diff tests/run-tests.py @ 10:db6f217dc45a

Uploaded tarball. Version 1.1. - Added stranded output. - Added, tested no-filter mode. - now prints all sites. - Changed handling of minor allele ties. - Added test datasets. - Revised help text.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/run-tests.py	Fri Sep 06 20:37:07 2013 -0400
@@ -0,0 +1,54 @@
+#!/usr/bin/env python
+import os
+import sys
+import subprocess
+
+DATASETS = [
+  'artificial',
+  'artificial-samples',
+  'artificial-nofilt',
+  'real',
+  'real-mit',
+  'real-mit-s',
+  'real-nofilt',
+]
+IN_EXT  = '.vcf.in'
+OUT_EXT = '.csv.out'
+ARGS_KEY = '##comment="ARGS='
+
+def main():
+
+  test_dir = os.path.dirname(os.path.relpath(sys.argv[0]))
+  if test_dir:
+    test_dir += os.sep
+
+  for dataset in DATASETS:
+    infile  = test_dir+dataset+IN_EXT
+    outfile = test_dir+dataset+OUT_EXT
+
+    if not os.path.exists(infile):
+      sys.stderr.write("Error: file not found: "+infile+"\n")
+      continue
+    if not os.path.exists(outfile):
+      sys.stderr.write("Error: file not found: "+outfile+"\n")
+      continue
+
+    options = read_options(infile)
+    script_cmd = 'allele-counts.py '+options+' -i '+infile
+    bash_cmd = 'diff '+outfile+' <('+script_cmd+')'
+    # print infile+":"
+    print script_cmd
+    subprocess.call(['bash', '-c', bash_cmd])
+
+
+def read_options(infile):
+  with open(infile, 'r') as infilehandle:
+    for line in infilehandle:
+      line.strip()
+      if ARGS_KEY == line[:len(ARGS_KEY)]:
+        return line[len(ARGS_KEY):-2]
+  return ''
+
+
+if __name__ == '__main__':
+  main()
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