--skipNonStandardChromosomes parameter added to skip nonstandard chromosomes

generate.py

@@ -47,6 +47,8 @@ def download_ucsc_file(filename):
 
 inputFile = sys.argv[1]
 db = sys.argv[2]
+skipNonStandardChromosomes = sys.argv[3] if 3 < len(sys.argv) else None
+
 basename = ntpath.basename(inputFile).replace(".txt.gz", "")
 
 download_ucsc_file("fetchChromSizes")
@@ -59,10 +61,15 @@ with open(chrom_sizes, 'w') as output_chrom_sizes:
 chromosomes = {}
 unknown_chromosomes = {}
 
+if skipNonStandardChromosomes == "--skipNonStandardChromosomes":
+    print("Skipping non standard chromosomes")
+
 with open(chrom_sizes) as f:
     lines = f.readlines()
     for line in lines:
-        chromosomes[line.split("\t")[0]] = True
+        chromosomeName = line.split("\t")[0]
+        if skipNonStandardChromosomes != "--skipNonStandardChromosomes" or "_" not in chromosomeName:
+            chromosomes[chromosomeName] = True
 
 output_file_unsorted = basename + ".bed"