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#!/bin/sh
# wget ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/wgs/assembly/build_2.40/S_lycopersicum_chromosomes.2.40.fa.gz
# GFF has to be downloaded manually from
#
# http://solgenomics.net/itag/release/2.3/list_files#
# File ITAG2.3_gene_models.gff3
#
#
# Create genes.gff
echo Decompressing the file
cp ITAG2.3_gene_models.gff3.gz genes.gff.gz
rm -f genes.gff
gunzip genes.gff.gz
echo Fixing start-end problem
cat genes.gff | ./fixStartEnd.pl > g
mv g genes.gff
# Append FASTA Sequences
echo "###" >> genes.gff
echo "##FASTA" >> genes.gff
zcat S_lycopersicum_chromosomes.2.40.fa.gz >> genes.gff
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