From: Brandon King <kingb@caltech.edu>
Date: Fri, 23 May 2008 21:43:56 +0000 (+0000)
Subject: Back porting Diane's opener.py from trunk to v0.1.x branch
X-Git-Tag: 0.1.4~2
X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=commitdiff_plain;h=e55d6eae5b97bb142b3f30ab82be5f6354a495ea;p=htsworkflow.git

Back porting Diane's opener.py from trunk to v0.1.x branch
---

diff --git a/gaworkflow/util/opener.py b/gaworkflow/util/opener.py
new file mode 100644
index 0000000..035bb24
--- /dev/null
+++ b/gaworkflow/util/opener.py
@@ -0,0 +1,57 @@
+"""
+Helpful utilities for turning random names/objects into streams.
+"""
+import os
+import gzip
+import bz2
+import types
+import urllib2
+
+def isfilelike(file_ref, mode):
+    """Does file_ref have the core file operations?
+    """
+    # if mode is w/a check to make sure we writeable ops
+    # but always check to see if we can read
+    read_operations = ['read', 'readline', 'readlines']
+    write_operations = [ 'write', 'writelines' ]
+    #random_operations = [ 'seek', 'tell' ]
+    if mode[0] in ('w', 'a'):
+        for o in write_operations:
+            if not hasattr(file_ref, o):
+                return False
+    for o in read_operations:
+        if not hasattr(file_ref, o):
+            return False
+          
+    return True
+
+def isurllike(file_ref, mode):
+    """
+    does file_ref look like a url?
+    (AKA does it start with protocol:// ?)
+    """
+    #what if mode is 'w'?
+    parsed = urllib2.urlparse.urlparse(file_ref)
+    schema, netloc, path, params, query, fragment = parsed
+    
+    return len(schema) > 0
+
+def autoopen(file_ref, mode='r'):
+    """
+    Attempt to intelligently turn file_ref into a readable stream
+    """
+    # catch being passed a file
+    if type(file_ref) is types.FileType:
+        return file_ref
+    # does it look like a file?
+    elif isfilelike(file_ref, mode):
+        return file_ref
+    elif isurllike(file_ref, mode):
+        return urllib2.urlopen(file_ref)
+    elif os.path.splitext(file_ref)[1] == ".gz":
+        return gzip.open(file_ref, mode)
+    elif os.path.splitext(file_ref)[1] == '.bz2':
+        return bz2.BZ2File(file_ref, mode)
+    else:
+        return open(file_ref,mode)
+