bin dir is created when necessary

generate.py

@@ -6,6 +6,8 @@ import sys
 import urllib.request
 from pathlib import Path
 
+BIN_PATH = "bin/"
+
 
 def transform(input_line):
     chromosome = input_line[2]
@@ -32,12 +34,15 @@ def transform(input_line):
 
 
 def downloadUcscFile(filename):
-    if not Path('bin/' + filename).is_file():
-        print('Beginning file download ' + filename + '...')
+    if not os.path.isdir(BIN_PATH):
+        os.makedirs(BIN_PATH)
 
+    if not Path(BIN_PATH + filename).is_file():
         url = 'http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/' + filename
-        urllib.request.urlretrieve(url, 'bin/' + filename)
-        os.chmod('bin/' + filename, 0o755)
+        print('Beginning file download ' + filename + ' (' + url + ')')
+
+        urllib.request.urlretrieve(url, BIN_PATH + filename)
+        os.chmod(BIN_PATH + filename, 0o755)
 
 
 inputFile = sys.argv[1]
@@ -49,7 +54,7 @@ downloadUcscFile("fetchChromSizes")
 chrom_sizes = basename + ".chrom.sizes"
 with open(chrom_sizes, 'w') as output_chrom_sizes:
     print('Fetching chrom sizes: ' + chrom_sizes)
-    subprocess.call(["bin/fetchChromSizes", db], stdout=output_chrom_sizes)
+    subprocess.call([BIN_PATH + "fetchChromSizes", db], stdout=output_chrom_sizes)
 
 chromosomes = {}
 unkown_chromosomes = {}
@@ -91,18 +96,15 @@ else:
 
 output.close()
 
-if not Path('bin').is_dir():
-    os.mkdir('bin')
-
-downloadUcscFile("sortBed")
+downloadUcscFile("bedSort")
 
 output_file_sorted = basename + "-sorted.bed"
 print('Sorting bed file: ' + output_file_sorted)
-subprocess.call(["bin/sortBed", output_file_unsorted, output_file_sorted])
+subprocess.call([BIN_PATH + "bedSort", output_file_unsorted, output_file_sorted])
 
 downloadUcscFile("bedToBigBed")
 
 output_big_bed = basename + ".bb"
 
 print('Creating big bed file: ' + output_big_bed)
-subprocess.call(["bin/bedToBigBed", output_file_sorted, chrom_sizes, output_big_bed])
+subprocess.call([BIN_PATH + "bedToBigBed", output_file_sorted, chrom_sizes, output_big_bed])