annotate Snakemake_files/Snakefile_pggb_heatmap_upset @ 3:e42d30da7a74 draft

Uploaded

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 all:
    input:
        "outputs/seqfile",
        "outputs/pggb_out/all_genomes.fa.smooth.final.gfa",
        "outputs/pav_matrix.tsv",
        "outputs/heatmap.svg.gz",
        "outputs/rarefaction_curves.txt"

rule get_data:
    input:
        "config.yaml"   
    output:
        "outputs/seqfile",
        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"]
                output_file.write(f"{genome_name}\t{genome_name}\t{fasta_file}\n")
                cmd = "sed 's/>/>"+str(name)+"#/g' "+fasta_file+" >outputs/genomes/"+str(name)+".fasta"
                os.system(cmd)
                gff_file = genome_info["gff3"]
                shutil.copy(gff_file, "outputs/genomes/"+str(name)+".gff")

rule pggb:
    input:
        expand("outputs/genomes/{sample}.fasta", sample=SAMPLES),
        expand("outputs/genomes/{sample}.gff", sample=SAMPLES),
    output:
        gfa="outputs/pggb_out/all_genomes.fa.smooth.final.gfa",
        png1="outputs/pggb_out/all_genomes.fa.lay.draw.png",
        png2="outputs/pggb_out/all_genomes.fa.og.viz_multiqc.png",
    shell:
        """
        cat outputs/genomes/*fasta >outputs/genomes/all_genomes.fa
        samtools faidx outputs/genomes/all_genomes.fa
        reference=$(head -1 outputs/genomes/strains.txt | awk '{{print $2}}')
        pggb -i outputs/genomes/all_genomes.fa -o outputs/pggb_out -V $reference -m
        mv outputs/pggb_out/all_genomes.*smooth.final.gfa {output.gfa}
        mv outputs/pggb_out/all_genomes.*lay.draw.png {output.png1}
        mv outputs/pggb_out/all_genomes.fa.*.og.viz_multiqc.png {output.png2}
        """

rule create_gene_paths:
    input:
        gff="outputs/genomes/{sample}.gff",
        gfa="outputs/pggb_out/all_genomes.fa.smooth.final.gfa",
    output:
        basename="outputs/genomes/{sample}.gene_segments",
        gene_length="outputs/genomes/{sample}.gene_segments.gene_length.txt",
        bed="outputs/genomes/{sample}.gene_segments.bed",
    shell:
        """
        perl $PANEX_PATH/Perl/CreateGenePathsFromGFA.pl {input.gfa} {input.gff} {output.basename}
        """

rule bedtools_intersect:
    input:
        samples="outputs/seqfile",
        bedfiles=expand("outputs/genomes/{sample}.gene_segments.bed", sample=SAMPLES)
    params:
        identity=30
    output:
        "outputs/pav_matrix.tsv",
    shell:
        """
        perl $PANEX_PATH/Perl/GeneratePAVfromBed.pl {input.samples} outputs/genomes {output} {params.identity}
        """

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}
        """