[EMBOSS] jaspextract does not work

[Peter Rice]

On 05/14/12 20:41, Hermann Norpois wrote:
> To whom it may conern.
>
> I have problems to install the jaspar database. My emboss database
> directory is /usr/share/EMBOSS/data. The jaspar files are dummies. This is
> okay.
> I downloaded Archive.zip from the jaspar site, extracted it to ~/jaspar and
> got 3 directories:
>
> drwxr-xr-x  5 hnorpois hnorpois 4096 2012-05-14 21:04 all_data
> drwxr-xr-x 10 hnorpois hnorpois 4096 2012-05-14 21:04 jaspar_collections
> drwxr-xr-x  4 hnorpois hnorpois 4096 2012-05-14 21:04 jaspar_CORE
>
> Now i started from the command line
> jaspextract
> and get
>
> Extract data from JASPAR
> JASPAR database directory [.]:
>
> I do not understand what to type after JASPAR database directory [.]:
>
> I tried all variations I can imagine (e.g.: ~/jaspar, ~/jaspar/all_data,
> ~/jaspar/all_data/FlatFileDir) but I always get the answer:
>
> Error: Unable to open directory '~/jaspar/'
>
> Could anybody give me an instruction?


The help (jaspextract -help) has a clue. The directory is 'The 
FlatFileDir directory containing the .pfm files and the matrix_list.txt 
file' so if you are in the jaspar directory you could reply with 
all_data/FlatFileDir/

You are being (reasonably) confused because EMBOSS is not interpreting 
the '~' in your response. That is an omission by us ... it will fill in 
the directory when it sees '~' for an input file, but not for an input 
directory. This will be fixed in the next release. Meanwhile a full or 
relative path will be fine.

Hope this helps,

Peter Rice
EMBOSS Team