tfextract not indexing?
Martín Sarachu
mad at biol.unlp.edu.ar
Mon Nov 11 19:18:00 UTC 2002
Hi,
tfextract is apparently running ok, but it's output are files are empty.
The command line is
> # tfextract -debug -warning -error -fatal -die -verbose
> Extract data from TRANSFAC
> Full pathname of transfac SITE.DAT: /home/work/dbs/transfac/site.dat
> #
and
> # ls -s /usr/local/emboss/share/EMBOSS/data/tf*
> 0 /usr/local/emboss/share/EMBOSS/data/tffungi
> 0 /usr/local/emboss/share/EMBOSS/data/tfinsect
> 0 /usr/local/emboss/share/EMBOSS/data/tfother
> 0 /usr/local/emboss/share/EMBOSS/data/tfplant
> 0 /usr/local/emboss/share/EMBOSS/data/tfvertebrate
...a sample from site.dat
> VV TRANSFAC SITES TABLE, V.2.4 25-08-1995
> XX
> //
> AC R00001
> XX
> ID HS$6-16_01
> XX
> DT 20.06.90 (created); .
> DT 24.08.95 10:48:05 (updated); EWI.
> XX
> TY DNA
> XX
> DE 6-16
> XX
> SE gGGAAAaTGAAACT
> XX
> EL ISRE
> XX
> SF -127
> ST -89
> XX
> ...
> ...
> SO 0811; B103
> ME gel shift competition
> RN [1]
> RA Suzuki-Yagawa Y., Kawakami K., Nagano K.
> RT Housekeeping Na,K-ATPase alpha1 subunit gene promoter is composed
> RT of multiple cis elements to which common and cell type-specific
> RT factors bind
> RL Mol. Cell. Biol. 12:4046-4055 (1992).
> DR EMBL; X52560; HSNFIL6(37:74).
> //
am I missing something?
Thanks,
martin
--
Martín Sarachu
mad at biol.unlp.edu.ar
EMBNet Argentina
http://www.ar.embnet.org
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