I am just getting started on Python, though I know a bit of R. I want to replicate something someone has already done. I am receiving this error on one of my kernels on Jupyter and I don't immediately know what to do about it. Does anyone have any input or experience with it?
Traceback (most recent call last):
File "parse.py", line 8, in <module>
from param import ranked_blast_output_schema, blast_outfmt6_schema
ImportError: cannot import name 'ranked_blast_output_schema' from 'param' (/Users/myaccount/miniconda3/lib/python3.8/site-packages/param/__init__.py)
Traceback (most recent call last):
File "lca_analysis.py", line 52, in <module>
if ("~" in blast_results["query"].iloc[0]):
File "/Users/myaccount/miniconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 894, in __getitem__
return self._getitem_axis(maybe_callable, axis=axis)
File "/Users/myaccount/miniconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 1500, in _getitem_axis
self._validate_integer(key, axis)
File "/Users/myaccount/miniconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 1443, in _validate_integer
raise IndexError("single positional indexer is out-of-bounds")
IndexError: single positional indexer is out-of-bounds
Ah okay. I am replicating a Jupyter notebook and I was told to run this link on bash.
lca_analysis.py --blast_type nt --fpath s3://org_name/contigs/CMS001_002_Ra_S1/blast_nt.m9 --filtered_blast_path s3://bucket_name/contig_quality/CMS001_002_Ra_S1/blast_nt_filtered.m9 --excluded_contigs_path s3://bucket_name/contig_quality/CMS001_002_Ra_S1/exclude_contigs_nt.txt --outpath s3://bucket_name/contig_quality/CMS001_002_Ra_S1/lca_nt.m9 --read_count_path s3://bucket_name/contigs/CMS001_002_Ra_S1/contig_stats.json --verbose True
But then, I had this error
Read counts have been loaded: s3://bucket_name/contigs/CMS001_002_Ra_S1/contig_stats.json| elapsed time: 0.73 seconds
/var/folders/ns/gdtc2hvx1g13_29wct4qkhd80000gq/T/tmp3m3k6w9o blast file downloaded to this tempfile
Traceback (most recent call last):
File "parse.py", line 8, in <module>
from param import ranked_blast_output_schema, blast_outfmt6_schema
ImportError: cannot import name 'ranked_blast_output_schema' from 'param' (/Users/myaccount/miniconda3/lib/python3.8/site-packages/param/__init__.py)
Traceback (most recent call last):
File "lca_analysis.py", line 52, in <module>
if ("~" in blast_results["query"].iloc[0]):
File "/Users/myaccount/miniconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 894, in __getitem__
return self._getitem_axis(maybe_callable, axis=axis)
File "/Users/myaccount/miniconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 1500, in _getitem_axis
self._validate_integer(key, axis)
File "/Users/myaccount/miniconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 1443, in _validate_integer
raise IndexError("single positional indexer is out-of-bounds")
IndexError: single positional indexer is out-of-bounds
I had just used pip install param to get param, and the install went just fine.
Related
C:\Users\Lenovo>python next.py
Traceback (most recent call last):
File "C:\Users\Lenovo\next.py", line 1, in <module>
import pywhatkit
File "C:\Users\Lenovo\pywhatkit.py", line 2, in <module>
pywhatkit.sendwhatmsg("+917878807006", "Hi", 10, 24)
AttributeError: partially initialized module 'pywhatkit' has no attribute 'sendwhatmsg' (most likely due to a circular import)
tell me how to resolve it
and my file name is not same as module name
I've installed all per-requisites from. Build fails with the following error by using ./waf command.
Traceback (most recent call last):
File "/usr/lib/python3.6/py_compile.py", line 125, in compile
_optimize=optimize)
File "<frozen importlib._bootstrap_external>", line 741, in source_to_code
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/usr/local/lib/python3/dist-packages/visualizer/visualizer/svgitem.py", line 123
raise AttributeError, 'unknown property %s' % pspec.name
^
SyntaxError: invalid syntax
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 3, in <module>
File "/usr/lib/python3.6/py_compile.py", line 129, in compile
raise py_exc
py_compile.PyCompileError: File "/usr/local/lib/python3/dist-packages/visualizer/visualizer/svgitem.py", line 123
raise AttributeError, 'unknown property %s' % pspec.name
^
SyntaxError: invalid syntax
I will appreciate any help. Thank you.
You can disable python. First you need to clean your previous failed build and then configure by disabling the python.
./waf distclean
./waf --disable-python configure
./waf
I am trying to follow instruction from Enthought support website To test of what I have done i run line:
_python.exe canopy-script.pyw -d
Unfortunately this gives Traceback:
Traceback (most recent call last):
File "canopy-script.pyw", line 776, in <module>
File "canopy-script.pyw", line 336, in bootstrap
File "canopy-script.pyw", line 363, in chainload
File "canopy-script.pyw", line 762, in _chainload
File "C:\Users\User\AppData\Local\Enthought\Canopy\App\appdata\canopy-1.7.4.3348.win-x86_64\Canopy-script.pyw", line 7, in <module>
from canopy.app.bootstrap import main
ImportError: No module named canopy.app.bootstrap
After "Search" I can see many of bootstrap.py files on the disc.
What would be the solution for this problem?
The current version of Canopy is 2.1.9. (You are running v 1.7.4).
To update Canopy, and for a link to release notes, please see "Installing a new Canopy version".
After you update, see:
https://support.enthought.com/hc/en-us/articles/360021798791--UnresolvableRequirements-or-Conflicting-requirements-when-installing-or-updating-packages
I just installed gsutil on OS X, exactly following Google's instruction, and am seeing errors of the following format when running any gsutil command:
Traceback (most recent call last):
File "/Users//gsutil/gsutil", line 22, in <module>
gsutil.RunMain()
File "/Users//gsutil/gsutil.py", line 101, in RunMain
sys.exit(gslib.__main__.main())
File "/Users//gsutil/gslib/__main__.py", line 175, in main
command_runner = CommandRunner()
File "/Users//gsutil/gslib/command_runner.py", line 107, in __init__
self.command_map = self._LoadCommandMap()
File "/Users//gsutil/gslib/command_runner.py", line 113, in _LoadCommandMap
__import__('gslib.commands.%s' % module_name)
File "/Users//gsutil/gslib/commands/disablelogging.py", line 16, in <module>
from gslib.command import COMMAND_NAME
ImportError: cannot import name COMMAND_NAME
This error occurs on several modules in the commands directory. The only thing I could do to get rid of these errors is to remove the following modules from the directory which reference COMMAND_NAME: disablelogging, enablelogging, getacl, getcors, getdefacl, getlogging, setacl, setcors, setdefacl.
Did I do the right thing here? Is this a bug in gsutil?
I'm trying to use PuDB with ipython as the shell, but when I drop to shell, I get the following error:
can't set attribute
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/atexit.py", line 24, in _run_exitfuncs
func(*targs, **kargs)
File "/Library/Python/2.7/site-packages/IPython/core/interactiveshell.py", line 2744, in atexit_operations
self.reset(new_session=False)
File "/Library/Python/2.7/site-packages/IPython/core/interactiveshell.py", line 1132, in reset
self.displayhook.flush()
File "/Library/Python/2.7/site-packages/IPython/core/displayhook.py", line 255, in flush
self.shell.user_ns['_oh'].clear()
KeyError: '_oh'
Error in sys.exitfunc:
Traceback (most recent call last):
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/atexit.py", line 24, in _run_exitfuncs
func(*targs, **kargs)
File "/Library/Python/2.7/site-packages/IPython/core/interactiveshell.py", line 2744, in atexit_operations
self.reset(new_session=False)
File "/Library/Python/2.7/site-packages/IPython/core/interactiveshell.py", line 1132, in reset
self.displayhook.flush()
File "/Library/Python/2.7/site-packages/IPython/core/displayhook.py", line 255, in flush
self.shell.user_ns['_oh'].clear()
KeyError: '_oh'
Version details:
PuDB 2011.3.1
IPython 0.12
Python 2.7.1
Mac OS X 10.7.3
This is a known issue, and should be fixed in IPython 0.12.1 or master. Does updating to current (0.12.1) IPython help?