--- a
+++ b/singlecellmultiomics/pyutils/handlelimiter.py
@@ -0,0 +1,95 @@
+# Handle limiter written by Buys de Barbanson, Hubrecht 2017
+# This class allows for writing many files at the same time without the
+# hassle of thinking about handle limitations.
+import gzip
+import time
+
+
+class HandleLimiter(object):
+
+    def __init__(self, maxHandles=32, pruneEvery=10000, compressionLevel=1):
+        self.openHandles = {}
+        self.seen = set()  # Which files have been opened before
+        self.maxHandles = maxHandles
+        self.pruneEvery = pruneEvery
+        self.pruneIntervalCounter = 0
+        self.compressionLevel = compressionLevel
+
+    def write(self, path, string, method=None, forceAppend=False):  # 0= plain, 1:gzip
+
+        if path not in self.openHandles:
+
+            self.openHandles[path] = {}
+            failedOpening = True
+            while failedOpening:
+                try:
+                    if path in self.seen or forceAppend:
+                        # Append when we already wrote to the file
+                        if method == 1:
+                            self.openHandles[path]['handle'] = gzip.open(
+                                path, 'ab', self.compressionLevel)
+                        else:
+                            self.openHandles[path]['handle'] = open(path, 'a')
+                    else:
+                        # Open as new file when it is the first write
+                        if method == 1:
+                            self.openHandles[path]['handle'] = gzip.open(
+                                path, 'wb', self.compressionLevel)
+                        else:
+                            self.openHandles[path]['handle'] = open(path, 'w')
+                        # Remember that we accessed this file
+                        self.seen.add(path)
+                    failedOpening = False
+                except Exception as e:
+                    failedOpening = True
+                    if len(self.openHandles) > 1:
+                        self.close()
+                    else:
+                        # This is mayorly bad...
+                        print(
+                            'Failed writing to %s, even after closing all other open file-handles. Out of options...' %
+                            path)
+                        print(e)
+                        # Raise the error to the parent method
+                        raise
+        if method == 0:
+            self.openHandles[path]['handle'].write(string)
+        else:
+            self.openHandles[path]['handle'].write(bytes(string, 'UTF-8'))
+        self.openHandles[path]['lastw'] = time.time()
+        self.pruneIntervalCounter += 1
+        if self.pruneIntervalCounter >= self.pruneEvery:
+            self.prune()
+
+    def prune(self):
+        if len(self.openHandles) > self.maxHandles:
+            toPrune = len(self.openHandles) - self.maxHandles
+            pathsToPrune = sorted(
+                self.openHandles.keys(), key=lambda path: (
+                    self.openHandles[path]['lastw']))[
+                :toPrune]  # ,reverse=True
+            for path in pathsToPrune:
+                if 'handle' in self.openHandles[path]:
+                    try:
+                        self.openHandles[path]['handle'].close()
+                    except Exception as e:
+                        pass
+
+                self.openHandles.pop(path)
+        self.pruneIntervalCounter = 0
+
+    def close(self):
+
+        k = self.openHandles.keys()
+        destroyed = []
+        for path in k:
+            if 'handle' in self.openHandles[path]:
+                try:
+                    self.openHandles[path]['handle'].close()
+                except BaseException:
+                    pass
+            else:
+                print('Closed broken file handle for %s' % path)
+            destroyed.append(path)
+        for delete in destroyed:
+            self.openHandles.pop(delete)