Description for usage of the scripts

# create full length viruses from contigs

for f in \*/contigs.fa; do echo ${f%%/contigs.fa}; python create_full_length_virus.py ${f} SARS_CoV2.fa ${f%%contigs.fa}/quast/contigs_reports/nucmer_output/contigs.all_snps ${f%%contigs.fa}/quast/contigs_reports/nucmer_output/contigs.coords ${f%%contigs.fa}/quast/report.tsv ${f%\*/contigs.fa}.bam all_strains/; done &> genome_replace_new.log

# add root >NC_045512.2|NC_045512.2|2020-01-31 with sequence

# run virusprepro (-> GitHub)

conda activate virustracker

bash VirusTracker/phylogeo_discrete/preprocessing/viralPrePro.sh strains_cds.fa "acr"

VirusTracker/phylogeo_discrete/preprocessing/software/ "NC_045512.2"

# copy samples.tsv file and create tree (optional)

Rscript visualize_tree.Rscript RAxML_bestTree.acr_raxml.phy SARS-CoV-2-tree.pdf

# Root the tree by putting NC in extra bracket (manually, replace acr with strains in name)
# run raxML -f A

raxmlHPC -f A -t RAxML_bestTree.strains_raxml.phy -s acr_cds_mapped_c.aln -m GTRCAT -n "strains_raxml.phy"

# add labels (edge lengths)

python3 add_labels.py RAxML_bestTree.strains_raxml.phy RAxML_nodeLabelledRootedTree.strains_raxml.phy

# take strains produced by this (RAxML_marginalAncestralStates.strains_raxml.phy)
# add all (leaf) strains to original mapping (acr_cds_mapped_c.aln -> strains_cds.aln)

cat acr_cds_mapped_c.aln > strains_cds.aln

while read -r line; do if [[ $line == \>* ]]; then echo -e "\n$line"; else echo -ne ${line^^}; fi; done < strains_cds.aln > strains_cds.aln1

echo -e "\n" >> strains_cds.aln1

while read -r line; do if [[ $line == \>* ]]; then echo -ne "$line "; else echo ${line}; fi; done < strains_cds.aln1 > strains_cds.aln

rm -f strains_cds.aln1

# remove leading ">"

sed -i '/^>/s/^.//' strains_cds.aln

cat RAxML_marginalAncestralStates.strains_raxml.phy >> strains_cds.aln

# replace ? by -

sed -i 's:?:-:g' strains_cds.aln

# add "label location" to first line
# run count_links.R script

Rscript count_links.R RAxML_nodeLabelledRootedTree.strains_raxml.phy strains_cds.aln > changes.tsv

sed -i 's:\[1\] ::g; s:"::g; s:$::g; s:::g' changes.tsv

#remove all empty changes