--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/directory_copier.py	Tue Jun 21 03:38:52 2016 -0400
@@ -0,0 +1,106 @@
+import gzip
+import optparse  # using optparse as hydra still python 2.6
+import os.path
+import re
+import shutil
+import sys
+
+def report_error(*args):
+    sys.stderr.write(' '.join(map(str,args)) + '\n')
+    sys.stderr.flush()
+    sys.exit(1)
+
+
+def check_pattern_get_new_name(a_file, ending, options):
+    if options.start:
+        if not(a_file.startswith(options.start)):
+            return None
+    name = a_file[:-len(ending)]
+    if name.endswith("."):
+        name = name[:-1]
+    if options.last:
+        if not(name.endswith(last)):
+            return None
+    if options.regex:
+        pattern = re.compile(options.regex)
+        if pattern.search(name) is None:
+            return None
+    if options.new_ending:
+        if options.new_ending[0] ==".":
+            return name + options.new_ending
+        else:
+            return name + "." + options.new_ending
+    if options.decompress:
+        if a_file.endswith(".gz"):
+            return a_file[:-3]
+    return a_file
+
+
+def check_and_get_new_name(a_file, options):
+    for ending in options.endings:
+        if a_file.endswith(ending):
+            return check_pattern_get_new_name (a_file, ending, options)
+    return None
+
+
+def link(a_file, new_name, path):
+    file_path = os.path.join(os.path.realpath(path), a_file)
+    sym_path = os.path.join(os.path.realpath("output"), new_name)
+    os.link(file_path, sym_path)
+
+
+def decompress(a_file, new_name, path):
+    file_path = os.path.join(os.path.realpath(path), a_file)
+    target_path = os.path.join(os.path.realpath("output"), new_name)
+    with gzip.open(file_path, 'rb') as f_in, open(target_path, 'wb') as f_out:
+        shutil.copyfileobj(f_in, f_out)
+
+
+def copy_and_link(path, options):
+    if options.decompress or options.link:
+        os.mkdir("output")
+    with open(options.list, 'w') as list_file:
+        files = os.listdir(path)
+        files.sort()
+        for a_file in files:
+            new_name = check_and_get_new_name(a_file, options)
+            if new_name:
+                list_file.write(new_name)
+                list_file.write("\n")
+                if options.decompress:
+                    if a_file.endswith(".gz"):
+                        decompress(a_file, new_name,path)
+                    else:
+                        link(a_file, new_name, path)
+                elif options.link:
+                    link(a_file, new_name, path)
+
+
+if __name__ == '__main__':
+    parser = optparse.OptionParser()
+    parser.add_option("--path", action="store", type="string",
+                      help="Path of directory to check. ")
+    parser.add_option("--ending", action="append", type="string", dest="endings",
+                      help="Ending that can be listed and if requested linked or decompressed. ")
+    parser.add_option("--start", action="store", type="string",
+                      help="String that must be at the start of the file name ")
+    parser.add_option("--last", action="store", type="string",
+                      help="String that must be the last bit of the file name before the endings")
+    parser.add_option("--regex", action="store", type="string",
+                      help="Regex for file names not including the endings")
+    parser.add_option("--new_ending", action="store", type="string", 
+                      help="New ending to replace any previous ending in list and if required links or decompressions. Note: If not set decompression will auto remove the compressioned part of the ending")
+    parser.add_option("--list", action="store", type="string",
+                      help="Path to where all files should be listed. ")
+    parser.add_option("--link", action="store_true", default=False,
+                      help="If set will cause links to be added in output directory. ")
+    parser.add_option("--decompress", action="store_true", default=False,
+                      help="If set will cause gz files to be decompressed or if not a supported decompression ending linked.")
+    (options, args) = parser.parse_args()
+
+
+    path = options.path.strip()
+    if path[-1] != '/':
+        path = path + "/"
+    copy_and_link(path, options)
+