[EMBOSS] SAM format

[Stephen Taylor]

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