seqret doesn't count more than 99?

Charles Plessy charles at moulinette.dyndns.org
Fri Apr 26 21:30:56 UTC 2002


Hello,

I downloaded the draft of the fugu genome (fasta format, 300Mb) and
renamed the headers using the following command line :

sed < fugu_02_04_28.fasta 's/>/>gnl|fugu|/' > fugu_newheaders_02_04_28.fasta

I'm not able to index a blast database correctly if the header doesn't
look «ncbi compliant» ant formatdb haddn't been run with the -o flag.

I created the blast database and indexed it with dbiblast. The reason
for not formatting the fasta file itself is to save space. This also
enforces a synchronicity between the blast hits names and the names
that I can give to seqret.

Here is now the prbolem :

charles at pc-1035-a:~$ seqret fugu:Scaffold_7
Reads and writes (returns) sequences
Output sequence [scaffold_7.fasta]:  ==> OK!

charles at pc-1035-a:~$ seqret fugu:Scaffold_99
Reads and writes (returns) sequences
Output sequence [scaffold_99.fasta]: ==> OK!

charles at pc-1035-a:~$ seqret fugu:Scaffold_100
Reads and writes (returns) sequences
Error: Unable to read sequence 'fugu:Scaffold_100'

==> KO :((

seqret can't fetch sequences names like Scaffold_xzy, where xyz >= 100.

Is it due to the lenght of the name?
I am puzzled with that problem... I can send you more info if you like.

Charles




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