> 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
