[BioPython] PDB -> FASTA

[Iddo]

Welcome aboard, and I am glad we managed to save one  Jedi from the dark 
side of  bioinformatics...;)

As to your question:  see the attached class. I should get that in 
Biopython, but I keep not doing that....

./I


Douglas Kojetin wrote:

> Hi All-
>
> I'm a beginner @ biopython (and I'm 'switching' from perl to python 
> ...).  First off, many thanks for the structrual biopython FAQ ... 
> very helpful!  My question:  can anyone help me with some ideas on how 
> to whip up a quick PDB->FASTA (sequence) script?
>
> From the structural biopython faq, I've been able to extract residue 
> information in the form of:
>
>  <Residue MET het=  resseq=1 icode= >
>
> I take it I would just need to grab the MET (split the residue object 
> and grab the r[1] index?) and convert into M, then append to a 
> sequence string ....
>
> but I didn't know if biopython had something that did an 
> autoconversion of MET->M, or vice versa (M->MET).
>
> Thanks for the input,
> Doug
>
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>


-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 North Torrey Pines Road
La Jolla, CA 92037 USA
T: (858) 646 3100 x3516
F: (858) 713 9930
http://ffas.ljcrf.edu/~iddo

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