alfons.elmeuportal.cat http://www.selenocisteina.info -- http://mail.python.org/mailman/listinfo/python-list
Re: mySQL problems
Hi, > Maybe there is a certain connection limit which hits if your client > programms reconnect in random order? I saw this on some PHP web sites. > > Probably some configuration adjustments and persistent connections > could help you in this situation. I know I can check it but I am not the admin of the server where the mySQL server is and before to check it with the sysadmin I would like to discard other possibilities (they ask me to do this before) :-( > Also, was the choice of MySQL a conscious one? Yes, the choice of MySQL is conscious because I have to manage huge amounts of data and I already have some experience in mySQL which makes it easier. Regards, Alfons. > > Regards > Tino -- ---- Alfons Nonell-Canals, PhD Chemogenomics Lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Barcelona Biomedical Research Park (PRBB) C/ Doctor Aiguader, 88 - 08003 Barcelona [EMAIL PROTECTED] - http://cgl.imim.es Tel. +34933160528 http://alfons.elmeuportal.cat http://www.selenocisteina.info -- http://mail.python.org/mailman/listinfo/python-list
Generate documentation for a Python developed software
Dear all, I have a complex program developed using Python. It contains lot of files and classes. Now I have the lazy task to documentate it. I have some notes about is class but I would like to know if there is something to auto-generate the doucmentation with the program code. I know I will have to explain each class and variable but, if an external software canprepare it, the template, it will be great! Thanks in advance! Regards, -- Alfons Nonell-Canals Chemogenomics Lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Parc de Recerca Biomèdica de Barcelona (PRBB) C/ Doctor Aiguader, 88 - 08003 Barcelona [EMAIL PROTECTED] - http://cgl.imim.es http://alfons.elmeuportal.cat http://www.selenocisteina.info -- http://mail.python.org/mailman/listinfo/python-list
PSP problem showing images
Hello, I have experience working with Python an dnow I would like to use it for web development. I worked with php from several years ago and I'm trying to move to PSP. I have no problem runing some tests, implement an small project with psp is pretty easy. But I have only one problem, me scrips don't show any image. I developed a script which generates some images (is a work about Chemistry) and returns a page with some results and these images. When I run the script from the web browser, "all" works fine: the images are created, some other staff is calculated and the final page with the results is fine except the images. It does not print the images! I chech the paths and all is fine. With it I thought tha maybe there is something wrong in the apache's configuration. And I'm almost sure the problem is there because the Handler used only manages .psp documents. I add some code to not apply the Handler to .png but... help? Do you have any idea/experience? Below is the configuration of the host... ServerAdmin u...@domain.com ServerName www.domain.com ServerAlias domain.com # Indexes + Directory Root. DirectoryIndex index.psp DocumentRoot /path/to/the/pages AddHandler mod_python .psp PythonHandler mod_python.psp PythonDebug On Sethandler None # Logfiles ErrorLog /var/log/apache2/domain.com-error.log CustomLog /var/log/apache2/domain.com-access.log combined Thanks in advance! Regards, Alfons. -- ---- Alfons Nonell-Canals, PhD Chemogenomics Lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Barcelona Biomedical Research Park (PRBB) C/ Doctor Aiguader, 88 - 08003 Barcelona alfons.non...@upf.edu - http://cgl.imim.es Tel. +34933160528 http://alfons.elmeuportal.cat http://www.selenocisteina.info -- http://mail.python.org/mailman/listinfo/python-list
Re: PSP problem showing images
Hi Lawrence, Yes, I've tried it! I've saw the code, copyed the src path ans pasted into the browser and it works. I think it not works only unther a psp hostname/directory, for this reason I thought the problem is in the apache2 (site) configuration pasted in my mail... Thanks! Alfons. Lawrence D'Oliveiro wrote: > In message , Alfons > Nonell-Canals wrote: > > >> I developed a script which generates some images (is a work about >> Chemistry) and returns a page with some results and these images. When I >> run the script from the web browser, "all" works fine: the images are >> created, some other staff is calculated and the final page with the >> results is fine except the images. It does not print the images! I chech >> the paths and all is fine. >> > > Did you view source to check the URLs in the “” directives? > Did you try copying and pasting the image URLs directly into new > windows/tabs, to see if they came up or you got an error page instead? > -- Alfons Nonell-Canals, PhD Chemogenomics Lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Barcelona Biomedical Research Park (PRBB) C/ Doctor Aiguader, 88 - 08003 Barcelona alfons.non...@upf.edu - http://cgl.imim.es Tel. +34933160528 http://alfons.elmeuportal.cat http://www.selenocisteina.info -- http://mail.python.org/mailman/listinfo/python-list
Re: PSP problem showing images
Anybody of you have any idea? Alfons Nonell-Canals wrote: > Hi Lawrence, > Yes, I've tried it! I've saw the code, copyed the src path ans pasted > into the browser and it works. I think it not works only unther a psp > hostname/directory, for this reason I thought the problem is in the > apache2 (site) configuration pasted in my mail... > > Thanks! > Alfons. > > > > Lawrence D'Oliveiro wrote: > >> In message , Alfons >> Nonell-Canals wrote: >> >> >> >>> I developed a script which generates some images (is a work about >>> Chemistry) and returns a page with some results and these images. When I >>> run the script from the web browser, "all" works fine: the images are >>> created, some other staff is calculated and the final page with the >>> results is fine except the images. It does not print the images! I chech >>> the paths and all is fine. >>> >>> >> Did you view source to check the URLs in the “” directives? >> Did you try copying and pasting the image URLs directly into new >> windows/tabs, to see if they came up or you got an error page instead? >> >> > > -- Alfons Nonell-Canals, PhD Chemogenomics Lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Barcelona Biomedical Research Park (PRBB) C/ Doctor Aiguader, 88 - 08003 Barcelona alfons.non...@upf.edu - http://cgl.imim.es Tel. +34933160528 http://alfons.elmeuportal.cat http://www.selenocisteina.info -- http://mail.python.org/mailman/listinfo/python-list
Combining sets/dictionaries
Hello, I have different sets/dictionaries/lists (whatever you want because I can convert them easily) and I would like to combine them. I don't want a consensus and something like it. I'd need to combine all elements of the first one with the all elements of the second one and third,... the numbers of dictionaries/sets/lists is variable as the number of elements for each one. For example, i have the following sets and I would like to obtain all possible combinations... ['I', 'O', 'N', 'P', 'S', 'C'] ['I', 'O', 'N', 'P', 'S', 'C'] ['I', 'O', 'N', 'P', 'S', 'C'] ['I', 'N', 'P', 'S', 'C'] ['I', 'N', 'P', 'S', 'C'] ['F', 'I', 'L', 'O', 'N', 'P', 'S', 'R', 'C'] ['I', 'O', 'N', 'P', 'S', 'C'] ['I', 'O', 'N', 'P', 'S', 'C'] ['F', 'I', 'L', 'O', 'N', 'P', 'S', 'R', 'C'] And it should be flexible because as I've said, the number of dictionaries/lists/sets is not always the same, as the number of elements. I don't like to ask this kid of questions but... today I'm totally lost and I need it to close one part of a nice project... Thanks in advance! Best regards, Alfons. -- Alfons Nonell-Canals, PhD Chemogenomics Lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Barcelona Biomedical Research Park (PRBB) C/ Doctor Aiguader, 88 - 08003 Barcelona alfons.non...@upf.edu - http://cgl.imim.es Tel. +34933160528 http://alfons.elmeuportal.cat http://www.selenocisteina.info -- http://mail.python.org/mailman/listinfo/python-list
Re: Combining sets/dictionaries
Hello, finally I've solved it using a "combinatorics" library which allows to do this kind of things. Here, here is an example: http://automatthias.wordpress.com/2007/04/28/cartesian-product-of-multiple-sets/ Thanks for your suggestions. Regards, Alfons. Carl Banks wrote: > On Sep 22, 3:08 am, Alfons Nonell-Canals > wrote: > >> Hello, >> I have different sets/dictionaries/lists (whatever you want because I >> can convert them easily) and I would like to combine them. I don't want >> a consensus and something like it. I'd need to combine all elements of >> the first one with the all elements of the second one and third,... the >> numbers of dictionaries/sets/lists is variable as the number of elements >> for each one. >> >> For example, i have the following sets and I would like to obtain all >> possible combinations... >> >> ['I', 'O', 'N', 'P', 'S', 'C'] >> ['I', 'O', 'N', 'P', 'S', 'C'] >> ['I', 'O', 'N', 'P', 'S', 'C'] >> ['I', 'N', 'P', 'S', 'C'] >> ['I', 'N', 'P', 'S', 'C'] >> ['F', 'I', 'L', 'O', 'N', 'P', 'S', 'R', 'C'] >> ['I', 'O', 'N', 'P', 'S', 'C'] >> ['I', 'O', 'N', 'P', 'S', 'C'] >> ['F', 'I', 'L', 'O', 'N', 'P', 'S', 'R', 'C'] >> > > This is the input. What do you want the output to look like given > this input? > > I can't really tell exactly what you mean by "all combinations", there > are different ways to combine sequences, and it doesn't sound like you > mean the formal mathematical definition of "combination". > > My best guess is that you want something like this. > > def all_union(seqs): > s = set() > for seq in seqs: > s.update(seq) > return s > > > Carl Banks > -- Alfons Nonell-Canals, PhD Chemogenomics Lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Barcelona Biomedical Research Park (PRBB) C/ Doctor Aiguader, 88 - 08003 Barcelona alfons.non...@upf.edu - http://cgl.imim.es Tel. +34933160528 http://alfons.elmeuportal.cat http://www.selenocisteina.info -- http://mail.python.org/mailman/listinfo/python-list
