KEGG-to-anvio error: got an unexpected keyword argument "axis" #7
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Hello,
I just ran this through the parsing step on our server and it seems to be working so it’s possibly a versioning issue. What version of pandas and numpy are your running? We just need to pinpoint what’s different in your distribution vs mine.
Regards,
Elaina
… On Jul 7, 2018, at 7:05 PM, Smitdere ***@***.***> wrote:
I am trying to run the parser KEGG-to-anvio to import GhostKoala annotations into my anvio contigs database. When running the script with python 2 I get the following error message:
Traceback (most recent call last):
File "KEGG-to-anvio", line 38, in
extracted= extracted.rename({'description':'function'},axis='columns')
File "/usr/lib/python2.7/dist-packages/pandas/core/frame.py", line 2834, in rename
**kwargs)
File "/usr/lib/python2.7/dist-packages/pandas/core/generic.py", line 650, in rename
'argument "{0}"'.format(list(kwargs.keys())[0]))
TypeError: rename() got an unexpected keyword argument "axis"
Below is the command that I am running:
python KEGG-to-anvio --KeggDB KO_Orthology_ko00001.txt -i user_ko.fixed.txt -o KeggAnnotations-AnviImportable.txt
Attached is my GhostKoala output.
I am getting this error despite removing the first two rows which have no Kegg annotation in the second column, as recommended in other posts that I've read on the github.
Thanks,
Derek
user_ko.txt
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Hi Robert,
This is related to the issue I was already discussing with you. I consulted
the author via github and they seem to think it is an issue of not having
the right versions of either pandas or numpy. Can you check what versions
we have in the singularity omics -i bio.img?
Thanks!
…On Mon, Jul 9, 2018 at 8:42 AM, Elaina ***@***.***> wrote:
Hello,
I just ran this through the parsing step on our server and it seems to be
working so it’s possibly a versioning issue. What version of pandas and
numpy are your running? We just need to pinpoint what’s different in your
distribution vs mine.
Regards,
Elaina
> On Jul 7, 2018, at 7:05 PM, Smitdere ***@***.***> wrote:
>
> I am trying to run the parser KEGG-to-anvio to import GhostKoala
annotations into my anvio contigs database. When running the script with
python 2 I get the following error message:
>
> Traceback (most recent call last):
> File "KEGG-to-anvio", line 38, in
> extracted= extracted.rename({'description':'function'},axis='columns')
> File "/usr/lib/python2.7/dist-packages/pandas/core/frame.py", line
2834, in rename
> **kwargs)
> File "/usr/lib/python2.7/dist-packages/pandas/core/generic.py", line
650, in rename
> 'argument "{0}"'.format(list(kwargs.keys())[0]))
> TypeError: rename() got an unexpected keyword argument "axis"
>
> Below is the command that I am running:
> python KEGG-to-anvio --KeggDB KO_Orthology_ko00001.txt -i
user_ko.fixed.txt -o KeggAnnotations-AnviImportable.txt
>
> Attached is my GhostKoala output.
>
> I am getting this error despite removing the first two rows which have
no Kegg annotation in the second column, as recommended in other posts that
I've read on the github.
>
> Thanks,
> Derek
> user_ko.txt
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub, or mute the thread.
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<#7 (comment)>,
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.
--
Derek Smith
PhD Candidate
University of Michigan
Department of Earth and Environmental Sciences
smitdere@umich.edu
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It may also be helpful to look at the KeggDB file your using. If there’s in issue with that file you’d get a similar error.
… On Jul 9, 2018, at 10:42 AM, Smitdere ***@***.***> wrote:
Hi Robert,
This is related to the issue I was already discussing with you. I consulted
the author via github and they seem to think it is an issue of not having
the right versions of either pandas or numpy. Can you check what versions
we have in the singularity omics -i bio.img?
Thanks!
On Mon, Jul 9, 2018 at 8:42 AM, Elaina ***@***.***> wrote:
> Hello,
>
> I just ran this through the parsing step on our server and it seems to be
> working so it’s possibly a versioning issue. What version of pandas and
> numpy are your running? We just need to pinpoint what’s different in your
> distribution vs mine.
>
> Regards,
> Elaina
>
> > On Jul 7, 2018, at 7:05 PM, Smitdere ***@***.***> wrote:
> >
> > I am trying to run the parser KEGG-to-anvio to import GhostKoala
> annotations into my anvio contigs database. When running the script with
> python 2 I get the following error message:
> >
> > Traceback (most recent call last):
> > File "KEGG-to-anvio", line 38, in
> > extracted= extracted.rename({'description':'function'},axis='columns')
> > File "/usr/lib/python2.7/dist-packages/pandas/core/frame.py", line
> 2834, in rename
> > **kwargs)
> > File "/usr/lib/python2.7/dist-packages/pandas/core/generic.py", line
> 650, in rename
> > 'argument "{0}"'.format(list(kwargs.keys())[0]))
> > TypeError: rename() got an unexpected keyword argument "axis"
> >
> > Below is the command that I am running:
> > python KEGG-to-anvio --KeggDB KO_Orthology_ko00001.txt -i
> user_ko.fixed.txt -o KeggAnnotations-AnviImportable.txt
> >
> > Attached is my GhostKoala output.
> >
> > I am getting this error despite removing the first two rows which have
> no Kegg annotation in the second column, as recommended in other posts that
> I've read on the github.
> >
> > Thanks,
> > Derek
> > user_ko.txt
> >
> > —
> > You are receiving this because you are subscribed to this thread.
> > Reply to this email directly, view it on GitHub, or mute the thread.
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <#7 (comment)>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AYUGFx_TlTMtRyd5rkydx7pPY87xoF5tks5uE0_EgaJpZM4VGhft>
> .
>
--
Derek Smith
PhD Candidate
University of Michigan
Department of Earth and Environmental Sciences
***@***.***
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Hi Elaina,
We have pandas v 0.19 on our servers. We also found that the following edit
at line 38 in KEGG-to-anvio seemed to fix the issue as well:
change:
extracted= extracted.rename({'description':'function'},axis='columns')
to:
extracted= extracted.rename(columns={'description':'function'})
Cheers,
…On Mon, Jul 9, 2018 at 10:55 AM, Elaina ***@***.***> wrote:
It may also be helpful to look at the KeggDB file your using. If there’s
in issue with that file you’d get a similar error.
> On Jul 9, 2018, at 10:42 AM, Smitdere ***@***.***> wrote:
>
> Hi Robert,
>
> This is related to the issue I was already discussing with you. I
consulted
> the author via github and they seem to think it is an issue of not having
> the right versions of either pandas or numpy. Can you check what versions
> we have in the singularity omics -i bio.img?
>
> Thanks!
>
> On Mon, Jul 9, 2018 at 8:42 AM, Elaina ***@***.***> wrote:
>
> > Hello,
> >
> > I just ran this through the parsing step on our server and it seems to
be
> > working so it’s possibly a versioning issue. What version of pandas and
> > numpy are your running? We just need to pinpoint what’s different in
your
> > distribution vs mine.
> >
> > Regards,
> > Elaina
> >
> > > On Jul 7, 2018, at 7:05 PM, Smitdere ***@***.***>
wrote:
> > >
> > > I am trying to run the parser KEGG-to-anvio to import GhostKoala
> > annotations into my anvio contigs database. When running the script
with
> > python 2 I get the following error message:
> > >
> > > Traceback (most recent call last):
> > > File "KEGG-to-anvio", line 38, in
> > > extracted= extracted.rename({'description':'function'},axis=
'columns')
> > > File "/usr/lib/python2.7/dist-packages/pandas/core/frame.py", line
> > 2834, in rename
> > > **kwargs)
> > > File "/usr/lib/python2.7/dist-packages/pandas/core/generic.py", line
> > 650, in rename
> > > 'argument "{0}"'.format(list(kwargs.keys())[0]))
> > > TypeError: rename() got an unexpected keyword argument "axis"
> > >
> > > Below is the command that I am running:
> > > python KEGG-to-anvio --KeggDB KO_Orthology_ko00001.txt -i
> > user_ko.fixed.txt -o KeggAnnotations-AnviImportable.txt
> > >
> > > Attached is my GhostKoala output.
> > >
> > > I am getting this error despite removing the first two rows which
have
> > no Kegg annotation in the second column, as recommended in other posts
that
> > I've read on the github.
> > >
> > > Thanks,
> > > Derek
> > > user_ko.txt
> > >
> > > —
> > > You are receiving this because you are subscribed to this thread.
> > > Reply to this email directly, view it on GitHub, or mute the thread.
> >
> > —
> > You are receiving this because you authored the thread.
> > Reply to this email directly, view it on GitHub
> > <#7#
issuecomment-403465546>,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AYUGFx_
TlTMtRyd5rkydx7pPY87xoF5tks5uE0_EgaJpZM4VGhft>
> > .
> >
>
>
>
> --
> Derek Smith
> PhD Candidate
> University of Michigan
> Department of Earth and Environmental Sciences
> ***@***.***
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub, or mute the thread.
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<#7 (comment)>,
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.
--
Derek Smith
PhD Candidate
University of Michigan
Department of Earth and Environmental Sciences
smitdere@umich.edu
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Hello, thanks for the information, I am running pandas v.0.22. They must have changed the functionality of pandas.rename because removing the 'axis='columns'' causes the script to become non-functional. -Elaina |
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I am trying to run the parser KEGG-to-anvio to import GhostKoala annotations into my anvio contigs database. When running the script with python 2 I get the following error message:
Traceback (most recent call last):
File "KEGG-to-anvio", line 38, in
extracted= extracted.rename({'description':'function'},axis='columns')
File "/usr/lib/python2.7/dist-packages/pandas/core/frame.py", line 2834, in rename
**kwargs)
File "/usr/lib/python2.7/dist-packages/pandas/core/generic.py", line 650, in rename
'argument "{0}"'.format(list(kwargs.keys())[0]))
TypeError: rename() got an unexpected keyword argument "axis"
Below is the command that I am running:
python KEGG-to-anvio --KeggDB KO_Orthology_ko00001.txt -i user_ko.fixed.txt -o KeggAnnotations-AnviImportable.txt
Attached is my GhostKoala output.
I am getting this error despite removing the first two rows which have no Kegg annotation in the second column, as recommended in other posts that I've read on the github.
Thanks,
Derek
user_ko.txt
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