Merge pull request #222 from nvictus/master

Fix get_header to work with different peek implementations

.travis.yml

@@ -1,7 +1,6 @@
 language: python
 python:
   # We don't actually use the Travis Python, but this keeps it organized.
-  - "2.7"
   - "3.6"
   - "3.7"
   - "3.8"

cooler/cli/cload.py

@@ -49,17 +49,28 @@ def get_header(instream, comment_char='#'):
         raise ValueError('Please, provide a comment char!')
     comment_byte = comment_char.encode()
     # get peekable buffer for the instream
-    inbuffer = instream.buffer
-    current_peek = inbuffer.peek()
+    read_f, peek_f = None, None
+    if hasattr(instream, 'buffer'):
+        peek_f = instream.buffer.peek
+        readline_f = instream.buffer.readline
+    elif hasattr(instream, 'peek'):
+        peek_f = instream.peek
+        readline_f = instream.readline
+    else:
+        raise ValueError('Cannot find the peek() function of the provided stream!')
+
+    current_peek = peek_f(1)
     while current_peek.startswith(comment_byte):
         # consuming a line from buffer guarantees
         # that the remainder of the buffer starts
         # with the beginning of the line.
-        line = inbuffer.readline()
+        line = readline_f()
+        if isinstance(line, bytes):
+            line = line.decode()
         # append line to header, since it does start with header
-        header.append(line.decode().strip())
+        header.append(line.strip())
         # peek into the remainder of the instream
-        current_peek = inbuffer.peek()
+        current_peek = peek_f(1)
     # apparently, next line does not start with the comment
     # return header and the instream, advanced to the beginning of the data
     return header, instream

tests/test_create_ingest.py

@@ -256,6 +256,11 @@ def test_cload_pairix(bins_path, pairs_path, ref_path):
             op.join(testdir, "data", "toy.bins.var.bed"),
             op.join(testdir, "data", "toy_hash.pairs"),
             op.join(testdir, "data", "toy.symm.upper.var.cool"),
+        ),
+        (
+            op.join(testdir, "data", "toy.bins.var.bed"),
+            op.join(testdir, "data", "toy_hash.pairs.gz"),
+            op.join(testdir, "data", "toy.symm.upper.var.cool"),
         )
     ],
 )