You hard drive or SMART tool reports errors when reading specific blocks similar to this message:
[3142.686141] end_request: I/O error, dev sda, sector 31415926
No matter how often you read the block, the hard drive still returns an error and does not reallocate the block.
Torrent files are essentially containers that store information about a set of files to be downloaded via P2P.
Unfortunately it is not easily possible to simply list the files that are stored in a torrent. Using our python script
torrentls.py you can easily accomplish that task.
Just like many other databases in computational biology, the downloads for the popular UniProt database are available in a custom text format which is documented on ExPASy.
While it is certainly not difficult writing a generic parser and one can use BioPython, I believe it is often easier to use a tested parser that only uses standard libraries.
Recently I started to add unit tests using setuptools to one of my packages.
In order to do this, I added a
test directory containing
setup.py was properly setup using the
However, when running
python setup.py test
I got this error message:
running test running egg_info writing MyPackage.egg-info/PKG-INFO writing top-level names to MyPackage.egg-info/top_level.txt writing dependency_links to MyPackage.egg-info/dependency_links.txt reading manifest file 'MyPackage.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'MyPackage.egg-info/SOURCES.txt' running build_ext Traceback (most recent call last): File "setup.py", line 29, in <module> 'Topic :: Scientific/Engineering :: Information Analysis' File "/usr/lib/python3.4/distutils/core.py", line 148, in setup dist.run_commands() File "/usr/lib/python3.4/distutils/dist.py", line 955, in run_commands self.run_command(cmd) File "/usr/lib/python3.4/distutils/dist.py", line 974, in run_command cmd_obj.run() File "/usr/lib/python3/dist-packages/setuptools/command/test.py", line 135, in run self.with_project_on_sys_path(self.run_tests) File "/usr/lib/python3/dist-packages/setuptools/command/test.py", line 116, in with_project_on_sys_path func() File "/usr/lib/python3/dist-packages/setuptools/command/test.py", line 160, in run_tests testLoader = cks File "/usr/lib/python3.4/unittest/main.py", line 92, in __init__ self.parseArgs(argv) File "/usr/lib/python3.4/unittest/main.py", line 139, in parseArgs self.createTests() File "/usr/lib/python3.4/unittest/main.py", line 146, in createTests self.module) File "/usr/lib/python3.4/unittest/loader.py", line 146, in loadTestsFromNames suites = [self.loadTestsFromName(name, module) for name in names] File "/usr/lib/python3.4/unittest/loader.py", line 146, in <listcomp> suites = [self.loadTestsFromName(name, module) for name in names] File "/usr/lib/python3.4/unittest/loader.py", line 117, in loadTestsFromName return self.loadTestsFromModule(obj) File "/usr/lib/python3/dist-packages/setuptools/command/test.py", line 26, in loadTestsFromModule for file in resource_listdir(module.__name__, ''): File "/usr/lib/python3/dist-packages/pkg_resources.py", line 954, in resource_listdir resource_name File "/usr/lib/python3/dist-packages/pkg_resources.py", line 1378, in resource_listdir return self._listdir(self._fn(self.module_path,resource_name)) File "/usr/lib/python3/dist-packages/pkg_resources.py", line 1415, in _listdir "Can't perform this operation for unregistered loader type" NotImplementedError: Can't perform this operation for unregistered loader type
You need a list of countries, ordered by continent, under a liberal license.
You need to calculate the center star approximation for a given set of sequences. Instead of calculating the sequence distances and center string by hand, you want the computer to do the hard work.
You need to parse a GFF3 file containing information about sequence features. You prefer to use a minimal, depedency-free solution instead of importing the GFF3 data into a database right away. However, you need to have a standard-compatible parser
If you Google GO OBO parser, there is something missing. You can easily find parsers in Perl, parsers in Java, but not even BioPython has a parser in Python. The format itself, however seems like it’s tailor-made for Python’s generator concept. Only a few SLOCs are needed to get it work without storing everything in RAM.
I used this parser in a prototype project that allows to search GO interactively (it’s fast). I’m not sure when/if I’ll publish that, but here is the parser code.
It is surprisingly difficult to compute simple statistics of FASTA files using existing software. I recently needed to compute the nucleotide count and relative GC frequency of a single sequence in FASTA format, but unless you install dependency-heavy native software like FASTX or you develop it by yourself using BioPython or similar, there doesn’t seem to be a simple, dependency-free solution for this simple set of problem.