[EMBOSS] jaspscan from the commandline

[Peter Rice]

On 15/05/2012 21:23, Hermann Norpois wrote:
> Hello,
>
> I tried to execute jaspscan from the command line and got the menu again.
> This is my syntax:
> (1) ~/embl/jtest$ jaspscan -sequence sequence.fasta -matrices @matrix_mouse
> -threshold 89.0
>
> matrix_mouse is a file and looks like this:
> ma0042.1, ma0090.1
>
> I tried it with upper case as well (MA..., MA...).
>
> matrix_mouse is in the same directory like sequence.fasta. It is the
> directory in which I start jaspscan.
>
> If I execute (1) I have to read:
>
> Scans DNA sequences for transcription factors
> Jaspar matrix set
>           C : Core
>           F : Fam
>           P : Phylofacts
>           N : CNE
>           O : POLII
>           S : SPLICE
>           B : PBM
>           L : PBM_HLH
>           H : PBM_HOMEO
>
> So jaspscan did not recognise my file matrix_mouse. I tried it with
> "@matrix_mouse",  '@matrix_mouse' etc .. Always the same. Could you please
> give me a hint concerning the correct syntax?

Your matrix.list file has a list of matrix names (the default is to use 
all matrices) but you still need to say which matrix set they belong to 
so jaspscan knows which directory to search.

You can simply add -menu c (or whatever section you are searching), or 
for the default value -auto which defaults all remaining prompted values.

> In addition: I would prefer an outputfile with the transcription factors in
> a list, e.g. like this
> accessionnumber of input sequence: TFa, TFb etc

The output is an EMBOSS "report" so you do have a choice of report 
formats available with the command line qualifier -rformat.

For example, you could use -rformat excel and then use excel or any 
other spreadsheet tool to select the columns you need.

We could also add more report formats to the next release, but I am not 
convinced this one is useful as it removes too much information.

However, we may be able to reduce the extra tags included in jaspscan 
output.

We may also be able to provide an applicationn that will post-propcess a 
standard report format and produce the summary you ask for, again in the 
next release.

Hope this helps

Peter Rice
EMBOSS Team