[EMBOSS] SAM format

[Peter Rice]

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.

regards,

Peter