I am glad to announce the second edition of Python for Bioinformatics. In
today's data driven biology, programming knowledge is essential in turning
ideas into testable hypothesis. Based on my extensive experience, Python
for Bioinformatics, Second Edition helps biologists get to grips with the
bas
-- Forwarded message --
From: Roberto Alsina
Date: Fri, Sep 10, 2010 at 12:00 AM
Subject: [pyar] Issue 1 of "PET: English Translation" a Python magazine is
out!
To: python-announce-l...@python.org, Python Argentina
This magazine is a community effort. It's done by Python guys in
On Mon, Jun 14, 2010 at 11:02 AM, madhuri vio wrote:
> TypeError: Need a file handle, not a string (i.e. not a filename)
This says that the error is that you are using a filename where you
should be using a filehandle.
So this line:
for seq_record in SeqIO.read("ls_MTbH37Rv.fasta", "fasta"):
Sh
On Fri, May 28, 2010 at 9:41 AM, Tino Wildenhain wrote:
> Did you consider adding a part dealing with postgresql too?
> (Especially interesting in the way you can write stored functions
> in python there)
That is a good idea for the next version/edition. But meanwhile I
could write something in m
On Fri, May 28, 2010 at 12:37 AM, John Bokma wrote:
> I feel more than uncomfortable with example code that uses: user="root"
What's wrong with this? It is just an example of connection string.
The reader will use his/her user/pass/dbname according to their own
settings.
> (e.g. p291). I never g
Hello, I want to announce that the publisher of "Python for
Bioinformatis" (CRC Press) allowed me to publish a chapter from my
book.
I decided to publish the chapter about "Python and databases". I think
it may be useful for somebody.
The official announcement and download link is here:
http://py4b
On Thu, May 27, 2010 at 9:13 PM, Robert Kern wrote:
> ElementTree writes exactly what you tell it to. In XML, whitespace is
> significant. If you want newlines and/or indentation to make it
> pretty-looking, then you need to add those to your elements.
This is not always true. Let me quote an XML
Hi,
Could you post a minimal version of the DB (a DB dump) to test it?
Just remove most information and leave on the ones needed to reproduce
the error. Also remove any personal/confidential information. Then
dump the DB so I can test it here.
Best,
SB.
--
http://mail.python.org/mailman/listinfo/
On Tue, Mar 16, 2010 at 2:18 PM, wrote:
> I have a few dozen simple Python CGI scripts.
> Are there any advantages or disadvantages to rewriting these CGI scripts as
> WSGI scripts?
It depends of the script. WSGI should be faster since you don't start
a Python instance for each call (as in CGI).
On Wed, Feb 24, 2010 at 3:41 PM, Dennis Lee Bieber
wrote:
> No there isn't... The problem is that you need to put the wildcards
> into the parameter instead of the placeholder.
Thank you, it works now.
Best,
SB
--
http://mail.python.org/mailman/listinfo/python-list
c.execute("SELECT bin FROM bins WHERE qtl LIKE '%:keys%'",{'keys':keywords})
This query returns empty. When it is executed, keywords = 'harvest'.
To check it, I do it on the command line and it works as expected:
sqlite> SELECT bin FROM bins WHERE qtl LIKE '%harvest%';
11C
11D
12F
I guess there
On Sun, Dec 13, 2009 at 2:10 PM, Carsten Haese wrote:
from sets import Set
aSet = Set(['Small', 'Extra-small', 'Medium'])
You don't need to import "Set" since it is built in now:
>>> a=set([1,2,2,3,4,5])
>>> a
set([1, 2, 3, 4, 5])
(I have Python 2.6.2 but I think that this is availabl
On Sun, Dec 13, 2009 at 12:48 PM, Victor Subervi
wrote:
> Who said I was expecting a string? I don't know what I'm expecting! I need
> to be able to parse this thing, whatever it is. You say it's a Python Set
> object. How do I parse it? Googling has been disappointing.
You can walk thought a set
On Mon, Oct 19, 2009 at 5:53 AM, Piter_ wrote:
> Great.
> I've been waiting it.
> Any place in Europe to get it?
Go here:
http://www.crcpress.com/product/isbn/9781584889298
And then look at the bottom of the page and choose your country, I
know they have offices in London.
> P.S. Is anyone writi
On Mon, Oct 19, 2009 at 5:43 AM, Bearophile wrote:
> A more pythonic code is:
...
> Note the use of xrange and names_with_underscores. In Python names are
> usually lower case and their parts are separated by underscores.
Regarding underscore (and code notation in general) I wrote in the
book (pa
I announced that Python for Bioinformatics was ready, now I want to
announce that is available and in stock in most book sellers.
Worldwide, use Amazon.
In Argentina, it is more convenient buying it from me at MercadoLibre:
http://articulo.mercadolibre.com.ar/MLA-64715574-libro-python-for-bioinform
On Sat, Aug 15, 2009 at 10:29 PM, Douglas Alan wrote:
> Python doesn't run in your typical web browser, but it is common to
> use Python for doing the server-side programming, along with a Python-
> based web development framework, such as Django.
> You could use Jython to make a JVM applet that wo
On Thu, Aug 6, 2009 at 11:52 AM, Bearophile wrote:
> The book looks interesting, but that doesn't look like a good way to
> show/offer the code. I suggest to also put it into a zip that can be
> downloaded.
Code is also in a directory in the DVD and also inside the virtual
machine. Anyway I think
"Python for Bioinformatics"
ISBN 1584889292
Amazon: http://www.tinyurl.com/biopython
Publisher: http://www.crcpress.com/product/isbn/9781584889298
This book introduces programming concepts to life science researchers,
bioinformaticians, support staff, students, and everyone who is
interested in ap
On Fri, Jul 24, 2009 at 7:28 PM, superpollo wrote:
> is there a pythonic and synthetic way (maybe some standard module) to "pack"
> an integer (maybe a *VERY* big one) into a string? like this:
What do you mean to pack? Maybe Pickle is what you want.
import cPickle
variable = 124348654333577698
c
On Mon, Mar 23, 2009 at 9:15 PM, Muddy Coder wrote:
> I wonder that does Python have certificate? You see, java, .NET, PHP,
> and so on, they have certificates for developers to get. Python is
> quite popular nowadays, I wonder is there such a thing? If so, I
> certainly want to get one. I searche
On Sun, Feb 22, 2009 at 10:07 AM, Garrett Cooper wrote:
>It's not building lib_renderPM_libart properly, or it's a typo
> that supposed to be librenderPM_libart, or bad LDFLAGS...
>More details need to be provided like an ls of your site-packages
> directory and a partial ls of your local
I don't understand what is wrong when I try to install ReportLab. This
is under Ubuntu and all build packages are installed.
Here is what I get when trying to install it: (I could install it with
apt-get, but I am testing virtualenv and easy_install).
(testbio149)vi...@maricurie:~/Public/testbio14
On Wed, Jan 7, 2009 at 6:42 PM, Oltmans wrote:
> I'm writing a program in which I will ask users to enter user name and
> password once only. It's a console based program that will run on
In general you don't store the password, but a "hash" of it. Then when
the user logs-in, you hash it and comp
On Thu, Jan 1, 2009 at 2:19 PM, Barak, Ron wrote:
> I have a very big text file: I need to find the place where the last line
> begins (namely, the offset of the one-before-the-last '\n' + 1).
> Could you suggest a way to do that without getting all the file into memory
> (as I said, it's a big fi
On Wed, Oct 22, 2008 at 3:49 AM, Terry Reedy <[EMAIL PROTECTED]> wrote:
> Depending on the answer you get here, you might send the same observation
> and question to [EMAIL PROTECTED]
OK, I've just sent it. Thank you.
--
http://mail.python.org/mailman/listinfo/python-list
If I put IDLE in the search box at python.org, the first hit is:
http://www.python.org/idle/
But this page is a directory without any index file:
Index of /idle
Icon NameLast modified Size
Description[DIR] Parent Directory -
[ ] Makefile
On Tue, Oct 21, 2008 at 2:50 PM, Paulo J. Matos <[EMAIL PROTECTED]> wrote:
> I was just wondering, if you wish to commercialize an application
> developed in Python, what's the way to go?
You choose the conditions. Nothing in Python license prevents you of
selling your work.
> I guess the only wa
On Sat, Sep 27, 2008 at 3:32 PM, Eric Wertman <[EMAIL PROTECTED]> wrote:
> I've been growing a library of my own functions, that use the names of
> unix commands. They are just conveniences, of course, but I'd suggest
> the same for sysadmins, it's handy.
Can you share it?
Best,
SB.
--
http://ma
On Wed, Sep 24, 2008 at 10:17 AM, Marin Brkic
<[EMAIL PROTECTED]> wrote:
> As far as I know py2exe is the only option which can do such a thing
> (make exe files from scripts). Is there a way to make those exe files
> a little smaller (for a small script they easily go up to 5-10 mb).
An alternati
On 9/9/08, Beema Shafreen <[EMAIL PROTECTED]> wrote:
> I am using Biopython to fetch pumed Id's ,The module i use is (from Bio
> import Entrez)
> But i am getting this error
from Bio import Entrez
> Traceback (most recent call last):
> File "", line 1, in ?
> ImportError: cannot import name
On 2/26/08, Andreas Tawn <[EMAIL PROTECTED]> wrote:
> Maybe http://www.rosettacode.org ? That's a wiki.
YES!!!. Thank you!!
--
Sebastián Bassi (セバスティアン). Diplomado en Ciencia y Tecnología.
Curso Biologia molecular para programadores: http://tinyurl.com/2vv8w6
GPG Fingerprint: 9470 0980 620D ABFC
Hello,
I know there is one site with wikimedia software installed, that is
made for comparing the syntax of several computer languages (Python
included). But don't remember the URL. Anyone knows this site?
--
Sebastián Bassi (セバスティアン). Diplomado en Ciencia y Tecnología.
Curso Biologia molecular
I'm happy to report the release of a PLOS paper: "A Primer on Python
for Life Science Researchers".
It is a six page education paper introducing Python. If you have a
friend that is a researchers in a biological area and you think that
he may need to know Python, please send him this e-mail:
URL:
On 10/18/07, Adam Atlas <[EMAIL PROTECTED]> wrote:
>
> Use the builtin function "eval".
What is the difference with os.system()?
--
Sebastián Bassi (セバスティアン). Diplomado en Ciencia y Tecnología.
Curso Biologia molecular para programadores: http://tinyurl.com/2vv8w6
GPG Fingerprint: 9470 0980 620D
On 9/17/07, Stodge <[EMAIL PROTECTED]> wrote:
> Good idea, but I can't guarantee that the two scripts will be run from
> the same directory - so where to store the pickle?
It doesn't matter if is the same directory or not, as long as both
programs has access to the pickle file (one program should
On 9/16/07, Stodge <[EMAIL PROTECTED]> wrote:
> python app1.py --location=c:\test1
> What I want to do is save the location parameter, so I can then do (in
> the same window):
> python app2.py
> And have app2.py automatically have access to the value of "location".
Do app1.py to save a pickle of t
Hello,
What are people using these days to generate HTML? I still use
HTMLgen, but I want to know if there are new options. I don't
want/need a web-framework a la Zope, just want to produce valid HTML
from Python.
Best,
SB.
--
Sebastián Bassi (セバスティアン). Diplomado en Ciencia y Tecnología.
Curso B
On 8/27/07, J. Cliff Dyer <[EMAIL PROTECTED]> wrote:
> Play with your log to get the range you want
Here you can get "true" random numbers (not pseudorandom, they claim
to use a quatum generaton (?)) by fetching them from:
http://random.irb.hr/
They give you a python class t insert into your code
On 8/19/07, W. Watson <[EMAIL PROTECTED]> wrote:
> Google? What's that? Thanks. I like to get a insider's view when I know
> experts are out there. So now I ask a deeper question. Are there matrix
> computation libraries or even statistical (regression, factor analysis)
> libraries?
If you are so
On 8/15/07, Mikael Olofsson <[EMAIL PROTECTED]> wrote:
> What is unclear here is in what order the keys should be visited. The
> following assumes that the keys should be considered in alphanumeric order.
Yes, my fault. The orden should be given by a string, like:
DCDBA
Using this dictionay.
A={'
On 8/15/07, Wildemar Wildenburger <[EMAIL PROTECTED]> wrote:
> Oh but it is:
> >>> ADictionary={"one":["A","B","C","D"],"two":["H","I"]}
> >>> result = set()
> >>> for one in ADictionary["one"]:
> ... for two in ADictionary["two"]:
> ... result.add(one + two)
That was easy :)
What abou
I have 2 (or more) groups of elements, and I want to get all possible
unique combinations from all of them. Is there a build-in method to do
it?
ADictionary={"one":["A","B","C","D"],"two":["H","I"]}
I want to have all possible combinations from "one" and "two", that is:
AH
BI
CH
DI
AI
BH
CI
DH
On 7/15/07, John Machin <[EMAIL PROTECTED]> wrote:
> So you imagine that there is an undocumented feature?
No, I just think that is documented but I am not able to understand
it. Reading the list I've learned several things that are not directly
inferred from documentation (that is not the same as
On 7/13/07, Simon Hibbs <[EMAIL PROTECTED]> wrote:
> place. At the end of it you'll have a good idea how OOP works, and how
> Python works. Learning OOp this way is easy and painless, and what you
...
But this tutorial states "I assume you know how object-oriented
programming works"
--
Sebastián
Hi,
In my CSV file, the first line has the name of the variables. So the
data I want to parse resides from line 2 up to the end. Here is what I
do:
import csv
lines=csv.reader(open("MYFILE"))
lines.next() #this is just to avoid the first line
for line in lines:
DATA PARSING
This works fine.
I have this code:
import xml.parsers.expat
def start_element(name, attrs):
print 'Start element:', name, attrs
def end_element(name):
print 'End element:', name
def char_data(data):
print 'Character data:', repr(data)
p = xml.parsers.expat.ParserCreate()
p.StartElementHandler = start_e
I would like to remove the namespace information from my elements and
have just the tag without this information. This
"{http://uniprot.org/uniprot}"; is preapended into all my output.
I understand that the solution is related with "_namespace_map" but I
don't know much more.
>>> for x in eleroot
On 5/4/07, Leo Jay <[EMAIL PROTECTED]> wrote:
> i want to compile a python by myself, but after configure and make, it
> seems that md5 is not built by default.
>
> what should i do to compile md5 as an module?
md5 module was deprecated, now it functions are in hashlib.
(see http://docs.python.org
On 2 May 2007 07:14:04 -0700, redcic <[EMAIL PROTECTED]> wrote:
> And i get an out.txt file looking like:
> 1,2,3
> 10,20,30
> Whereas what I'd like to get is:
> 1,2,3,
> 10, 20, 30
> which is more readable.
The idea behind csv module is to produce and read csv files that are
"machine r
On 26 Apr 2007 14:48:29 -0700, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> Is there a better solution to avoid browser timeouts?
Raising timeout in Apache, by default is 300 seconds.
Limiting jobs size (both in the html form and from script size since
you should not trust on client validations)
On 26 Apr 2007 14:48:29 -0700, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> In order to work around this problem, I started printing empty strings
> (i.e. print "") so that the browser does not timeout.
How do you print something while doing the query and waiting for the results?
I saw some page
On 13 Apr 2007 21:14:36 -0700, Jia Lu <[EMAIL PROTECTED]> wrote:
> I donot want to use a real DB like MySQL ... But I need something to
> save about more than 1000 articles.
> Is there any good ways?
SQLite is a good option, as you were told. But what about put them in
a dictionary and then cPic
On 15 Apr 2007 15:44:47 -0700, [EMAIL PROTECTED]
<[EMAIL PROTECTED]> wrote:
> But errors and bugs do happen, inside data too; so often it's better
> to be on safe side if the safe code is fast enough.
Yes, I agree since I've seen lot of errors in data. But this data
comes from a taxonomy tree made
On 4/15/07, Peter Otten <[EMAIL PROTECTED]> wrote:
> Depending on your input data you may need to add some cycle detection.
> For example, try it with
> tree_path(1, {1:[2], 2:[1]}, [])
I guess this should make the program enter into a endless loop. But
the data won't have such a redundancy, becau
On 14 Apr 2007 09:32:07 -0700, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> def tree_path(key,tree,indent):
> print '\t'*indent,key
> if tree.has_key(key):
> for m in tree[key]:
> tree_path(m,tree,indent+1)
> return
Thank you. It worked!.
I changed it a bit to re
I have a two column list like:
2,131
6,335
7,6
8,9
10,131
131,99
5,10
And I want to store it in a tree-like structure.
So if I request 131, it should return all the child of 131, like 2, 10
and 5 (since 5 is child of 10).
If I request 335, it should return: 6 and 7.
If I request 9, it should retu
On 4/13/07, Jack <[EMAIL PROTECTED]> wrote:
> I wonder what everybody uses for Python editor/IDE on Linux?
> I use PyScripter on Windows, which is very good. Not sure if
> there's something handy like that on Linux. I need to do some
> development work on Linux and the distro I am using is Xubuntu.
On 4/3/07, Jaroslaw Zabiello <[EMAIL PROTECTED]> wrote:
> After executing
>./configure
> you have to edito
>Modules/Setup
> file and uncomment the following line:
> #zlib zlibmodule.c -I$(prefix)/include -L$(exec_prefix)/lib -lz
> Then continue with normal make; make install.
Thank you. I
I was trying to install Python 2.5 compiling from sources. I used:
./compile
It run OK.
Then:
make altintall
After a lot of output, got this:
Listing /usr/local/lib/python2.5/xml/sax ...
Compiling /usr/local/lib/python2.5/xml/sax/__init__.py ...
Compiling /usr/local/lib/python2.5/xml/sax/_exception
On 21 Mar 2007 12:18:50 -0700, Paddy <[EMAIL PROTECTED]> wrote:
> I just had a link to Tim peters first post on doctest:
> http://groups.google.com/group/comp.lang.python/msg/1c57cfb7b3772763
AFAIK, Google doesn't offer a permalink to usenet/group post (since a
mayor "upgrade" they made some
On 3/18/07, bruce peng <[EMAIL PROTECTED]> wrote:
> how to redirect the putput of the
> program to a file?
like this:
program_name -parameters > outfile.txt
--
http://mail.python.org/mailman/listinfo/python-list
On 17 Mar 2007 17:28:56 -0700, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
> I use os.system() to execute a system command in python.
> Can you please tell me how can I parse (in python) the output of the
> os.system() ?
Maybe you mean to parse the output of the program you run using
os.system.
On 3/15/07, Rob Clewley <[EMAIL PROTECTED]> wrote:
> Matplotlib supports boxplots in a very straightforward fashion and is
> reasonably documented (just google it!) I actually just submitted a
> patch for extra boxplot features in matplotlib, which you can find on
> the sourceforge patch tracker.
Hello,
Is there a graphic package for Python that provides support for box plots? (see
http://en.wikipedia.org/wiki/Box_plot and
http://en.wikipedia.org/wiki/Image:R-speed_of_light_boxplot.png for
information on box plots).
I have N sets of data, each with X "points".
Example:
Set 1:
Point 1: 0.
Hello,
I found http://www2.sfk.nl/svg as a Python module for writing SVG.
Last update was in 2004 and I am not sure if there is something
better.
Any recommendation for generating SVG graphics?
Best,
SB.
--
http://mail.python.org/mailman/listinfo/python-list
I am writing a paper where I refer to Python. Is there a paper that I
can refer the reader to? Or just use the Python web page as a
reference?
--
http://mail.python.org/mailman/listinfo/python-list
On 1 Sep 2006 00:57:04 -0700, crystalattice <[EMAIL PROTECTED]> wrote:
> I'd write for 2.4, even though 2.5 should be coming out "shortly".
> There aren't many significant changes to the whole language between 2.4
> and 2.5. Probably the best thing is write for 2.4 and have a sidenote
> stating wh
Hello all,
I am working on a Python book, since it could be completed in about a
year (writing time + edition + publishing) or more, I would like to
know what version to target since I don't want to release a book that
will be outdated just after is printed.
I use 2.4 for everyday work but most we
On 2/23/06, Diez B. Roggisch <[EMAIL PROTECTED]> wrote:
> "äöü".decode("ascii")
> should do the trick -- you get an UnicodeError when there is anything ascii
> can't encode.
Thank you. This is good enought for me.
Best regards,
SB.
--
Bioinformatics news: http://www.bioinformatica.info
Lriser: ht
Hello,
How do I detect non-ascii letters in a string?
I want to detect the condition that a string have a letter that is not
here: string.ascii_letters
Best regards,
SB.
--
Bioinformatics news: http://www.bioinformatica.info
Lriser: http://www.linspire.com/lraiser_success.php?serial=318
--
http
Hola,
Aca con una pregunta basica:
A veces veo que hay programas que tienen varias instrucciones en la
misma linea, cuando lo que aprendi de Python era que se usaba el
espaciado para mantener la estructura (indent).
Por ejemplo:
if name != 'comic': return
Hay un return despues de los dos puntos, n
On 9/30/05, Reinhold Birkenfeld <[EMAIL PROTECTED]> wrote:
> after Guido's pronouncement yesterday, in one of the next versions of Python
> there will be a conditional expression with the following syntax:
> X if C else Y
I don't understand why there is a new expression, if this could be
accomplis
On 19 Sep 2005 12:25:16 -0700, [EMAIL PROTECTED]
<[EMAIL PROTECTED]> wrote:
> >>> rs='AUGCUAGACGUGGAGUAG'
> >>> rs[12:15]='GAG'
> Traceback (most recent call last):
> File "", line 1, in ?
> rs[12:15]='GAG'
> TypeError: object doesn't support slice assignment
You should try Biopython (www.bi
On 7/20/05, Cyril Bazin <[EMAIL PROTECTED]> wrote:
> The question of the type of the data sutructure depends of your use of the
> data.
> You could avoid some confusion without naming your columns "lines"...
Yes, that is because they are "plant lines", that is why is called "lines" :)
> Anyway
On 20 Jul 2005 11:51:56 -0700, Graham Fawcett <[EMAIL PROTECTED]> wrote:
> You get the idea: model the data in the way that makes it most useable
> to you, and/or most efficient (if this is a large data set).
I don't think this could be called a large dataset (about 40Kb all the file).
It would b
On 20 Jul 2005 10:47:50 -0700, Graham Fawcett <[EMAIL PROTECTED]> wrote:
> # zip is your friend here. It lets you iterate
> # across your line names and corresponding values
> # in parallel.
This zip function is new to me, the only zip I knew was pkzip :). So
will read about it.
--
On 20 Jul 2005 10:47:50 -0700, Graham Fawcett <[EMAIL PROTECTED]> wrote:
> This looks a lot like 2D data (row/column), not 3D. What's the third
> axis? It looks, too, that you're not really interested in storage, but
> in analysis...
I think it as 3D like this:
1st axis: [MARKER]Name, like TDF1,
Hello,
I have to parse a text file (was excel, but I translated to CSV) like
the one below, and I am not sure how to store it (to manipulate it
later).
Here is an extract of the data:
Name,Allele,RHA280,RHA801,RHA373,RHA377,HA383
TDF1,181,
,188,
,190,
,193,*,*,,,
,None,,,*,*,*
,,
On 16 Jul 2005 09:51:55 -0700, [EMAIL PROTECTED]
<[EMAIL PROTECTED]> wrote:
> i want to get a small certificate or diploma in python.
> it should be online cuz i live in pakistan and wont have teast centers
> near me.
> it should be low cost as i am not rich.
> and hopefully it would be something l
Thanks, you are right!
On 6/20/05, Konstantin Veretennicov <[EMAIL PROTECTED]> wrote:
> > > type="image/svg+xml" name="wmap" wmode="transparent">
>
> Works for me...
--
http://www.spreadfirefox.com/?q=affiliates&id=24672&t=1";>La
web sin popups ni spyware: Usa Firefox en lugar de Internet
Ex
Hello,
I am using HTMLgen. It is very nice. But I can't make it to generate
an arbitrary command.
For example I want to output this:
Each time I put "<" it gets escaped from HTML, instead of being inserted inside.
--
http://www.spreadfirefox.com/?q=affiliates&id=24672&t=1";>La
web sin popups
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