Removed ensembl function.

config.yaml

 #Directories to be specified
-workdir: /home/bftan/CNA_results        #directory to write output
-gisticdir: /home/bftan/Tools/GISTIC2    #directory to install GISTIC2
+#workdir: /home/bftan/CNA_results        #directory to write output
+#gisticdir: /home/bftan/Tools/GISTIC2    #directory to install GISTIC2
 
-#workdir: /home/beatrice/CNA_analysis
-#gisticdir: /home/beatrice/CNA_analysis/run_gistic2
+workdir: /home/beatrice/CNA_analysis
+gisticdir: /home/beatrice/CNA_analysis/run_gistic2
 
 #Input details to download from firehose
 cancer_type: SKCM

scripts/ParseResults.py

@@ -46,13 +46,30 @@ def parse_gistic_results(results_file, known_genes, census_genes):
                 start, end = bp.split("-")
                 cnv_type = 'amp' if stats[0].startswith("Amplification") else 'del'
                 qval = log10(float(stats[5])) * -1   #Convert q-value to log10(q-value)
-                list_genes = genes_locus(chrom, int(start), int(end))
+                #list_genes = genes_locus(chrom, int(start), int(end))
+                result_dir, conf = results_file.split("all_lesions")
+                gene_file = os.path.join(result_dir, cnv_type + "_genes" + conf)
+                list_genes = gistic_genes(gene_file, CNV_id)
                 known_overlap = set(list_genes).intersection(set(known_genes))
                 census_overlap = set(list_genes).intersection(set(census_genes))
                 cnv_data = [chrom, start, end, cnv_type, qval, list(known_overlap), list(census_overlap), list_genes]
                 regions.append(cnv_data)
     return regions
 
+def gistic_genes(gene_file, CNV_id):
+        """Extract list of genes for a given recurrent CNV from GISTIC2 output."""
+        out_genes = []
+        with open(gene_file, 'r') as genes:
+            for i in range(3):
+                genes.readline()
+            column_CNV = genes.readline().split("\t").index(CNV_id)
+            for line in genes:
+                if len(line.split("\t")) >= column_CNV:
+                    gene = line.split("\t")[column_CNV]
+                    if gene != '':
+                        out_genes.append(gene)
+        return out_genes
+
 def parse_rubic_results(results_gains, results_losses, known_genes, census_genes):
     """Create a list of lists with the recurrent regions called by GISTIC2."""
     regions = []
@@ -63,21 +80,23 @@ def parse_rubic_results(results_gains, results_losses, known_genes, census_genes
                 chrom, start, end, qval_left, qval_right, genes = lesion.split("\t")
                 CNV_id = "chr" + chrom + ":" + start + "-" + end
                 cnv_type = 'amp' if result_file.endswith('gains.txt') else 'del'
-                list_genes = genes_locus(chrom, int(start), int(end))
+                #list_genes = genes_locus(chrom, int(start), int(end))
+                list_genes = genes.strip().split(",")
+                print(list_genes)
                 known_overlap = set(list_genes).intersection(set(known_genes))
                 census_overlap = set(list_genes).intersection(set(census_genes))
                 cnv_data = [chrom, start, end, cnv_type, (qval_left, qval_right),  list(known_overlap), list(census_overlap), list_genes]
                 regions.append(cnv_data)
     return regions
 
-def genes_locus(chrom, start, end):
-    """Get list of gene IDs at certain location."""
-    IDs = []
-    gene_info = ensembl.genes_at_locus(chrom, start, end)
-    for gene in gene_info:
-        ID = gene.gene_id
-        IDs.append(ID)
-    return IDs
+#def genes_locus(chrom, start, end):
+#    """Get list of gene IDs at certain location."""
+#    IDs = []
+#    gene_info = ensembl.genes_at_locus(chrom, start, end)
+#    for gene in gene_info:
+#        ID = gene.gene_id
+#        IDs.append(ID)
+#    return IDs
 
 def gene_file_IDs(gene_file, top_nr):
     """Parse a file with a list of genes (one gene per line or first column).
@@ -90,11 +109,12 @@ def gene_file_IDs(gene_file, top_nr):
                     continue
                 else:
                     gene = line.split("\t")[0]
-                    try:
-                        gene_ID = ensembl.gene_ids_of_gene_name(gene)
-                        list_genes = list_genes + gene_ID
-                    except:
-                        pass
+                    list_genes.append(gene)
+                    #try:
+                    #    gene_ID = ensembl.gene_ids_of_gene_name(gene)
+                    #    list_genes = list_genes + gene_ID
+                    #except:
+                    #    pass
     if top_nr != np.inf:
         list_genes = list_genes[0:top_nr]
     return list_genes