Commit 0233d1b2 authored by Beatrice Tan's avatar Beatrice Tan

Update Circos.smk

parent db6d0312
......@@ -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}"
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