Question: error to import NcbimakeblastdbCommandline
0
gravatar for flogin
4 days ago by
flogin150
flogin150 wrote:

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?

blast biopython python • 55 views
ADD COMMENTlink written 4 days ago by flogin150
1

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

ADD REPLYlink written 4 days ago by cpad011212k
1
gravatar for Joe
3 days ago by
Joe15k
United Kingdom
Joe15k wrote:

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 COMMENTlink written 3 days ago by Joe15k

Thanks, was really a version error :D

ADD REPLYlink written 3 days ago by flogin150
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