[Biophp-dev] Re: front end blast

[S Clark]

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This has been very confusing - but I am wondering if perhaps you haven't
got the right type of database files for the BLASTALL.EXE program?

It just sunk in as I re-read your last couple of emails that you are giving=
 a=20
"(something).txt" file as your database name - are you trying to use a plain
=46ASTA file for a BLAST database?

If so, I don't think that works.  There is a utility that converts the FASTA
file into a set of BLAST database files, which should all have the same
"database name" but with different file extensions.  So, if spopuri.txt is =
a=20
=46ASTA file of text sequences, you should use the "formatdb" (I guess this=
=20
would be "formatdb.exe" on windows) to convert the txt file to a set of BLA=
ST
database files - the command would be something like:

formatdb -i spopuri.txt -p F -n spopuri

(I am not 100% certain I have that command right, so you may need to
double-check in the documentation to make sure I'm not wrong about that)

Then when you call the blast frontend, the database name should just
be called "spopuri" (without the file extensions).  Then, the command
that the BLAST frontend should be trying to run would look something like:

C:\blast\blastall.exe -p 'blastn' -d 'spopuri' -i 'C:\WINDOWS\Temp\BQF273.T=
MP'=20
=2D -o 'C:\WINDOWS\Temp\BRF274.TMP' -v '25' -b '25' -T 'T'

Other than that, I don't THINK there is anything wrong with the output file=
 -
this file is created outside of PHP by the blastall program, not by PHP
itself.  The PHP frontend is only choosing what the filename will be (so th=
at
it will know what file to look in for the results when blastall.exe finishes
running).

Does any of that information help?  If not, I think the only thing left
that I can think of to try will be for me to create a "test" set of BLAST
database files and a specific "test" query to run, and I can try putting
that up where you can download it and try it out. =20

I am HOPING it is just a database format issue, though.  Let me know!

Sean

On Tuesday 30 December 2003 02:39 am, you wrote:
> Hi,
> Hope that you've spent a nice holidays.
> Concerning the last frontend_blast.php that you sent form me. The script
> return this message when it run. The following information was passed by
> the form:
> Sequence: atgcgatcgatcgat
> Database name: spopuri.txt
> Program: blastx
> Maximum "e-value": 10.0
> (Now attempting to run blastx query on the spopuri.txt database.)
> Got results! The results are:
>
> Until there, all is going for the best but no results are shown after the
> last line mentionned "got results! the results are " .... Only the form of
> "Example BLAST Frontend  Page" is re- shown after that ligne. !
>
> it works but does not return the result !
>
> Thank you and I wish you happy new year ! :)
>
> ANIBA.
>
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> >
> > Sorry about being so slow right now!
> >
> > I've come up with one more thing to try - we're about to leave
> > for the holidays, so I haven't had time to test this, but I've
> > made another test version of the blast frontend.
> > There are two changes - one is that it will ALWAY use
> > 'blast_results.html' as the filename for the results (and
> > without the temporary directory, so it SHOULD show up in the
> > same directory as the BLAST data files), and it should also
> > now get the entire text from the command line output instead of
> > just the last line. That assumes that I haven't done this too
> > quickly and made a stupid mistake somewhere, but give it a try
> > and see what it does. If I get a chance during the holiday I
> > will check email and see how it goes. Good luck!
> >
> > On Monday 22 December 2003 04:23 am, you wrote:
> > > hi clark !
> > > ------
> > > C:\WINDOWS\Temp\BQF273.TMP
> > > The resulting output will be stored temporarily in:
> > > C:\WINDOWS\Temp\BRF274.TMP Opened C:\WINDOWS\Temp\BQF273.TMP to save
> > > the sequence to it. Successfully wrote 52 characters of data to
> > > C:\WINDOWS\Temp\BQF273.TMP. Setting -i value to
> > > C:\WINDOWS\Temp\BQF273.TMP Setting -o value to
> > > C:\WINDOWS\Temp\BRF274.TMP
> > > Preparing to attempt to run C:\blast\blastall.exe -p 'blastn' -d
> > > 'seq1.txt' -i 'C:\WINDOWS\Temp\BQF273.TMP' -o
> > > 'C:\WINDOWS\Temp\BRF274.TMP' -v '25' -b '25' -T 'T' (If it doesn't
> > > work, try running this exact command from a console prompt to see wha=
t,
> > > if any, the error is.) Like, Dude! Something went wrong!
> > > If there is a line of output from the attempt, you'll see it here:
> > > -----
> > > when i go to C:\windows\temp\BQF273.tmp and i open it with wordpad or
> > > IE i find the sequence i entered, which prove that the file was opened
> > > with writing, but the file C:\windows\temp\BQR274.tmp contains no
> > > output result , it seems like the file was not opened or the writing
> > > result operation did not happen ! I THINK THAT the $resultfname is not
> > > open to write in it the blast results when the blast runs !! whereas =
we
> > > open $queryfname to write in it blastsequence ?,??? do u think it cou=
ld
> > > be that the problem ? ANIBA
> > >
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> > > > Another distracting business trip (what's a mere 700 mile drive?) b=
ut
> > > > while I'm here I'm going to try to get some time to make one last
> > > > attempt to figure out what's going on. It sounds like we've got it
> > > > boiled down to something to do with getting blastall.exe on windows
> > > > to properly generate the output file...
> > > >
> > > > Hopefully be able to post a further 'debug' attempt sometime
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