Mercurial > repos > dereeper > pangenome_explorer
view Snakemake_files/Snakefile_orthofinder_heatmap_upset @ 6:35d71348e81e draft
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author | dereeper |
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date | Thu, 30 May 2024 12:12:30 +0000 |
parents | e42d30da7a74 |
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import glob import os import shutil import yaml configfile: "config.yaml" SAMPLES = [] with open("config.yaml", "r") as yaml_file: genome_data = yaml.safe_load(yaml_file) for genome_name, genome_info in genome_data["input_genomes"].items(): name = genome_info["name"] SAMPLES.append(name) rule final: input: expand("outputs/genomes/{sample}.fasta", sample=SAMPLES), expand("outputs/genomes/{sample}.gff", sample=SAMPLES), expand("outputs/genomes/{sample}.pep", sample=SAMPLES), "outputs/pav_matrix.tsv", "outputs/heatmap.svg.gz", "outputs/rarefaction_curves.txt" rule get_data: input: "config.yaml" output: "outputs/genomes/strains.txt", expand("outputs/genomes/{sample}.fasta", sample=SAMPLES), expand("outputs/genomes/{sample}.gff", sample=SAMPLES), run: with open(input[0], "r") as yaml_file, open(output[0], "w") as output_file: genome_data = yaml.safe_load(yaml_file) for genome_name, genome_info in genome_data["input_genomes"].items(): fasta_file = genome_info["fasta"] name = genome_info["name"] gff_file = genome_info["gff3"] shutil.copy(gff_file, "outputs/genomes/"+str(name)+".gff") shutil.copy(fasta_file, "outputs/genomes/"+str(name)+".fasta") output_file.write(f"{name}\t{name}\n") rule gffread: input: fasta = "outputs/genomes/{sample}.fasta", gff = "outputs/genomes/{sample}.gff" output: "outputs/genomes/{sample}.pep" shell: """ gffread -y {output} -g {input.fasta} {input.gff} """ rule orthofinder: input: expand("outputs/genomes/{sample}.pep", sample=SAMPLES) params: identity=80 output: pav="outputs/Orthogroups.tsv" shell: """ mkdir -p outputs/proteomes sed -i '/^>/! s/\./N/g' outputs/genomes/*.pep cp -rf outputs/genomes/*.pep outputs/proteomes orthofinder -f outputs/proteomes mv outputs/proteomes/OrthoFinder/R*/Orthogroups/Orthogroups.tsv outputs/Orthogroups.tsv """ rule convert_matrix: input: pav="outputs/Orthogroups.tsv" output: "outputs/pav_matrix.tsv" shell: """ perl $PANEX_PATH/Perl/ConvertOrthofinderMatrix.pl outputs/genomes {input} {output} outputs/genomes/strains.txt """ rule heatmap_upset: input: pav="outputs/pav_matrix.tsv" output: heatmap="outputs/heatmap.svg.gz", html="outputs/heatmap.svg.heatmap_plotly.html", upsetr="outputs/upsetr.svg", binpav="outputs/heatmap.svg.pangenes_01matrix.txt" shell: """ perl $PANEX_PATH/Perl/GenerateHeatmapFromPAV.pl {input.pav} outputs/heatmap.svg mv outputs/heatmap.svg.upsetr.svg {output.upsetr} """ rule micropan: input: binpav="outputs/heatmap.svg.pangenes_01matrix.txt" output: txt="outputs/rarefaction_curves.txt", pdf="outputs/rarefaction_curves.pdf", svg="outputs/rarefaction_curves.svg", heaps="outputs/heaps.tsv" shell: """ Rscript $PANEX_PATH/R/micropan_rarefaction.R -f {input.binpav} -p {output.pdf} -a {output.heaps} -o {output.txt} pdf2svg {output.pdf} {output.svg} """