dewshr / ncbi-genbank-file-parser Goto Github PK
View Code? Open in Web Editor NEWThis program can be used to parse the NCBI GenBank file to create a tabulated csv file.
License: MIT License
This program can be used to parse the NCBI GenBank file to create a tabulated csv file.
License: MIT License
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!
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.
Hi,
Could you add a licence to this code ? I think it is certainly an oversight.
Thank you in advance,
Jan
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.