NameError: name 'utils' is not defined

[jorvis]

NameError: name 'utils' is not defined

[jorvis]

I'm a little confused by that. Your command line shows you invoking Perl to run the script, but then the stack trace is python. I'm assuming that is a mis-paste.

I'm not at a spot at the moment where I can edit and test this. If you open the tbl.py module there and replace each instance of " utils." with " biocode.utils." does this fix the problem?

[arsilan324]

I am sorry it was typo. I should have written python3 instead of perl; (fixed now) in the code above.
The code is here
https://github.com/jorvis/biocode/blob/master/gff/convert_gff3_to_ncbi_tbl.py

Even replacing utils with biocode.utils in the code doesn't work. Instead it says
NameError: name 'biocode' is not defined

[jorvis]

Would you mind making your input file available somewhere? Or you could email it to me at Gmail with this user name.

…

On Feb 9, 2018 5:57 PM, "arsilan324" ***@***.***> wrote: I am sorry it was typo. I should have written python3 instead of perl; (fixed now) in the code above. The code is here https://github.com/jorvis/biocode/blob/master/gff/ convert_gff3_to_ncbi_tbl.py Even replacing utils with utils with biocode.utils in the code doesn't work. Instead it says NameError: name 'biocode' is not defined — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#53 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAUMkw9Eu3v5djWRaXaSPl9l4VNKaVf7ks5tTNtlgaJpZM4SAmQY> .

[arsilan324]

I just wrote you email with the dropbox links..

[bernt-matthias]

as a follow up: replacing "utils." with " biocode.utils." does this fix the problem

[jorvis]

Thanks for the report. Corrected in commit 3e095dd

[eloguh]

I have the same problem, i can't resolve it, NameError: name 'biocode' is not defined

[jorvis]

@eloguh Did you happen to see if your script has the changes from the commit linked above? If not, maybe you still have the older script version. There are 4 lines of code that were corrected.

[eloguh]

what i did was correct the import El mié., 2 feb. 2022 21:05, Joshua Orvis ***@***.***> escribió:

…

@eloguh <https://github.com/eloguh> Did you happen to see if your script has the changes from the commit linked above? If not, maybe you still have the older script version. There are 4 lines of code that were corrected. — Reply to this email directly, view it on GitHub <#53 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AXK3BFI63MN4BREFIVF5YPDUZGFBVANCNFSM4EQCMQMA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[jorvis]

If you're not using a GitHub checkout then you should probably replace your tbl file with this one:

https://raw.githubusercontent.com/jorvis/biocode/3e095dd233dcf3353654f3958b6117a6f2d3ea44/lib/biocode/tbl.py

That's a critical part which uses the module name as needed.

[eloguh]

thanks El mié., 2 feb. 2022 22:08, Joshua Orvis ***@***.***> escribió:

…

If you're not using a GitHub checkout then you should probably replace your tbl file with this one: https://raw.githubusercontent.com/jorvis/biocode/3e095dd233dcf3353654f3958b6117a6f2d3ea44/lib/biocode/tbl.py That's a critical part which uses the module name as needed. — Reply to this email directly, view it on GitHub <#53 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AXK3BFLB7PC3BMDSWFCCWRTUZGMOTANCNFSM4EQCMQMA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[jorvis]

I'm surprised you're seeing this if you're using an updated version of biocode, as I've made a release since this bugfix was added.

[eloguh]

I still do not control much the general operation of the upload of codes El mié., 2 feb. 2022 22:39, Joshua Orvis ***@***.***> escribió:

…

I'm surprised you're seeing this if you're using an updated version of biocode, as I've made a release since this bugfix was added. — Reply to this email directly, view it on GitHub <#53 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AXK3BFP3XVT2IWFDAA6PEMTUZGQCVANCNFSM4EQCMQMA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>