[Biopython] Generating a fasta file from atomic coordinate file

[Jared Adolf-Bryfogle]

Hey Ahmad,

I have a script called get_seq.py in the bio-jade module, which uses
BioPython.

pip install bio-jade.

The script will be installed to your path and you can use get_seq.py --help
for more info. You may need to source your bashrc/profile afterward or open
a new terminal to see it.

If you have any issues, please let me know.  I may need to but out a new
version.

https://bio-jade.readthedocs.io/en/latest/apps_public_api/apps.public.general.html#get-seq-py

https://github.com/SchiefLab/Jade

-Jared


Jared Adolf-Bryfogle, Ph.D.
Research Associate
Lab of Dr. William Schief
The Scripps Research Institute

On Tue, Mar 20, 2018 at 1:42 PM, Ahmad Abdelzaher <underoath006 at gmail.com>
wrote:

> Hello,
>
> Can I generate a properly formatted fasta sequence from the atomic
> coordinates of a pdb file? I sort of know how to code it, but hopefully
> there's some ready method in one of Biopython's modules that can do that.
>
> Any other suggestions?
>
> Regards.
>
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