[Bioperl-guts-l] Create is own mRNA Feature

Ewan Birney birney at ebi.ac.uk
Mon Feb 10 08:59:55 EST 2003


On Mon, 10 Feb 2003 Frederic.Fleche at aventis.com wrote:

> Hi Bioperl World,
> 
> 
> First of all, many thanks for developing very useful biological oriented
> tools.
> I am a newbie in Bioperl and I would like to know what is the way to add his
> own mRNA feature to an embl file which looks like this :
> 
> FT   mRNA            join(1001..1062,1768..1945,7968..8051,8376..8051,
> FT                   11711..11804,11895..12037,13172..13421,
> FT                   14062..14157,14933..15111,15908..15990,
> FT                   20244..20393,24155..25871)
> FT                   /label="CYP26"
> 
> 
> 
> In fact I know that if I want to add exons features to an embl file which
> look like these :
> 
> FT   exon            1001..1062
> FT                   /label="exon 1"
> FT   exon            1768..1945
> FT                   /label="exon 2"
> 
> I have to use code like the following :
> 
> $feat = new Bio::SeqFeature::Generic ( -start => $exon_start, 
> 				       -end => $exon_end,
> 				       -strand => 1, 
> 				       -primary => 'exon',
> 				       -tag    => { label => "exon $n" }
> 

Build a location object and then use that rather than start/end to 
intialise the location:



$loc = new Bio::Location::Split ();

$loc->add_sub_Location( new Bio::Location::Simple( -start => 1001, -end => 
1062, -strand => 1);

$loc->add_sub_Location( new Bio::Location::Simple( -start => 1768, -end => 
1945, -strand => 1);

...etc...

$feat = new Bio::SeqFeature::Generic( -primary -> 'mRNA', -location => 
$loc);




We should make the Bio::SeqFeature::Gene* classes work nicer so that this 
is easier, but it doesn't work at the moment, and you have to build things 
up by hand...





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