dewshr / ncbi-genbank-file-parser Goto Github PK

Just wondering how to run this on ubuntu? Sorry, couldn't see this in the readme file. I am getting the error: syntax error near unexpected token `newline'. Thanks!

Hi,

Could you add a licence to this code ? I think it is certainly an oversight.

Thank you in advance,
Jan

First off, the shebang is missing from the top, after adding

#usr/bin/env python

and running I've been getting an error.

I've tried running your script a few times to test the output, but haven't been able to get it to run properly.
Here is my output of running the script:

Enter your NCBI gene bank file name: ctg1.cluster001.gbk
2


Parsing started
1
Traceback (most recent call last):
  File "/home/seq/gbknuctest.py", line 128, in <module>
    ntgenbank()
  File "/home/seq/gbknuctest.py", line 50, in ntgenbank
    nm_version = (nm_and_version.split('.')[1]).strip('\n')
IndexError: list index out of range

The output file is blank besides the headers, but the .txt file generated is complete.
What i'm trying to get out of this ultimately is to have a csv containing every CDS and it's corresponding nucleotide sequence to add to an annotations summary file. While your script does much more than this, I haven't been able to find one that pulls the nucleotide sequence for every CDS in the file.

Not sure if this is due to an update in python or not, I'm currently running on python 2.7.15

Thanks in advance.