revert nopen

goatools/base.py

@@ -1,13 +1,17 @@
 """Utilities used in Gene Ontology Enrichment Analyses."""
 
+import bz2
 import gzip
 import logging
 import os
+import os.path as op
 import sys
 import traceback
 
 from ftplib import FTP
 from os.path import isfile
+from subprocess import PIPE, Popen
+from urllib.request import urlopen
 
 import requests
 
@@ -31,6 +35,86 @@ def get_logger(name: str):
 logger = get_logger("goatools")
 
 
+def nopen(f, mode="r"):
+    r"""
+    open a file that's gzipped or return stdin for '-'
+    if f is a number, the result of nopen(sys.argv[f]) is returned.
+    >>> nopen('-') == sys.stdin, nopen('-', 'w') == sys.stdout
+    (True, True)
+    >>> nopen(sys.argv[0])
+    <...file...>
+    # expands user and vars ($HOME)
+    >>> nopen("~/.bashrc").name == nopen("$HOME/.bashrc").name
+    True
+    # an already open file.
+    >>> nopen(open(sys.argv[0]))
+    <...file...>
+    >>> nopen(0)
+    <...file...>
+    Or provide nicer access to Popen.stdout
+    >>> files = list(nopen("|ls"))
+    >>> assert 'setup.py\n' in files or b'setup.py\n' in files, files
+    """
+    if isinstance(f, int_types):
+        return nopen(sys.argv[f], mode)
+
+    if not isinstance(f, basestring):
+        return f
+    if f.startswith("|"):
+        # using shell explicitly makes things like process substitution work:
+        # http://stackoverflow.com/questions/7407667/python-subprocess-subshells-and-redirection
+        # use sys.stderr so we dont have to worry about checking it...
+        p = Popen(
+            f[1:],
+            stdout=PIPE,
+            stdin=PIPE,
+            stderr=sys.stderr if mode == "r" else PIPE,
+            shell=True,
+            bufsize=-1,  # use system default for buffering
+            preexec_fn=prefunc,
+            close_fds=False,
+            executable=os.environ.get("SHELL"),
+        )
+        if sys.version_info[0] > 2:
+            import io
+
+            p.stdout = io.TextIOWrapper(p.stdout)
+            p.stdin = io.TextIOWrapper(p.stdin)
+            if mode != "r":
+                p.stderr = io.TextIOWrapper(p.stderr)
+
+        if mode and mode[0] == "r":
+            return process_iter(p, f[1:])
+        return p
+
+    if f.startswith(("http://", "https://", "ftp://")):
+        fh = urlopen(f)
+        if f.endswith(".gz"):
+            return ungzipper(fh)
+        if sys.version_info[0] < 3:
+            return fh
+        import io
+
+        return io.TextIOWrapper(fh)
+    f = op.expanduser(op.expandvars(f))
+    if f.endswith((".gz", ".Z", ".z")):
+        fh = gzip.open(f, mode)
+        if sys.version_info[0] < 3:
+            return fh
+        import io
+
+        return io.TextIOWrapper(fh)
+    elif f.endswith((".bz", ".bz2", ".bzip2")):
+        fh = bz2.BZ2File(f, mode)
+        if sys.version_info[0] < 3:
+            return fh
+        import io
+
+        return io.TextIOWrapper(fh)
+
+    return {"r": sys.stdin, "w": sys.stdout}[mode[0]] if f == "-" else open(f, mode)
+
+
 def ungzipper(fh, blocksize=16384):
     """
     work-around to get streaming download of http://.../some.gz