[BioPython] How to produce html report with biopython blast

[Peter]

>  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