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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
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
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
Pyrex hasn't been updated in 8 years, so I guess people aren't using it anymore.
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