Mercurial > repos > dereeper > pangenome_explorer
view Snakemake_files/Snakefile_wget_roary_heatmap_upset_COG @ 9:24676ef2945d draft
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author | dereeper |
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date | Thu, 30 May 2024 16:18:04 +0000 |
parents | e42d30da7a74 |
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import glob import os import shutil import re import subprocess import yaml configfile: "config.yaml" SAMPLES = [] with open("config.yaml", "r") as yaml_file: genome_data = yaml.safe_load(yaml_file) if "ids" in genome_data.keys(): for id in genome_data["ids"]: SAMPLES.append(id) if "input_genbanks" in genome_data.keys(): for gb_path in genome_data["input_genbanks"]: cmd = "grep 'ACCESSION' "+gb_path returned_value = subprocess.getoutput(cmd) words = returned_value.split() name = words[1] #words = returned_value.split() #SAMPLES.append(words[1]) words = gb_path.split("/") genbank_file_name = words[-1] x = genbank_file_name.replace(".", "_") cmd = "sed -i 's/ACCESSION "+name+"/ACCESSION "+x+"/g' "+gb_path subprocess.getoutput(cmd) cmd_locus = "grep 'LOCUS' "+gb_path returned_value = subprocess.getoutput(cmd_locus) words_locus = returned_value.split() name_locus = words_locus[1] cmd = "sed -i 's/LOCUS "+name_locus+"/LOCUS "+x+"/' "+gb_path subprocess.getoutput(cmd) cmd = "grep 'ACCESSION' "+gb_path returned_value = subprocess.getoutput(cmd) words = returned_value.split() SAMPLES.append(words[1]) rule final: input: "outputs/pav_matrix.csv", "outputs/GCskew.txt", "outputs/pav_matrix.tsv", "outputs/heatmap.svg.gz", "outputs/cog_output.txt", "outputs/fastani.out", "outputs/rarefaction_curves.txt" rule ncbi_datasets: input: "config.yaml" output: expand("outputs/genomes/{sample}.fasta", sample=SAMPLES), expand("outputs/genomes/{sample}.gb", sample=SAMPLES), genomes="outputs/genomes/genomes.txt" shell: """ perl $PANEX_PATH/Perl/get_data.pl {input} outputs/genomes """ rule gcskew: input: "outputs/genomes/{sample}.fasta" output: "outputs/genomes/{sample}.fasta.gcskew.txt" shell: """ python3 $PANEX_PATH/SkewIT/src/gcskew.py -i {input} -o {input}.gcskew.txt -k 1000 -w 1000 """ rule concat_gcskew: input: expand("outputs/genomes/{sample}.fasta.gcskew.txt", sample=SAMPLES) output: out2="outputs/GCskew.txt" shell: """ cat {input} >>{output.out2} """ rule genbank2gff3: input: "outputs/genomes/{sample}.gb" output: gff1="outputs/genomes/{sample}.gb.gff", gff2="outputs/genomes/{sample}.gb.rmdup.gff" shell: """ perl $PANEX_PATH/Perl/bp_genbank2gff3.pl -o outputs/genomes {input} perl $PANEX_PATH/Perl/remove_duplicates_in_gff.pl {output.gff1} {output.gff2} """ rule roary: input: expand("outputs/genomes/{sample}.gb.rmdup.gff", sample=SAMPLES) params: identity=80 output: pav="outputs/pav_matrix.csv", newick="outputs/accessory_binary_genes.fa.newick" shell: """ roary -f outputs/roary_outdir -i {params.identity} outputs/genomes/*gb.rmdup.gff cp -rf outputs/roary_outdir/gene_presence_absence.csv {output.pav} cp -rf outputs/roary_outdir/accessory_binary_genes.fa.newick {output.newick} """ rule convert_matrix: input: pav="outputs/pav_matrix.csv" output: "outputs/pav_matrix.tsv" shell: """ perl $PANEX_PATH/Perl/ConvertRoaryMatrix.pl outputs/genomes {input} {output} outputs/genomes/strains.txt """ rule cog: input: pav="outputs/pav_matrix.tsv" output: cog="outputs/cog_output.txt", cogstat="outputs/cog_stats.txt", cogstat2="outputs/cog_stats2.txt", cogofclusters="outputs/cog_of_clusters.txt" shell: """ perl $PANEX_PATH/Perl/GetCogOfCluster.pl {input} outputs/genomes {output.cog} {output.cogstat} {output.cogstat2} {output.cogofclusters} 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} """ rule fastani: input: "outputs/genomes/genomes.txt" output: out="outputs/fastani.out", matrix="outputs/fastani.out.matrix", completematrix="outputs/fastani.out.matrix.complete", pdf="outputs/fastani.out.pdf", svg="outputs/fastani.out.svg" shell: """ fastANI --rl {input} --ql {input} -o {output.out} -t 4 --matrix perl $PANEX_PATH/Perl/convertANI.pl {output.matrix} outputs/genomes/genomes2.txt >{output.completematrix} Rscript $PANEX_PATH/R/heatmap_ani.R -f {output.completematrix} -o {output.pdf} pdf2svg {output.pdf} {output.svg} """