[Debian-med-packaging] Bug#792510: blast_formatter: need internet access even if run locally

[Yann Dumont]

Just one point, as I read your answer : the GI number mentioned in my
message is from the query file, not from the subject file. It is just
a precision, since the work-around will still work.

You are very welcome, since I only do troubleshooting and you may do
the hardest part of the debugging !

2015-07-22 17:17 GMT+02:00 Aaron M. Ucko <ucko at debian.org>:
>> Is there any way to by-pass this ? Telling blast to write sequence in
>> the ASN file systematically ? Is it a expected behaviour ?
>
> AFAICT, blastx and the like have no such option at present, but I expect
> it would be relatively straightforward to implement one.  Also, it might
> be possible to run blast_formatter with environment settings telling it
> to retrieve sequence data from your local BLAST database; I'm not sure
> what the precise syntax would be, but will investigate and get back to
> you.
>
> Meanwhile, I suppose you could work around the issue by disguising the
> well-known sequence IDs prior to running makeblastdb:
>
>   sed -e '/^>/y,|,!,; s/^>\([a-z]\)/>lcl|\1' foo.aa > foo-disguised.aa
>
> Of course, you'd then likely want a compensatory transformation on the
> output side.
>
> Thanks for all your help diagnosing the problem!
>
> --
> Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
> http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu