tfextract problem

[Martín Sarachu]

Hi,

we're having a problem with transfac, it generates empty files.

Here is the output:

> # tfextract
> Extract data from TRANSFAC
> Full pathname of transfac SITE.DAT: /home/dbs/flatfiles/transfac/site.dat
> # ls -1s /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
> #

It does not give any error. Here's a sample of 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); .
........
> 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).
> //

We're using EMBOSS 2.4.1

Thanks for helping,

martin

-- 
Martín Sarachu
mad at biol.unlp.edu.ar
EMBNet Argentina
http://www.ar.embnet.org