Added circos zoomed plot.

Snakefile

@@ -14,7 +14,7 @@ include: "rules/GenePrioritization.smk"
 
 #Rules to compare different inputs.
 include: "rules/ComparisonRegions.smk"
-include: "rules/Circos.yaml"
+include: "rules/Circos.smk"
 include: "rules/SampleSizes.smk"
 include: "rules/UseControl.smk"
 
@@ -42,8 +42,9 @@ onerror:
 rule all:
     """Define desired output from pipeline."""
     input:
-        os.path.join(config["gisticdir"], "gistic2")
-        #"Reports/Results.html"
+        "Samplesize/Report.txt"
+        #"Reports/Overlap_plots/12.png"
+        #expand("Reports/Overlap_plots/{region}.png", region=range(22))
 
 
 rule help:

rules/Circos.yaml → rules/Circos.smk

-from Circos import InputCircos
+from Circos import InputCircos, bed_to_circos
 
 rule circos_input:
     """Make input files for making a circos diagram."""
@@ -60,3 +60,31 @@ rule add_legend_circos:
         offset = ((c_w - l_w), 0)
         circos.paste(legend, offset)
         circos.save(output[0])
+
+rule circos_input_zoom:
+    """Make input files for making a circos diagram."""
+    input:
+        bed="Reports/Overlap_known_genes.bed"
+    output:
+        gistic="Reports/Circos/Zoom/GISTIC.txt",
+        rubic="Reports/Circos/Zoom/RUBIC.txt",
+        genes="Reports/Circos/Zoom/Genes.txt",
+    run:
+        bed_to_circos(input.bed, output.rubic, output.gistic, output.genes)
+
+rule make_circos_zoom:
+    """Compare locations of known genes, recurrent regions from RUBIC and recurrent regions from GISTIC2."""
+    input:
+        gistic="Reports/Circos/Zoom/GISTIC.txt",
+        rubic="Reports/Circos/Zoom/RUBIC.txt",
+        genes="Reports/Circos/Zoom/Genes.txt",
+    output:
+        plots="Reports/Overlap_plots/12.png"
+    params:
+        workflow.basedir + "/scripts/circos/circos_zoom.conf",
+        chrom='hs12'
+    conda:
+        workflow.basedir + "/envs/circos.yaml"
+    shell:
+        "circos -conf {params[0]} -outputfile {output[0]} -param gistic_file={input.gistic} -param rubic_file={input.rubic} \
+         -param gene_file={input.genes} -param chrom={params.chrom}"

rules/ComparisonRegions.smk

@@ -55,24 +55,3 @@ rule bed_known_genes:
         workflow.basedir + "/envs/bedtools.yaml"
     shell:
         "bedtools intersect -a {input.known} -b {input.gistic} {input.rubic} -names GISTIC RUBIC -wo > {output}"
-
-
-def get_regions(bed_file):
-    plot_names = []
-    with open(bed_file, 'r') as bed:
-        bed.readline()
-        for line in bed:
-            chrom, start = line.split("\t")[0:2]
-            plot_names.append(chrom + "." + start)
-    return plot_names
-
-#rule compare_regions:
-#    """Compare locations of known genes, recurrent regions from RUBIC and recurrent regions from GISTIC2."""
-#    input:
-#        overlap="Reports/Overlap_regions.bed"
-#    params:
-#        known=os.path.join(workflow.basedir, config["prev_found_genes"]) if config["prev_found_genes"].startswith("input_files") else config["prev_found_genes"]
-#    output:
-#        plots=expand("Reports/Overlap_plots/{region}.png", region=get_regions(input.overlap))
-#    shell:
-#        "R {workflow.basedir}/scripts/plot_regions.R"

rules/SampleSizes.smk

@@ -14,7 +14,7 @@ rule seg_subsets:
 rule run_gistic_subsets:
     """Run GISTIC2 for the segmentation files with different subsets."""
     input:
-        gistic_directory=config["gisticdir"],
+        gistic_directory=os.path.join(config["gisticdir"], "gistic2"),
         seg="Samplesize/Input/Size{rand_nr}.Rep{rep_nr}.txt"
     output:
         "Samplesize/GISTIC/Size{rand_nr}.Rep{rep_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt"
@@ -50,9 +50,9 @@ rule run_rubic_subsets:
 rule report_sizes:
     """Report the difference when using different sample sizes."""
     input:
-        #gistic=expand("Samplesize/GISTIC/Size{rand_nr}.Rep{rep_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt", rand_nr=config["sizes"], rep_nr=config["repeats"]),
-        rubic_gains=expand("Samplesize/RUBIC/Size{rand_nr}.Rep{rep_nr}/gains.txt", rand_nr=config["sizes"], rep_nr=config["repeats"]),
-        rubic_losses=expand("Samplesize/RUBIC/Size{rand_nr}.Rep{rep_nr}/losses.txt", rand_nr=config["sizes"], rep_nr=config["repeats"])
+        gistic=expand("Samplesize/GISTIC/Size{rand_nr}.Rep{rep_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt", rand_nr=config["sizes"], rep_nr=config["repeats"]),
+        #rubic_gains=expand("Samplesize/RUBIC/Size{rand_nr}.Rep{rep_nr}/gains.txt", rand_nr=config["sizes"], rep_nr=config["repeats"]),
+        #rubic_losses=expand("Samplesize/RUBIC/Size{rand_nr}.Rep{rep_nr}/losses.txt", rand_nr=config["sizes"], rep_nr=config["repeats"])
     output:
         report="Samplesize/Report.txt",
         plots="Samplesize/Plots/"

scripts/Circos.py

@@ -45,3 +45,19 @@ class InputCircos:
                         qval = str(max([float(left_q), float(right_q)]))
                         out_line = ["hs" + chrom, start, end, qval]
                         out.write(" ".join(out_line) + "\n")
+
+def bed_to_circos(bed_file, rubic_file, gistic_file, gene_file):
+    rubic = open(rubic_file, 'w')
+    gistic = open(gistic_file, 'w')
+    genes = open(gene_file, 'w')
+    with open(bed_file, 'r') as bed:
+        for line in bed:
+            gene_chrom, gene_start, gene_end, gene_name, tool_name, tool_chrom, tool_start, tool_end, \
+            amp_name, overlap_bp = line.split("\t")
+            chrom = 'hs' + gene_chrom.strip("chr")
+            genes.write(" ".join([chrom, gene_start, gene_end]) + "\n")
+            if tool_name == 'GISTIC':
+                gistic.write(" ".join([chrom, tool_start, tool_end]) + "\n")
+            else:
+                rubic.write(" ".join([chrom, tool_start, tool_end]) + "\n")
+    rubic.close(), gistic.close(), genes.close()

scripts/circos/circos_zoom.conf

+<<include etc/colors_fonts_patterns.conf>>
+<<include ideogram.conf>>
+<<include ticks.conf>>
+
+<image>
+<<include etc/image.conf>>
+</image>
+
+karyotype = data/karyotype/karyotype.human.txt
+chromosomes_units           = 1000000
+chromosomes                 = conf(chrom)
+chromosomes_display_default = no
+
+<highlights>
+
+z          = 5
+
+
+<highlight>
+file       = conf(gistic_file)
+r0 = 0.9r
+r1 = 0.7r
+fill_color = lgrey
+</highlight>
+
+<highlight>
+file       = conf(rubic_file)
+r0 = 0.7r
+r1 = 0.5r
+fill_color = lyellow
+</highlight>
+
+<highlight>
+file       = conf(gene_file)
+r0 = 1.0r
+r1 = 0.9r
+fill_color = black
+</highlight>
+
+</highlights>
+<<include etc/housekeeping.conf>>

wrappers/GISTIC2/wrapper.py

@@ -8,9 +8,9 @@ from snakemake.shell import shell
 
 #Convert file locations to absolute paths
 segments = os.path.abspath(snakemake.input.seg)
-gistic_dir = os.path.abspath(snakemake.input.gistic_directory).split("gistic2")[0]
+gistic_dir = os.path.abspath(snakemake.input.gistic_directory).split("/gistic2")[0]
 outfolder = os.path.abspath(snakemake.output[0]).split("all_lesions")[0]
-
+print(outfolder)
 #Select reference file
 ref = snakemake.params.get("ref", "")
 ref_file = snakemake.params.get("ref_file", "")