diff Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG @ 3:e42d30da7a74 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Snakemake_files/Snakefile_wget_PGAP_heatmap_upset_COG	Thu May 30 11:52:25 2024 +0000
@@ -0,0 +1,131 @@
+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/pav_matrix.csv",
+  "outputs/GCskew.txt",
+  "outputs/pav_matrix.tsv",
+  "outputs/heatmap.svg",
+  "outputs/cog_output.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}.pep", 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 $PANEX_PATH/Perl/remove_duplicates_in_gff.pl {output.gff1} {output.gff2}
+        """
+
+
+rule pgap:
+    input:
+        expand("outputs/genomes/{sample}.pep", sample=SAMPLES)
+    params:
+        identity=80
+    output:
+        pav="outputs/pav_matrix.csv",
+        newick="outputs/accessory_binary_genes.fa.newick"
+    shell:
+        """
+        listforpgap=$(cat genbank_ids | tr '\n' '+')
+        alias consense='/usr/bin/phylip consense';alias dnaml='phylip /usr/bin/dnaml' 
+        cp -rf /usr/local/bin/PGAP-1.2.1/Blast_Filter.pl .
+        perl /usr/local/bin/PGAP-1.2.1/PGAP.pl --strains $listforpgap --cluster --evolution --method GF --input outputs/genomes --output outputs/pgap_outdir
+        cp -rf outputs/pgap_outdir/1.Orthologs_Cluster.txt {output.pav}
+        cp -rf outputs/pgap_outdir/4.PanBased.Neighbor-joining.tree {output.newick}
+        """
+
+rule convert_matrix:
+    input:
+        pav="outputs/pav_matrix.csv"
+    output:
+        "outputs/pav_matrix.tsv"
+    shell:
+        """
+        perl $PANEX_PATH/Perl/ConvertPGAPMatrix.pl outputs/genomes outputs/pav_matrix.csv outputs/pav_matrix.tsv outputs/genomes/strains.txt
+        """
+
+rule heatmap_upset:
+    input:
+        pav="outputs/pav_matrix.tsv"
+    output:
+        heatmap="outputs/heatmap.svg",
+        upsetr="outputs/upsetr.svg"
+    shell:
+        """
+        perl $PANEX_PATH/Perl/GenerateHeatmapFromPAV.pl {input.pav} {output.heatmap}
+        mv {output.heatmap}.upsetr.svg {output.upsetr}
+        """
+
+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
+        """
+