[BioPython] TMHMM

[Timothy Wu]

(sorry for the previous post, I accidently sent it before I finish it)

Hi,

Two things;

1. Is there a TMHMM module (and hopfully documented) in BioPython?

2. I had posted a similar question to the Python mailing list a long time
ago, but unfortunately I had not get a satisfiable answer. I hope I can find
some help here.

>From viewing TMHMM html source (http://www.cbs.dtu.dk/services/TMHMM/) I
think the form fields are:

seqfile --> file, which I don't know how to use, so I will not use it.
SEQ --> text box, which should be aa sequences
outform --> radio buttons, valid values are '-noshort', '-noplot', '-short'.
I would like to have it as '-short'
version --> a check box, valid value is '-v1'

I tested using urllib with something like this:

-----------------------------------------
params = urllib.urlencode({
'configfile':'/usr/opt/www/pub/CBS/services/TMHMM-2.0/TMHMM2.cf',
'SEQ':'VVDGLHQAETISSQGFKELFEGYGNFNNTRNGVEVENLKQAVIQKGADAIRTGSGSLGGTV',
'version': '-short'
})

f = urllib.urlopen("http://www.cbs.dtu.dk/cgi-bin/nph-webface", params)
sec = f.read()
-----------------------------------------

Of course, a successful TMHMM query requires me to read the return page from
urlopen, and parse another url
from within to obtain the final result page. But this is only the code to
obtain the intermediate page.

My problem is, notice my above strange code. For the 'version' field, I need
to fill in either '-v1' or leave it empty.
For outform (which I didn't include), I should have '-short'. But that
doesn't work! Had I done that it would return "Read: Field not declared;
'outform'".

I can get it to work if I only fill in "configfile" and "SEQ" fields. But I
would get the equivalent of having 'noshort' value in 'outform' (extensive
with graphics). The only way I am going to get the '-short' effect (one line
per protein) is to fill in '-short' in the version field. This is very
bizarre.

Is there something I am missing? SignalP which also is provided by the same
script also show this bizarre nature. I have also tried a perl script to do
the same thing. Strange behavior also result but not like the Python one:

-----------------------------------------
my $agent = new LWP::UserAgent;
my $request = POST($GS_URL,
Content_Type => 'form-data',
Content => [
configfile => '/usr/opt/www/pub/CBS/services/TMHMM-2.0/TMHMM2.cf',
 SEQ => 'VVDGLHQAETISSQGFKELFEGYGNFNNTRNGVEVENLKQAVIQKGADAIRTGSGSLGGTV',
outform => '-short',
]
);
-----------------------------------------

The script works. But if I swap the lines between configfile and seq
parameters, it doesn't. I am not really familier with Perl so I have no idea
why this is the way it is.
Anyone can tell me why I had to fill in '-noshort' in the supposingly wrong
field 'version'? Thanks a bunch.

Timothy