[EMBOSS] Searching for repeats in fuzznuc

[Phillip San Miguel]

Peter Rice wrote:
> [...]
>   
>
> % fuzznuc -pattern @tg.pat
>
> Hope that helps,
>
> Peter
>   
Hi Peter,
    Along these lines, I've noticed that dreg wants the pattern file 
name to be all caps. Eg.

# cat test.pat
 >CCHC
TG[CT].{6}TG[CT].{12}CA[CT](?:...){4,5}TG[CT]
# dreg -rformat gff -stdout -auto -sequence HEX0238L06merge.fasta @test.pat
Error: Unable to open regular expression file 'TEST.PAT'
Error: Bad regular expression pattern:
   '@TEST.PAT'
Died: dreg terminated: Bad value for '-pattern' with -auto defined
# ln -s test.pat TEST.PAT
# dreg -rformat gff -stdout -auto -sequence HEX0238L06merge.fasta @test.pat
##gff-version 2.0
##date 2007-06-21
##Type DNA HEX0238L06Merged_Contigs
HEX0238L06Merged_Contigs        dreg    misc_feature    25288   25329   
0.000   +       .       Sequence "HEX0238L06Merged_Contigs.1" ; note 
"*pat CCHC"

Phillip