From 15a274d3c53caef27676f6bbe4dd0341ee263062 Mon Sep 17 00:00:00 2001 From: Aysun Urhan Date: Mon, 18 Sep 2023 18:45:05 +0200 Subject: [PATCH] Create comparativeStudy.sh --- comparativeStudy.sh | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 comparativeStudy.sh diff --git a/comparativeStudy.sh b/comparativeStudy.sh new file mode 100644 index 0000000..87d16f2 --- /dev/null +++ b/comparativeStudy.sh @@ -0,0 +1,34 @@ +# Roary +roary gff3-input*.gff -f output/roary -p 4 -v + +# Ptolemy +java -jar ptolemy.jar extract -g ptolemy-input-list.txt -o output/ptolemy +java -jar ptolemy.jar syntenic-anchors --db output -o output/ptolemy +java -jar ptolemy.jar canonical-quiver -s output/ptolemy/syntenic_anchors.txt --db output/ptolemy -o output/ptolemy --dump + +# PPanGGoLin +ppanggolin workflow --anno ppanggolin-input-list.txt -output output/ppanggolin +ppanggolin write -p output/ppanggolin/pangenome.h5 --families_tsv -o output/ppanggolin +ppanggolin write -p output/ppanggolin/pangenome.h5 --all_gene_families -o output/ppanggolin -f +ppanggolin write -p output/ppanggolin/pangenome.h5 --all_genes -o output/ppanggolin -f + +# PIRATE +./PIRATE -i gff3-input -s "50,70,95" -o output/pirate +perl pirate-scripts/subsample_outputs.pl -i output/pirate/PIRATE.gene_families.tsv -g +output/pirate/modified_gffs/ -o output/pirate/gene_families.prev_locus.tsv --field "prev_locus" +perl pirate-scripts/gene_cluster_to_binary_fasta.pl -i output/pirate/PIRATE.gene_families.tsv output/pirate/binary_presence_absence.fasta +FastTree -fastest -nocat -nome -noml -nosupport -nt output/pirate/binary_presence_absence.fasta > output/pirate/binary_presence_absence.nwk 2>/dev/null + +# Panaroo +python convert_refseq_to_prokka_gff.py -g input.gff -f input.fasta -o output.gff # repeat for all inputs +panaroo -i gff3-input/*.gff -o output/panaroo -t 4 -verbose # strict mode +panaroo -i gff3-input/*.gff -o output/panaroo --mode relaxed -t 4 -verbose # relaxed mode + +# Combining Panaroo and Ptolemy +panaroo -i gff3-input/*.gff -o output/panaroo --mode relaxed -t 4 -verbose # obtain gene clusters +java -jar ptolemy.jar extract -g ptolemy-input-list.txt -o output # index graph +python createSA.py output/panaroo output # create syntenic anchor file input to Ptolemy +java -jar ptolemy.jar canonical-quiver -s output/syntenic_anchors.txt --db output -o output -dump + +# Perform GO enrichment study +python runGOE.py go.obo orf2go.tsv studyinput.txt goestudy.out