cjlee112 / pygr Goto Github PK

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

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