[Bioperl-l] How to get the intron phase

[Filipe Garrett]

Hi all,

I'm new to bioperl and I was looking for a way to obtain the intron 
phases from genes in a FASTA format like this:

 >CG3427-RA type=transcript; 
loc=2R:complement(2273725..2274587,2274647..2274996,2275280..2275413,2275634..2275804,2275864..2276117,2276188..2276549,2277349..2277510,2277748..2277924,2278864..2279008,2279228..2279373,2279935..2280127,2280182..2280323,2280392..2280478,2280739..2280836,2281121..2281172,2285453..2285599,2300275..2300819); 
ID=CG3427-RA; name=Epac-RA; 
db_xref=FlyBase:FBtr0086132,FlyBase:FBgn0033102,Gadfly:CG3427-RA; 
release=r4.1; species=dmel; len=4028
CTCTCCAGCGGCGCACAACTCGATCGCTGGCCCAGAGGTTCAGTTCGGTT
TGGTTCGGTTCGGTTTGAATCTCTGCCTCTGTTTACGCCTCTATATC...

I've looked at the script directory and found the phase method inside 
the Bio::SeqFeature::Gene::Intron object, but the examples are from data 
parsed from a GFF file.

Can I bypass the GFF stuff and use the FASTA header information directly?

Thanks in advance,

Bests