With the help of gthextractfasta one can extract the used fasta sequences from
GenomeThreader output files containing intermediate results. That is, all 
sequences which are represented in the intermediate files are printed in
fasta format on stdout. Strictly speaking, the sequences are not extracted from
the intermediate file, but from the corresponding sequence files.

gthextractfasta is called as follows:

gthextractfasta [options] intermediate_files

If no intermediate_file is given as imput, stdin is used instead. This allows
to use gthextractfasta in a UNIX pipe.

gthextractfasta offers the following options:

-containedcdna		extract cDNA/EST sequences 
-noncontainedcdna
-containedprotein	extract protein sequences
-noncontainedprotein   	
-containedgenomic   	extract genomic sequences 
-noncontainedgenomic

-cdna
-cdnacomplement
-protein
-proteincomplement
-genomic
-genomiccomplement

-gzip
-bzip2
-v
-help
