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View Code? Open in Web Editor NEWPython graph database framework for bioinformatics
Home Page: http://code.google.com/p/pygr
License: Other
Python graph database framework for bioinformatics
Home Page: http://code.google.com/p/pygr
License: Other
Pygr README =========== Introduction ------------ Pygr is an open source software project used to develop graph database interfaces for the popular Python language, with a strong emphasis on bioinformatics applications ranging from genome-wide analysis of alternative splicing patterns, to comparative genomics queries of multi-genome alignment data. For more information see http://pygr.org Latest Release -------------- http://code.google.com/p/pygr/downloads/list Documentation ------------- This distribution includes the full Pygr documentation source, but you will need the Sphinx documentation tool to build the formatted docs. You can get Sphinx via: easy_install -U Sphinx To build HTML versions of the docs using Sphinx: cd doc make html The docs are also available online: http://pygr.org/docs/latest-release/ Core Prerequisites ----------------- 1) Python >= 2.3 To build Pygr from source code, you need Pyrex Apps Prerequiites ----------------- MySQL-python >= 1.2.0 MySQL >= 3.23.x Note: While pygr's core functionality is solely dependent on a sane python environment, the aformentioned apps requirements must be installed if one wishes to utilize the apps modules and test code. Supported Platforms ------------------- In theory, pygr should work on any platform that adequately supports python. Here are the OS's we've successfully tested on: o Linux 2.2.x/2.4.x o OS X o OpenBSD o Windows XP Installation ------------ Installing pygr is quite simple. 1) tar -xzvf pygr-0.3.tar.gz 2) cd pygr 3) python setup.py install Once the test framework has completed successfully, the setup script will install pygr into python's respective site-packages directory. If you don't want to install pygr into your system-wide site-packages, replace the "python setup.py install" command with "python setup.py build". This will build pygr but not install it in site-packages. Using Pygr ---------- Check out the tutorials in the online docs! Pygr contains several modules imported as follows: from pygr import seqdb # IMPORT SEQUENCE DATABASE MODULE If you did not install pygr in your system-wide site-packages, you must set your PYTHONPATH to the location of your pygr build. For example, if your top-level pygr source directory is PYGRDIR then you'd type something like: setenv PYTHONPATH PYGRDIR/build/lib.linux-i686-2.3 where the last directory name depends on your specific architecture. License ------- New BSD license. Author ------ Chris Lee <[email protected]> and the rest of the Pygr developer team. Please see http://code.google.com/p/pygr for a current list of the participating developers. Also see http://github.com/cjlee112/pygr/ for a list of other developers who have created their own branches of the Pygr git repository.
Compatibility issue with Arch/Python3 (Arch linux installs defaults python3 on /usr/bin/python) so when runing pip install pygr
the result is:
Collecting pygr
Using cached pygr-0.8.2.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-build-tge2rfff/pygr/setup.py", line 19
print 'Setuptools not imported, falling back to distutils'
^
SyntaxError: Missing parentheses in call to 'print'
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-tge2rfff/pygr/
Collecting pyhgvs
Could not find a version that satisfies the requirement pyhgvs (from versions: )
No matching distribution found for pyhgvs
Pyrex hasn't been updated in 8 years, so I guess people aren't using it anymore.
I am running a script that uses pygr. I got this error. What does it mean and what should I change?
Traceback (most recent call last):
File "pwmScanning.py", line 239, in <module>
genome = read_genome("/u/home/a/annly200/project-vitamind/REF/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa")
File "pwmScanning.py", line 45, in read_genome
genome = seqdb.SequenceFileDB(fn)
File "/u/home/a/annly200/.conda/envs/pygr_conda/lib/python2.7/site-packages/pygr/seqdb.py", line 424, in __init__
seqLenDict = classutil.open_shelve(fullpath, 'r')
File "/u/home/a/annly200/.conda/envs/pygr_conda/lib/python2.7/site-packages/pygr/classutil.py", line 457, in open_shelve
return dbfile.shelve_open(filename, flag=mode, useHash=useHash)
File "/u/home/a/annly200/.conda/envs/pygr_conda/lib/python2.7/site-packages/pygr/dbfile.py", line 167, in shelve_open
d = open_index(filename, flag, useHash, mode) # construct Shelf only if OK
File "/u/home/a/annly200/.conda/envs/pygr_conda/lib/python2.7/site-packages/pygr/dbfile.py", line 106, in open_index
d = open_anydbm(filename, flag)
File "/u/home/a/annly200/.conda/envs/pygr_conda/lib/python2.7/site-packages/pygr/dbfile.py", line 46, in open_anydbm
raise WrongFormatError(msg)
pygr.dbfile.WrongFormatError: db type could not be determined
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