Update Circos.smk

rules/Circos.smk

@@ -82,23 +82,23 @@ def get_plot_region(gene_name, locations_known_genes):
                 plot_region = chrom_region + ":" + str(start_region) + "-" + str(end_region)
     return plot_region
 
-rule make_CIRCOS_zoom_plots:
-    """Compare locations of known genes, recurrent regions from RUBIC and recurrent regions from GISTIC2."""
-    input:
-        gistic="Reports/Circos/Zoom/GISTIC.txt",    #all gistic regions
-        rubic="Reports/Circos/Zoom/RUBIC.txt",      #all rubic regions
-        genes="Reports/Circos/Zoom/Genes.txt",
-        known="Reports/Locations_known_genes.bed",   #use locations known genes to extract list of known genes and run rule for each gene    maybe also not overlapping, but region around gene
-        list_genes = lambda
-    params:
-        known="Reports/Locations_known_genes.bed",
-        genes="Reports/Circos/Zoom/Genes.txt",
-        conf=workflow.basedir + "/scripts/circos/circos_zoom.conf",
-        chrom=get_plot_region(wildcards.gene, input.known)
-    output:
-        plot=expand("Reports/Overlap_plots/{gene}.png", gene=get_list_genes(params.genes, params.known))
-    conda:
-        workflow.basedir + "/envs/circos.yaml"
-    shell:
-        "circos -conf {params.conf} -outputfile {output.plot} -param gistic_file={input.gistic} -param rubic_file={input.rubic} \
-         -param gene_file={input.genes} -param chrom={params.chrom}"
+#rule make_CIRCOS_zoom_plots:
+#    """Compare locations of known genes, recurrent regions from RUBIC and recurrent regions from GISTIC2."""
+#    input:
+#        gistic="Reports/Circos/Zoom/GISTIC.txt",    #all gistic regions
+#        rubic="Reports/Circos/Zoom/RUBIC.txt",      #all rubic regions
+#        genes="Reports/Circos/Zoom/Genes.txt",
+#        known="Reports/Locations_known_genes.bed",   #use locations known genes to extract list of known genes and run rule for each gene    maybe also not overlapping, but region around gene
+#        list_genes = lambda
+#    params:
+#        known="Reports/Locations_known_genes.bed",
+#        genes="Reports/Circos/Zoom/Genes.txt",
+#        conf=workflow.basedir + "/scripts/circos/circos_zoom.conf",
+#        chrom=get_plot_region(wildcards.gene, input.known)
+#    output:
+#        plot=expand("Reports/Overlap_plots/{gene}.png", gene=get_list_genes(params.genes, params.known))
+#    conda:
+#        workflow.basedir + "/envs/circos.yaml"
+#    shell:
+#        "circos -conf {params.conf} -outputfile {output.plot} -param gistic_file={input.gistic} -param rubic_file={input.rubic} \
+#         -param gene_file={input.genes} -param chrom={params.chrom}"