annotate Snakemake_files/Snakefile_wget_cactus_heatmap_upset_COG2 @ 3:e42d30da7a74 draft

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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)
    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/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),
        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",
        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 cactus:
    input:
        expand("outputs/genomes/{sample}.fasta", sample=SAMPLES),
        expand("outputs/genomes/{sample}.gb.rmdup.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 create_gene_paths:
    input:
        gff="outputs/genomes/{sample}.gb.rmdup.gff",
        gfa="outputs/cactus_outdir/full.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 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 bedtools_intersect:
    input:
        strains="outputs/genomes/strains.txt",
        bedfiles=expand("outputs/genomes/{sample}.gene_segments.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}
        """

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}
        """