Nicole Redaschi <redaschi at ebi.ac.uk> writes:
> we also had requests from other people to make the taxonomy flatfile we
> produce for in-house use publically available. You can find it on our ftp
> site ftp://ftp.ebi.ac.uk/pub/databases/taxonomy.
OK, I have the data and I am using the icarus files from the EBI to
replace the old ones in the SRS 5.1 distribution.
The -e and -f output options do not seem to work very well - they give
the bare values and not the line from the entry. Seems to be because of
the funny way the fields are saved in taxonomy.is which throws away
the line code:
> fields: ~ {$In:entry $Out $Skip:1}
> ('//' |
> /([A-Z][^:]+): ([^\n]*)\n/
> {$s=$2 $Wrt:[$fn.$Trim:$1 s:$Trim:$s]} |
> ln {$App}
> )+ x{$Wrt:[children s:' ']}
> ~
The links to TAX_UP and TAX_DOWN are fun in their way - but can I get
*all* ancestors or descendants directly rather than one at a time?
getz -e '[taxonomy-taxon:caenorhabditis elegans] > tax_up > tax_up \
> tax_up > tax_up > tax_up > tax_up > tax_up > tax_up > tax_up \
> tax_up > tax_up > tax_up > tax_up > tax_up > tax_up > tax_up \
> tax_up'
1
0
no rank
1
root
--
----------------------------------------------------------------------
Peter Rice | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/
