[Biopython] Generating a fasta file from atomic coordinate file

[João Rodrigues]

Hi Ahmad,

You can use Bio.Seq directly on the PDB file:

from Bio import SeqIO
records = SeqIO.parse('1xyz.pdb', 'pdb-atom'):
with open('1xyz.fasta', 'w') as handle:
    SeqIO.write(records, handle, "fasta")

Not sure if there is a way to couple SeqIO directly to the Bio.PDB code (a
method that allows to read the sequence from the SMCRA object), that would
be cool to add.

Cheers,

João

2018-03-20 12:47 GMT-07:00 Jared Adolf-Bryfogle <jadolfbr at gmail.com>:

> 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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>
>
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