cp ../../_A_01_evigene_1_3cvs-gffmerged/output/dropset/* ../input/
cp ../../_A_01_evigene_1_3cvs-gffmerged/output/okayset/* ../input/

mv ../input/3cv_gffmerged_cds.drop.aa ../input/3cv_gffmerged_cds.drop.aa.fasta
mv ../input/3cv_gffmerged_cds.okalt.aa ../input/3cv_gffmerged_cds.okalt.aa.fasta
mv ../input/3cv_gffmerged_cds.okay.aa ../input/3cv_gffmerged_cds.okay.aa.fasta
mv ../input/3cv_gffmerged_cds.drop.cds ../input/3cv_gffmerged_cds.drop.cds.fasta
mv ../input/3cv_gffmerged_cds.okalt.cds ../input/3cv_gffmerged_cds.okalt.cds.fasta
mv ../input/3cv_gffmerged_cds.okay.cds ../input/3cv_gffmerged_cds.okay.cds.fasta
mv ../input/3cv_gffmerged_cds.drop.fasta ../input/3cv_gffmerged_cds.drop.tr.fasta
mv ../input/3cv_gffmerged_cds.okalt.fasta ../input/3cv_gffmerged_cds.okalt.tr.fasta
mv ../input/3cv_gffmerged_cds.okay.fasta ../input/3cv_gffmerged_cds.okay.tr.fasta

mkdir ../intermediate_1_preparing-files
mkdir ../intermediate_2_prepare-network
mkdir ../intermediate_3_sequence-sets-per-group-type
mkdir ../output

# phureja_sequences_keep.txt was generated manually prior and copied over

cat ../input/3cv_gffmerged_cds.drop.aa.fasta ../input/3cv_gffmerged_cds.okalt.aa.fasta ../input/3cv_gffmerged_cds.okay.aa.fasta > ../input/pantr_aa.fasta
cat ../input/3cv_gffmerged_cds.drop.cds.fasta ../input/3cv_gffmerged_cds.okalt.cds.fasta ../input/3cv_gffmerged_cds.okay.cds.fasta > ../input/pantr_cds.fasta
cat ../input/3cv_gffmerged_cds.drop.tr.fasta ../input/3cv_gffmerged_cds.okalt.tr.fasta ../input/3cv_gffmerged_cds.okay.tr.fasta > ../input/pantr_tr.fasta