You have a Python script or package that is running perfectly. After you make some alterations, "all of a sudden" you can't run it because it can't find a variable or name:
AttributeError: 'module' object has no attribute 'foobar'
But if you search for that name, it doesn't …
“Suddenly” (as is traditional to commence these sort of stories), I started having problems with some of the Python installations on my local machine. As is the way of things, I had three distinct sources of Python:
IPython notebooks are an incredibly useful way to do reproducible research and illustrate chunks of code. Obviously you'd like to put some of them on the web. Surely there must be an easy way to include them in a Pelican-based website. So why hasn't anyone done it yet?
They have …
REDCap is a fabulously useful tool for creating web databases, including a useful scheme for defining the database schema ("data dictionaries") in plain CSV files. However, difficulties arise when designing complex schema. It is cumbersome to code multiuple occurences of essentially the same field (e.g. sample_1 ... sample_2 ...). If …
You need to convert a time difference into a floating point quantity, like 2.5 days. Or you may want to do something related like round a fdatetime difference up or down, e.g. 3 or 2 days for our previous example.
When you subtract a …
Way, way back, this site ran on various permutations of PHP-based frameworks. Getting sick of ugly URLs and having to vigilantly update the software so as to avoid hacks (and still periodically falling victim to various hacks), I went in search of a Python-based framework that I could customize …
(Originally published on BiocodersHub.)
If you’re doing bioinformatics in Python, you’re probably using Biopython. Actually, Biopython is a good reason for using Python. But it can be formidable to newcomers: there’s a lot there and there’s not a huge amount of learning material. This then is …
Buried in the Python standard library, unicodedata contains most the information needed to interrogate and translate unicode characters. Unfortunately, it's underdocumented. More accurately, the docs are a terse list of what it does, but not why you might want to use it or how you use it. Unfortunately it's also …
See Problem 8: Find the greatest product of five consecutive digits in a 1000-digit number.
This is fairly straightforward. First we define the number, using Python's implicit string continuation:
numstr = '73167176531330624919225119674426574742355349194934' '96983520312774506326239578318016984801869478851843' '85861560789112949495459501737958331952853208805511' '12540698747158523863050715693290963295227443043557' '66896648950445244523161731856403098711121722383113' '62229893423380308135336276614282806444486645238749' '30358907296290491560440772390713810515859307960866' '70172427121883998797908792274921901699720888093776' '65727333001053367881220235421809751254540594752243' '52584907711670556013604839586446706324415722155397' '53697817977846174064955149290862569321978468622482' '83972241375657056057490261407972968652414535100474' '82166370484403199890008895243450658541227588666881' '16427171479924442928230863465674813919123162824586' '17866458359124566529476545682848912883142607690042' '24219022671055626321111109370544217506941658960408' '07198403850962455444362981230987879927244284909188' '84580156166097919133875499200524063689912560717606' '05886116467109405077541002256983155200055935729725' '71636269561882670428252483600823257530420752963450' …
See Project Euler Problem 112: Find the point at which the porportion of bouncy numbers is 99%.
This is a simple problem to state, but has some tricks. First in the conversion of a number into its component digits. This can be neatly done with the [int (x) for x …
See Problem 7: What is the 10001st prime number?
This solution is fairly simple (and largely stolen from Aaron Gallagher):
def iter_primes ():
# handle trivial case
yield 2
val = 1
primesq_pairs = []
while True:
curr = None
while (curr is None):
val += 2
curr = val
for prime, square in primesq_pairs:
if (curr < square …
See Problem 20.
Again, this rescues a lot of code from previous problems, but the solution is less than perfect. The Euler guidelines say that every problem should be computable within a minute, but despite much tweaking, this solution takes significantly longer.
For speed, primes should be generated only once …
(Originally published on BiocodersHub)
Following several lengthy and passionate discussions in different venues on what language to use for teaching bioinformatics, I've started cutting and pasting my reply. And here it is.
You'll get a lot of different opinions on this because:
Note
This package has been taken over by TODO, who has substantially re-engineered it and chnaged some of the API. This page is maintained for largely historical purposes.
The problem of sanitizing data (checking correctness and transforming to a useful form) is widespread throughout programming:
(Previously published on BiocodersHub.)
Previously I'd spoken about how Biopython represents sequence data with the Seq class. But there is also the SeqRecord class:
Interactive command-line programs need to query users for information, be it text, choices from a list, or simple yes-or-no answers. qanda is a module of simple functions to prompt users for such information, allowing validation and cleanup of answers, default responses, consistent formatting and presentation of help text, hints …
In a way, tuples are one of the most magical parts of Python. How does the interpreter distinguish between a method call, a bracketed portion of a mathematical expression and an actual tuple?:
calc_midpoint (1, None, [2, 3], False) x = w + (x * y) a = (b, c)
The really smart thing …
So I was writing a web application using WSGI and - after working for a long time - it started erroring out with:
AssertionError: write() argument must be string
from deep inside the WSGI handler. Now, this usually means that you're returning unicode, which WSGI can't handle. However, it's quite happy to …
Who would of thunk it? print is a reserved word everywhere.
Perhaps this is buried in some specification, but it seems that you can't use print as the name of a method of a class. (It makes sense you can't override the global name, but in an object? Perhaps it's …
Note
Although I used psicons heavily for a while, better and more humane tools have come along. In particular, I'd recommend snakemake. This page is left here for historical interest
Scientific analysis can be problematic:
Recently, I had the need to get an informative name from a range of Python objects for generating a useful error message. Where problems started was that these objects could include classes (new-style and old), functions, lambdas and built-in types. And here the logic started getting tricky.
Many geospatial locations within the UK are given with the Ordnance Survey system. While common and highly accurate, this coordinate system is peculiar to the UK and incompatible with many modern cartography tools. This module presents functions for converting between these and the most widely spread longitude-latitude system.
So, epydoc used to be the neatest and bestest documentation tool available for Python. It produced documentation from introspecting code and thus was the easiest way to the most accurate API documentation. However, it looks like the project has been abandoned. Attempts to run it over code result in sometimes …
Let me explain: Ete2, a Python module for representing phylogenies, has a number of dependencies (MySQLdb, Numpy, PyQt, etc.) that it doesn’t necessarily need and it can be installed without them. If you don’t use the associated functionality, you won’t need these dependencies. But, irritatingly, ete2 tries …
Over the years, Apple has fallen in and out of love with Applescript, its "official" scripting language for MacOS. True, Applescript isn't going to go away any day now and true, it is a very simple language and easy to use. But if you don't want to have to learn …
In which an oddity in SQLAlchemy is spotted, and it turns out to be a bug not a misunderstanding.
The merge function in SQLAlchemy lets an object seem to get pushed to the database, but actually stores and returns a copy of the object. This is handy for when …
Matplotlib is cool. Did I say it was cool? I meant very cool. While principally a plotting library, it can be used for image manipulation and drawing.
Which is where our first problem occurs (as of the 0.8.4 version of matplotlib and possibly earlier). Should you try …
This package presents a number of methods for querying webservices for bibliographic information, and includes two scripts for querying and renaming files by ISBN.
This package can be installed by the usual Pythonic methods:
use your favourite installation tool:
% easy_install biblio.webquery
or download the source, unpack it …
Not that I'm picking on ElementTree or anything but ...
Normally XML documents will declare their character encoding in their opening tag. And, normally, this will be utf8. (This may be a standard.) So this is a common sight:
xml version='1.0' encoding='utf8'?>
An oddity in ElementTree is that …
Good news: you can get reliable and easy access to a proper, fully-featured database from within Python.
Bad news: you may have to tinker to get it to (a) install properly. And if not done properly, this may cause it to (b) not work properly.
Good news: Download a .dmg …
Pydee is new and nifty graphical frontend for using Ipython. Unfortunately, there's no monolithic binary package available for installing (at least not on the Mac), and so users have to install and compile all the prerequisites. Given the the number of steps and small but important details, it's easy to …
One of those weird things that always slips my mind and always seems less obvious than it should be.
Parsing a date (object) from a string representation in Python seems oddly neglected or cumbersome as compared to the rest of the standard library that surrounds it. (Witness the number of …
Add this to list of list of things I'm surprised I didn't know about Python. How do you use a percent / modulo ''%'' symbol in a string?
I had to do this the other day and it stumped me. How could it be that in <insert large number of years> I've …
Note
rst2beamer has been wildly successful and used far beyond what I imagined. Further development has been taken on by Ryan Krauss and subsequently others. The source has been moved to its own repo on github and that (and the PyPi page) should be used as the primary sources. No …
Biodiversity assessment demands objective measures, because ultimately conservation is an issue of economics, prioritizing the use of limited resources for preserving taxa. The most general framework for such metrics are those that assess evolutionary distinctiveness as judged by how much of a phylogeny is conserved. However, their applicability is …
While some people have reporting installing PIL on MacOSX without problems, there are legion reports that say otherwise. Frequently this revolve around PIL installing without JPEG support. There are a myriad of solutions (involving editing make files, configure flags, using fink to install dependencies, using package managers, casting goat entrails …
I've gotten used to manipulating members of Python objects with getattr, setattr etc. But a recent similar problem had me stumped. I had a class that I wanted to create a large number of similar behaving properties on (they would all manipulate an internal dictionary):
>>> f = Foo() >>> f.contributor = 'xyz' …
Around version 2.2, Python rejigged its classes with some useful extensions. Unfortunately these enhancements have been explained so poorly that they appear in little published code.
One such enhancement is __slots__. An attribute of this name in a class restricts what attributes can be created in objects of that …
Phylogenies are smoking guns. An evolutionary history carrys in its very shape the fingerprints of every process that effected its creation: extinctions, key adaptations, radiations, colonizations, changes in the tempo and mode of macroevolution.
Unfortunately analysing phylogenies is difficult. The calculations of interest to any investigator are sometimes intricate …