In article <browns02-2111961622070001 at mcrcr1.med.nyu.edu>,
browns02 at mcrcr.med.nyu.edu (Stuart M. Brown) writes:
>I am trying to build a simple tool (in VMS) that will take the output
>from a BLAST search and create a file containing alist of accession
>numbers that can be used as input for FETCH and/or PILEUP. In addition
>to the many wierd things that BLAST does with its database names for
>sequences, I seem to have run into an inconsistancy in how FETCH and
>PILEUP read list files. If I give FETCH an accession number, it has
>no trouble returning the database entry to my directory, but if I put
>that same accession number into a list file, FETCH ignores it. What is
>going on here?
Just a simple question, before more complicated
explanations... did you put the period period marker (..)
at the beginning of the list, and after that, I think you
HAVE to put the database before the accession number (like
genbank:U46228).
For more help, read the 2-18 section of the user's guide,
for example, entries have to be at the beginning of the line (no
space before). Note that several GCG programms CAN'T read the
begin and end attributes, you have to check for fetch. The
conversion to make a programm able to read it is not so
difficult.
Hope this helps,
Francois.
--
Francois Jeanmougin
Service de bioinformatique / bioinformatics service
IGBMC BP 163 67404 Illkirch France
tel :(France) 03 88 65 32 71 / (international) (+33) 3 88 65 32 71
e-mail : jeanmougin at igbmc.u-strasbg.fr
"C'est pas parcequ'on monte au banc, qu'il faut descendre a jeun." (Thiefaine)
