[BioPython] How to produce html report with biopython blast

[Bruno Santos]

My problem was not changing the align_view argument. Now it is working fine.
Thank you very much.  

Peter said:
>Probably you want hsp.align_length here.  I'd have to double check
>that all three
>parsers are consistent here (for text, html and xml blast).

That's exactly what I want, the hsp.align_length is not present in Class
Diagram for blast present on Biopython tutorial so it will be a good idea to
add it. Since I usually do what Christof suggest to calculate the
len(hsp.match) because I thought that information was not present in the
xml, only when I write the xml to a file and checked the file I noticed it
is present. 

I also have almost finished writing some documentation for Bio.Sequencing
module to work with ace files I will probably be able to finish it during
this week if I have time. So then I need to know how I can upload the file
so it be included in the BioPython documentation. 

Peter said:
>I'm not sure.  Are you sending emails from one email address via
>another account? 

Yes I always write the mails from this e-mail account so no idea why this is
happening. 

Thank very much once more. 
Bruno Santos

-----Mensagem original-----
De: p.j.a.cock at googlemail.com [mailto:p.j.a.cock at googlemail.com] Em nome de
Peter
Enviada: quarta-feira, 16 de Abril de 2008 14:55
Para: Bruno Santos
Cc: biopython at biopython.org
Assunto: Re: [BioPython] How to produce html report with biopython blast

>  Hi,
>
>  I am using  python to launch some BLAST searches, but instead of parsing
results
>  in Python  I only want to produce a html file. To do that I am using the
keyword
>  html='T',  but this don't seem to be enough to python produce the file.
Can anyone
>  tell me  how can I achieve my objective?

Are you running standalone blast or using the NCBI online version?

With Bio.Blast.NCBIWWW.qblast() use the argument format_type="HTML"

With Bio.Blast.NCBIStandalone.blastall() I would try html=True (not
literally a string "T",
but I can see why you were mislead) and/or the align_view argument
(see the stand
alone blast documentation).

>  Another  question I want to ask is in which method of blast_record I can
get
>  the hsp.align-len, that is basically the length of the aligned hit? This
value is
>  present in the xml file but in the class diagram available in Biopython
tutorial
>  and cookbook I can't see a method that returns this value

Probably you want hsp.align_length here.  I'd have to double check
that all three
parsers are consistent here (for text, html and xml blast).

> P.S.-I am  having lots of problems with sending messages to biopython
lists it
> always say  the message is awaiting approval because it contain a
suspicious
> header. Can  anyone tell me what I need to do to change this behavior?

I'm not sure.  Are you sending emails from one email address via
another account?

Peter