[BioPython] Protparam using BioPython

[Shameer Khadar]

Dear Peter,

Thanks for your reply. I was looking for a script based on Bio.SeqUtils.
I got the following script from a website, its working perfect for me. But
the problem is i have around 1000 sequence (in raw format without headers)
and i thought to process it using a foreach equivalent in python(I am a
python newbie). But its only a couple of minutes back i came to know that
there is no foreach in python, but some better alternative is available
!!!.  It will be great if you can help to process my file using this
program.

program :
from Bio.SeqUtils import ProtParam, ProtParamData
def PrintDictionary(MyDict):
        for i in MyDict.keys():
                print "%s\t%.2f" %(i, MyDict[i])
        print "MAEGEITTFTALTEKFNLPPGNYKKPKLLYCSNGGHFL"
X = ProtParam.ProteinAnalysis("")
print "Instability index of test protein: %.2f" % X.instability_index()

first few lines of my file :
AEGEFAHLYGTFRED
AEGEFAHLZGTFRED
AEGEFGATYGVYTSD
AEGEFGATZGVYTSD
AEGEFGATYGVZTSD
AEGEFGATZGVZTSD
AEGEFLYGEIQGTQD

Thank you once again,
Shameer

On 4/20/07, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> Shameer Khadar wrote:
> > Dear All,
> >
> > I am looking for a script to run Protparam for a 1000 sequence. It will
> be
> > great if anyone can point me to a program / web page to get it done.
>
> Do you mean the Biopython module Bio.SeqUtils.ProtParam which does
> protein analysis (e.g. isoelectric point).
>
> Did you mean the Expasy ProtParam tool available online?  If you only
> have a few sequences doing them online by hand would be easy:
> http://www.expasy.org/tools/protparam.html
>
> Or did you mean something else?
>
> Peter
>
> P.S. did you mean 1000 different sequences, or a single 1000 amino acid
> sequence?
>
>