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 <u...@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/?a...@monk.mit.edu -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
