[BioPython] How to produce html report with biopython blast
Peter
biopython at maubp.freeserve.co.uk
Wed Apr 16 13:55:11 UTC 2008
> 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
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