On 24/01/2011 11:45, Peter Rice wrote:
On 24/01/11 11:09, Stephen Taylor wrote:
Hi again Peter,
On 01/20/11 09:17, Stephen Taylor wrote:
Is there a bug in the gff3 output of fuzznuc?
##gff-version 3
##sequence-region chr21 1 46944323
#!Date 2011-01-20
#!Type DNA
#!Source-version EMBOSS 6.3.1
chr21 fuzznuc nucleotide_motif 13362906 13362942 37.000 + .
ID="chr21.1";note="*pat pattern"
It would be nice to actually show the pattern matched in the note field.
or both. What it shows is the "name" of the pattern, which usually
defaults to pattern.
Please can you define 'usually' i.e. What are the 'rules' for getting it
to show the pattern? Usual behaviour when I run it, is it shows
note="*pat pattern".
The pattern name defaults to 'pattern'. This will always be the case
when the user specifies a pattern on the command line with no other options.
Where multiple patterns are defined in an input file ('filename syntax
for the pattern), each has a unique name in the file.
The pattern name can also be set via the -pname qualifier.
So it makes sense to include the pattern string in the qualifier value,
and to rename it to "Pattern" in the report output.
I see. Many thanks for clearing that up.
Steve
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