How to assemble mRNAs from gff file?

[JonB]

I have a gff file of genes that exist in mulitple isoforms and often several versions of mRNAs. I want to assemble all the exons for each gene to represent the longest isoform. I have tried bedtools and gffread, but I only get the sequences for each feature in the gff file. Any tips on how to do this?

Here's an example of my file:

##gff-version 3
###
scis396	noncoding	gene	286737	287339	.	-	.	ID=scign021128;Name=scign021128
scis396	noncoding	mRNA	286737	287339	3015	-	.	ID=scitn021128.1;Parent=scign021128;Name=scitn021128.1
scis396	noncoding	exon	286737	287339	.	-	.	Parent=scitn021128.1
###
scis673	noncoding	gene	85677	115116	.	+	.	ID=scign002358;Name=scign002358
scis673	noncoding	mRNA	113016	115116	6254	+	.	ID=scitn002358.1;Parent=scign002358;Name=scitn002358.1
scis673	noncoding	exon	113016	113049	.	+	.	Parent=scitn002358.1
scis673	noncoding	exon	113444	114538	.	+	.	Parent=scitn002358.1
scis673	noncoding	exon	114973	115116	.	+	.	Parent=scitn002358.1
scis673	noncoding	mRNA	85677	115099	3835	+	.	ID=scitn002358.2;Parent=scign002358;Name=scitn002358.2
scis673	noncoding	exon	85677	85697	.	+	.	Parent=scitn002358.2
scis673	noncoding	exon	113896	114538	.	+	.	Parent=scitn002358.2
scis673	noncoding	exon	114973	115099	.	+	.	Parent=scitn002358.2

[yueluo]

Google solves most problems, take a look at the following links (keywords: gff3, fasta)

http://gmod.827538.n3.nabble.com/Extracting-gene-sequences-from-GFF3-and-FASTA-library-for-Multi-FASTA-loading-into-Tripal-td3478935.html

http://www.biostars.org/p/46281/