diff Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG @ 3:e42d30da7a74 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG	Thu May 30 11:52:25 2024 +0000
@@ -0,0 +1,196 @@
+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)
+    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()
+            SAMPLES.append(words[1])
+
+
+
+rule final:
+ input:
+  "outputs/GCskew.txt",
+  "outputs/cactus_outdir/output_cactus.sv.gfa.gz",
+  "outputs/cactus_outdir/full.gfa",
+  "outputs/cactus_outdir/full.gfa.png",
+  "outputs/cactus_outdir/output_cactus.sv.gfa.pangenome.fasta",
+  "outputs/pav_matrix.tsv",
+  "outputs/heatmap.svg.gz",
+  "outputs/cog_output.txt",
+  "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),
+        expand("outputs/genomes/{sample}.prt", sample=SAMPLES),
+        expand("outputs/genomes/{sample}.nuc", sample=SAMPLES),
+        genomes="outputs/genomes/genomes.txt",
+        strains="outputs/genomes/strains.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",
+    shell:
+        """
+        perl $PANEX_PATH/Perl/bp_genbank2gff3.pl -o outputs/genomes {input}
+        """
+
+rule cactus:
+    input:
+        expand("outputs/genomes/{sample}.fasta", sample=SAMPLES),
+        expand("outputs/genomes/{sample}.gb.gff", sample=SAMPLES),
+    params:
+        reference=SAMPLES[0]
+    output:
+        gfasv="outputs/cactus_outdir/output_cactus.sv.gfa.gz",
+        gfafull="outputs/cactus_outdir/full.gfa"
+    shell:
+        """
+        mkdir outputs/cactus_work
+        cactus-pangenome outputs/jobstore outputs/genomes/seqfile --outDir outputs/cactus_outdir --outName output_cactus --reference {params.reference} --workDir outputs/cactus_work --vcf --mapCores 12 --gfa clip full --viz
+        zcat outputs/cactus_outdir/output_cactus.full.gfa.gz >{output.gfafull}
+        """
+
+
+
+
+rule gfatools:
+    input:
+        "outputs/cactus_outdir/output_cactus.sv.gfa.gz"
+    output:
+        "outputs/cactus_outdir/output_cactus.sv.gfa.pangenome.fasta"
+    shell:
+        """
+        gfatools gfa2fa -s {input} > {output}
+        """
+
+rule minigraph:
+    input:
+        cds_fasta="outputs/genomes/{sample}.nuc",
+        gfa="outputs/cactus_outdir/output_cactus.sv.gfa.gz",
+    output:
+        gaf="outputs/genomes/{sample}.nuc.pangenome.gaf",
+    shell:
+        """
+        minigraph -x lr {input.gfa} {input.cds_fasta} > {output.gaf}
+        """
+
+rule odgi:
+    input:
+        "outputs/cactus_outdir/full.gfa"
+    output:
+        og="outputs/cactus_outdir/full.gfa.og",
+        png="outputs/cactus_outdir/full.gfa.png",
+    shell:
+        """
+        odgi build -g {input} -o {output.og}     
+        odgi viz -i {output.og} -o {output.png}
+        """
+
+rule gaf2bed:
+    input:
+        "outputs/genomes/{sample}.nuc.pangenome.gaf"
+    output:
+        "outputs/genomes/{sample}.nuc.pangenome.gaf.bed",
+    shell:
+        """
+        awk '{{print $6"\\t"$8"\\t"$9"\\t"$1}}' {input} >{output}
+        """
+
+rule bedtools_intersect:
+    input:
+        strains="outputs/genomes/strains.txt",
+        bedfiles=expand("outputs/genomes/{sample}.nuc.pangenome.gaf.bed", sample=SAMPLES)
+    output:
+        "outputs/pav_matrix.tsv",
+    shell:
+        """
+        perl $PANEX_PATH/Perl/GeneratePAVfromBed.pl {input.strains} outputs/genomes {output}
+        """
+
+
+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}
+        """