tanghaibao /
goatools
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| Total Lines | 69 |
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Small methods make your code easier to understand, in particular if combined with a good name. Besides, if your method is small, finding a good name is usually much easier.
For example, if you find yourself adding comments to a method's body, this is usually a good sign to extract the commented part to a new method, and use the comment as a starting point when coming up with a good name for this new method.
Commonly applied refactorings include:
If many parameters/temporary variables are present:
Complex classes like nopen() often do a lot of different things. To break such a class down, we need to identify a cohesive component within that class. A common approach to find such a component is to look for fields/methods that share the same prefixes, or suffixes.
Once you have determined the fields that belong together, you can apply the Extract Class refactoring. If the component makes sense as a sub-class, Extract Subclass is also a candidate, and is often faster.
| 1 | """Utilities used in Gene Ontology Enrichment Analyses.""" |
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| 23 | def nopen(f, mode="r"): |
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| 24 | r""" |
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| 25 | open a file that's gzipped or return stdin for '-' |
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| 26 | if f is a number, the result of nopen(sys.argv[f]) is returned. |
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| 27 | >>> nopen('-') == sys.stdin, nopen('-', 'w') == sys.stdout |
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| 28 | (True, True) |
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| 29 | >>> nopen(sys.argv[0]) |
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| 30 | <...file...> |
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| 31 | # expands user and vars ($HOME) |
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| 32 | >>> nopen("~/.bashrc").name == nopen("$HOME/.bashrc").name |
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| 33 | True |
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| 34 | # an already open file. |
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| 35 | >>> nopen(open(sys.argv[0])) |
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| 36 | <...file...> |
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| 37 | >>> nopen(0) |
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| 38 | <...file...> |
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| 39 | Or provide nicer access to Popen.stdout |
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| 40 | >>> files = list(nopen("|ls")) |
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| 41 | >>> assert 'setup.py\n' in files or b'setup.py\n' in files, files |
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| 42 | """ |
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| 43 | if isinstance(f, int_types): |
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| 44 | return nopen(sys.argv[f], mode) |
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| 45 | |||
| 46 | if not isinstance(f, basestring): |
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| 47 | return f |
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| 48 | if f.startswith("|"): |
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| 49 | # using shell explicitly makes things like process substitution work: |
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| 50 | # http://stackoverflow.com/questions/7407667/python-subprocess-subshells-and-redirection |
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| 51 | # use sys.stderr so we dont have to worry about checking it... |
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| 52 | p = Popen(f[1:], stdout=PIPE, stdin=PIPE, |
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| 53 | stderr=sys.stderr if mode == "r" else PIPE, |
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| 54 | shell=True, bufsize=-1, # use system default for buffering |
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| 55 | preexec_fn=prefunc, |
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| 56 | close_fds=False, executable=os.environ.get('SHELL')) |
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| 57 | if sys.version_info[0] > 2: |
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| 58 | import io |
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| 59 | p.stdout = io.TextIOWrapper(p.stdout) |
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| 60 | p.stdin = io.TextIOWrapper(p.stdin) |
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| 61 | if mode != "r": |
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| 62 | p.stderr = io.TextIOWrapper(p.stderr) |
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| 63 | |||
| 64 | if mode and mode[0] == "r": |
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| 65 | return process_iter(p, f[1:]) |
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| 66 | return p |
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| 67 | |||
| 68 | if f.startswith(("http://", "https://", "ftp://")): |
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| 69 | fh = urlopen(f) |
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| 70 | if f.endswith(".gz"): |
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| 71 | return ungzipper(fh) |
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| 72 | if sys.version_info[0] < 3: |
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| 73 | return fh |
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| 74 | import io |
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| 75 | return io.TextIOWrapper(fh) |
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| 76 | f = op.expanduser(op.expandvars(f)) |
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| 77 | if f.endswith((".gz", ".Z", ".z")): |
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| 78 | fh = gzip.open(f, mode) |
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| 79 | if sys.version_info[0] < 3: |
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| 80 | return fh |
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| 81 | import io |
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| 82 | return io.TextIOWrapper(fh) |
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| 83 | elif f.endswith((".bz", ".bz2", ".bzip2")): |
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| 84 | fh = bz2.BZ2File(f, mode) |
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| 85 | if sys.version_info[0] < 3: |
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| 86 | return fh |
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| 87 | import io |
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| 88 | return io.TextIOWrapper(fh) |
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| 89 | |||
| 90 | return {"r": sys.stdin, "w": sys.stdout}[mode[0]] if f == "-" \ |
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| 91 | else open(f, mode) |
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| 92 | |||
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