diff Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG @ 3:e42d30da7a74 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Snakemake_files/Snakefile_wget_pggb_heatmap_upset_COG	Thu May 30 11:52:25 2024 +0000
@@ -0,0 +1,197 @@
+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()
+            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/GCskew.txt",
+  "outputs/pggb_out/all_genomes.fa.smooth.final.gfa",
+  "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 $PANEX_PATH/Perl/bp_genbank2gff3.pl -o outputs/genomes {input}
+        """
+
+rule pggb:
+    input:
+        expand("outputs/genomes/{sample}.fasta", sample=SAMPLES),
+        expand("outputs/genomes/{sample}.gb.gff", sample=SAMPLES),
+    output:
+        gfa="outputs/pggb_out/all_genomes.fa.smooth.final.gfa",
+        png1="outputs/pggb_out/all_genomes.fa.lay.draw.png",
+        png2="outputs/pggb_out/all_genomes.fa.og.viz_multiqc.png",
+        vcf="outputs/all_genomes.vcf",
+    shell:
+        """
+        samtools faidx outputs/genomes/all_genomes.fa
+        reference=$(head -1 outputs/genomes/strains.txt | awk '{{print $2}}')
+        pggb -i outputs/genomes/all_genomes.fa -o outputs/pggb_out -V $reference -m -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}
+        mv outputs/pggb_out/all_genomes.*vcf {output.vcf}
+        """
+
+rule odgi:
+    input:
+        gfa="outputs/pggb_out/all_genomes.fa.smooth.final.gfa",
+    output:
+        og="outputs/pggb_out/all_genomes.fa.smooth.final.gfa.og",
+        distance="outputs/pggb_out/all_genomes.fa.smooth.final.gfa.og.distance",
+    shell:
+        """
+        odgi build -g {input} -o {output.og} 
+        odgi similarity -i {output.og} -d >{output.distance}
+        """
+
+
+rule create_gene_paths:
+    input:
+        gff="outputs/genomes/{sample}.gb.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:
+        strains="outputs/genomes/strains.txt",
+        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.strains} outputs/genomes {output} {params.identity}
+        """
+
+
+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}
+        """