[Biopython-dev] Re: [BioPython] GRAVY index program anyone?

[Yair Benita]

on 1/8/03 9:40, Andrew Dalke at dalke at dalkescientific.com wrote:

> Yair:
>> Here is one of my functions. I have a collection of many protein
>> analysis
>> functions, maybe its time to put together a module.

> Andrew: 
> It would be.
Thanks for the feedback, Andrew. I already implemented your suggestions.

I recall we discussed this issue a few months ago. We talked about a "Tools"
module which will hold all analysis functions. The "Tools" module evolved to
something different and the analysis methods were forgotten.

My own modules have two analysis classes which are initialized with an
appropriate sequence object and have these methods:

class DnaAnalysis
    nucleotide content
    GC content
    Codon adaptation index

class ProteinAnalysis
    Amino acid content
    Molecular weight
    Aromaticity
    Calculate scale -> sliding window with any given dictionary.
    Instability index
    Flexibility
    isoelectric point
    Gravy
    secondary structure -> using Garnier
    
I guess there is some redundancy with existing modules. How should we
proceed with that? Maybe some of you prefer to separate DNA and Protein or
even make separate functions instead of classes.

I will clean up my code and send it soon.
Yair
-- 
Yair Benita
Pharmaceutical Proteomics
Faculty of Pharmacy
Utrecht University