This python script depends on external libraries, namely:
Both packages are easy-installable:
$ easy_install GFFutils $ easy_install pyfasta
Just locate the GFF file and the FASTA file, and then run the script:
$ ./gff_loader.py athaliana.gff athaliana.fa
This by default, extracts the mRNA IDs and pull out all subfeatures (CDS)
that have the same parent and concatenate the seqs together, reverse-complement
if needed. However sometimes the GFF does not use the standard names, this is
when you need to do:
$ ./gff_loader.py athaliana.gff athaliana.fa --parents Gene --children exon
If the GFF has meant coding sequences, but uses a different term.