Dear Olivier, > I try to make indexes for the release 87 of EMBL with new first line > format: > > * I downloaded EMBOSS-3.0.0 > > * gunzip, tar xvf ... > > * I replaced the files with the files in the fixes directory
There was a new fix last week for the embl87 format. As you see the "emblnew" format, I assume you are using the latest fix. > but when I try the seqret application I obtained this output: > > >.1; .1; Human cytomegalovirus strain AD169 complete genome > gggccgcgtggtgggtcctcgaggggcgggggggtgtttttagcgggggggtgaaacttg > gagttgcgtgtgtggacggcgactagttgcgtgtggtgcggaggacggcgacggcgaata > aaagcgacgtgcggcgcgcacggcgaaaagaagacgcgtgtctgtgtctgtgtgattccc > ... That is what you see without the fixes. Can you check all the fix files were copied, including ajax/ajseqread.c which seqret uses to read the new format. > I tried to index these new files with EMBLNEW format (in place of EMBL) > as specified in the README file in the fixes directory but it is not a > valid format. emblnew is a sequence format, not an indexing format (dbiflat, dbxflat, and anything reading embl files should read both formats with the new fixes. > Does anyone index the new format EMBL flat file successfully? Yes, I did ... but if anyone else has problems please let me know. I will try tomorrow to set up a simple test for everyone to check on a short embl database. regards, Peter _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
