diff env/lib/python3.7/site-packages/galaxy/util/ucsc.py @ 0:26e78fe6e8c4 draft

"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.7/site-packages/galaxy/util/ucsc.py	Sat May 02 07:14:21 2020 -0400
@@ -0,0 +1,39 @@
+"""
+Utilities for dealing with UCSC data.
+"""
+
+
+class UCSCLimitException(Exception):
+    pass
+
+
+class UCSCOutWrapper(object):
+    """File-like object that throws an exception if it encounters the UCSC limit error lines"""
+
+    def __init__(self, other):
+        self.other = iter(other)
+        # Need one line of lookahead to be sure we are hitting the limit message
+        self.lookahead = None
+
+    def __iter__(self):
+        return self
+
+    def __next__(self):
+        if self.lookahead is None:
+            line = next(self.other)
+        else:
+            line = self.lookahead
+            self.lookahead = None
+        if line.startswith("----------"):
+            next_line = next(self.other)
+            if next_line.startswith("Reached output limit"):
+                raise UCSCLimitException(next_line.strip())
+            else:
+                self.lookahead = next_line
+        return line
+
+    def next(self):
+        return self.__next__()
+
+    def readline(self):
+        return self.next()