[EMBOSS] can't access databases indexed by dbifasta

[Marcus Claesson]

That works fine now, thanks!

But I continue struggling with upcoming problems and you must be tired
of me asking questions all the time... (It's either me or the emboss man
pages that are bad, probably a mix ;))

Anyway, when I want to create a second database ecoli_aa, dbifasta seems
to overwrite the old indexfiles.

This works all fine:

[marcus]$ dbifasta -idformat ncbi -directory /var/data/blast_db
-filenames ecoli.nt -fields des -dbname ecoli_nt -release 0.0 -date
00/00/00
[marcus]$ seqret ecoli_nt: -auto -stdout|head
>AE000111 AE000111.1 Escherichia coli K-12 MG1655 section 1 of 400 of
the complete genome
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
ACAA

I add a second database: 

[marcus]$ dbifasta -idformat ncbi -directory /var/data/blast_db
-filenames ecoli.aa -fields des -dbname ecoli_aa -release 0.0 -date
00/00/00

And when I seqret the old ecoli_nt I get the new ecoli_aa entries
instead:

[marcus]$ seqret ecoli_nt: -auto -stdout|head
>AAC73112.1 (AE000111) thr operon leader peptide [Escherichia coli]
MKRISTTITTTITITTGNGAG
>AAC73113.1 (AE000111) aspartokinase I, homoserine dehydrogenase I
[Escherichia coli]
MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA
LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA
ALICRGEKMSIAIMAGV


I tried to run dbifasta for both fasta files at the same time but it
didn't work:
dbifasta -idformat ncbi -directory /var/data/blast_db -filenames
ecoli.nt ecoli.aa -fields des -dbname ecoli_nt ecoli_aa -release 0.0
-date 00/00/00

How can new databases be added without overwriting the old indexfiles?


/Marcus




On Wed, 2004-02-18 at 13:50, Gary Williams, Tel 01223 494522 wrote:
> "Gary Williams, Tel 01223 494522" wrote:
> > 
> > Marcus Claesson wrote:
> > > But this doesn't work and I don't know why since I added the 'des
> > > field'. Are queries like these suppose to work by the way?
> > >
> > > [marcus]$ seqret ecoli_nt:\*mitochondrio\* -auto -stdout
> > > Error: Unable to read sequence 'ecoli_nt:*mitochondrio*'
> > > Died: seqret terminated: Bad value for '-sequence' with -auto defined
> > 
> > The correct syntax should be:
> > seqret ecoli_nt-des:\*mitochondrio\* -auto -stdout
> > See:
> > http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Themes/UniformSequenceAddress.html#keys
> 
> I think that the '*' are not required, so:
> seqret ecoli_nt-des:mitochondrio -auto -stdout