Extracting protein or nucleotide sequences from an assembly using a GFF file
You will need a gff3 file and the genome assembly it is based on.
To get the protein sequences of the genes identified in the gff3 file
/opt/perun/PASA_r20140417/misc_utilities/gff3_file_to_proteins.pl name_of_gff_file name_of_assembly prot > name_of_outputfile
To get the nucleotide equivalent (coding sequence) of the protein sequence
/opt/perun/PASA_r20140417/misc_utilities/gff3_file_to_proteins.pl name_of_gff_file name_of_assembly CDS > name_of_outputfile
To get the nucleotide equivalent (coding sequence) plus a certain amount of flanking sequence on both ends
/opt/perun/PASA_r20140417/misc_utilities/gff3_file_to_proteins.pl name_of_gff_file name_of_assembly CDS number_of_flanking_bases > name_of_outputfile
To get the nucleotide gene sequence
/opt/perun/PASA_r20140417/misc_utilities/gff3_file_to_proteins.pl name_of_gff_file name_of_assembly gene > name_of_outputfile
Note that the number of gene sequences returned may not be equivalent to the number of protein or CDS sequences returned due to alternative CDS/protein models
To get the nucleotide gene sequence plus a certain amount of flanking sequence
/opt/perun/PASA_r20140417/misc_utilities/gff3_file_to_proteins.pl name_of_gff_file name_of_assembly gene number_of_flanking_bases > name_of_outputfile