error to import NcbimakeblastdbCommandline
1
0
Entering edit mode
21 months ago
flogin ▴ 270

Hello guys, I'm with a problem to import the function NcbimakeblastdbCommandline from Bio.Blast.Applications.

This is my list of packages:

Package                            Version  
---------------------------------- ---------
alabaster                          0.7.10   
anaconda-client                    1.6.14   
anaconda-navigator                 1.8.7    
anaconda-project                   0.8.2    
asn1crypto                         0.24.0   
astroid                            1.6.3    
astropy                            3.0.2    
attrs                              18.1.0   
Babel                              2.5.3    
backcall                           0.1.0    
backports.shutil-get-terminal-size 1.0.0    
bcbio-gff                          0.6.4    
beautifulsoup4                     4.6.0    
bio                                0.1.0    
biopython                          1.72     
bitarray                           0.8.1    
bkcharts                           0.2      
blaze                              0.11.3   
bleach                             2.1.3    
bokeh                              0.12.16  
boto                               2.48.0   
Bottleneck                         1.2.1    
certifi                            2018.4.16
cffi                               1.11.5   
chardet                            3.0.4    
click                              6.7      
cloudpickle                        0.5.3    
clyent                             1.2.2    
colorama                           0.3.9    
conda                              4.5.11   
conda-build                        3.10.5   
conda-verify                       2.0.0    
contextlib2                        0.5.5    
cryptography                       2.2.2    
cycler                             0.10.0   
Cython                             0.28.2   
cytoolz                            0.9.0.1  
dask                               0.17.5   
datashape                          0.5.4    
decorator                          4.3.0    
distributed                        1.21.8   
docutils                           0.14     
entrypoints                        0.2.3    
et-xmlfile                         1.0.1    
ete3                               3.1.1    
fastcache                          1.0.2    
filelock                           3.0.4    
Flask                              1.0.2    
Flask-Cors                         3.0.4    
gevent                             1.3.0    
glob2                              0.6      
gmpy2                              2.0.8    
greenlet                           0.4.13   
h5py                               2.7.1    
heapdict                           1.0.0    
html5lib                           1.0.1    
idna                               2.6      
imageio                            2.3.0    
imagesize                          1.0.0    
ipykernel                          4.8.2    
ipython                            6.5.0    
ipython-genutils                   0.2.0    
ipywidgets                         7.2.1    
isort                              4.3.4    
itsdangerous                       0.24     
jdcal                              1.4      
jedi                               0.12.0   
Jinja2                             2.10     
jsonschema                         2.6.0    
jupyter                            1.0.0    
jupyter-client                     5.2.3    
jupyter-console                    5.2.0    
jupyter-core                       4.4.0    
jupyterlab                         0.32.1   
jupyterlab-launcher                0.10.5   
jupyterthemes                      0.19.6   
kiwisolver                         1.0.1    
lazy-object-proxy                  1.3.1    
lesscpy                            0.13.0   
llvmlite                           0.23.1   
locket                             0.2.0    
lxml                               4.2.1    
MarkupSafe                         1.0      
matplotlib                         2.2.2    
mccabe                             0.6.1    
mistune                            0.8.3    
mkl-fft                            1.0.0    
mkl-random                         1.0.1    
more-itertools                     4.1.0    
mpmath                             1.0.0    
msgpack                            0.5.6    
msgpack-python                     0.5.6    
multipledispatch                   0.5.0    
navigator-updater                  0.2.1    
nbconvert                          5.3.1    
nbformat                           4.4.0    
networkx                           2.1      
nltk                               3.3      
nose                               1.3.7    
notebook                           5.6.0    
numba                              0.38.0   
numexpr                            2.6.5    
numpy                              1.14.3   
numpydoc                           0.8.0    
odo                                0.5.1    
olefile                            0.45.1   
openpyxl                           2.5.3    
packaging                          17.1     
pandas                             0.23.0   
pandocfilters                      1.4.2    
parso                              0.2.0    
partd                              0.3.8    
path.py                            11.0.1   
pathlib2                           2.3.2    
patsy                              0.5.0    
pep8                               1.7.1    
pexpect                            4.5.0    
pickleshare                        0.7.4    
Pillow                             5.1.0    
pip                                18.0     
pkginfo                            1.4.2    
pluggy                             0.6.0    
ply                                3.11     
prometheus-client                  0.3.1    
prompt-toolkit                     1.0.15   
psutil                             5.4.5    
ptyprocess                         0.5.2    
py                                 1.5.3    
pycodestyle                        2.4.0    
pycosat                            0.6.3    
pycparser                          2.18     
pycrypto                           2.6.1    
pycurl                             7.43.0.1 
pyflakes                           1.6.0    
Pygments                           2.2.0    
pylint                             1.8.4    
pyodbc                             4.0.23   
pyOpenSSL                          18.0.0   
pyparsing                          2.2.0    
PySocks                            1.6.8    
pytest                             3.5.1    
pytest-arraydiff                   0.2      
pytest-astropy                     0.3.0    
pytest-doctestplus                 0.1.3    
pytest-openfiles                   0.3.0    
pytest-remotedata                  0.2.1    
python-awk                         0.0.2    
python-dateutil                    2.7.3    
pytz                               2018.4   
PyWavelets                         0.5.2    
PyYAML                             3.12     
pyzmq                              17.0.0   
QtAwesome                          0.4.4    
qtconsole                          4.3.1    
QtPy                               1.4.1    
requests                           2.18.4   
rope                               0.10.7   
ruamel-yaml                        0.15.35  
scikit-image                       0.13.1   
scikit-learn                       0.19.1   
scipy                              1.1.0    
seaborn                            0.8.1    
Send2Trash                         1.5.0    
setuptools                         39.1.0   
simplegeneric                      0.8.1    
singledispatch                     3.4.0.3  
six                                1.11.0   
snowballstemmer                    1.2.1    
sortedcollections                  0.6.1    
sortedcontainers                   1.5.10   
Sphinx                             1.7.4    
sphinxcontrib-websupport           1.0.1    
spyder                             3.2.8    
SQLAlchemy                         1.2.7    
statsmodels                        0.9.0    
sympy                              1.1.1    
tables                             3.4.3    
tblib                              1.3.2    
terminado                          0.8.1    
testpath                           0.3.1    
toolz                              0.9.0    
tornado                            5.0.2    
traitlets                          4.3.2    
typing                             3.6.4    
unicodecsv                         0.14.1   
urllib3                            1.22     
wcwidth                            0.1.7    
webencodings                       0.5.1    
Werkzeug                           0.14.1   
wheel                              0.31.1   
widgetsnbextension                 3.2.1    
wrapt                              1.10.11  
xlrd                               1.1.0    
XlsxWriter                         1.0.4    
xlwt                               1.3.0    
yahmm                              1.1.3    
zict                               0.1.3

When I put these lines in my code:

from Bio.Blast.Applications import NcbiblastnCommandline
from Bio.Blast.Applications import NcbimakeblastdbCommandline

Returns:

Traceback (most recent call last):
  File "blast_v01.py", line 21, in <module>
    from Bio.Blast.Applications import NcbimakeblastdbCommandline
ImportError: cannot import name 'NcbimakeblastdbCommandline'

As we can see only the line from Bio.Blast.Applications import NcbimakeblastdbCommandline produce the error.

How can I solve this problem?

python blast biopython • 590 views
ADD COMMENT
1
Entering edit mode

check the functions available in Bio.Blast.Applications. Make sure that you are using correct version.

ADD REPLY
1
Entering edit mode
21 months ago
Joe 19k

It looks to me like you have a VERY low version number for Bio = 0.1.0, when the tool is on a release well over 1.73 (which is what I currently have).

First step is to update the package I think.

ADD COMMENT
0
Entering edit mode

Thanks, was really a version error :D

ADD REPLY

Login before adding your answer.

Traffic: 2311 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6