Python Popen.stdin方法代码示例

# 需要导入模块: from subprocess import Popen [as 别名]
# 或者: from subprocess.Popen import stdin [as 别名]
def main (filepath):
    # abort if it is directory
    if os.path.isdir(filepath):
        sys.exit("azcat: '%s' is a directory. Aborted." % filepath)

    try:
        with open(filepath, "r") as f:
            s = f.read()
    except IOError as e:
        sys.exit("azcat: cannot open '%s': %s" % (f, str(e)))
    except UnicodeDecodeError:
        sys.exit("azcat: file seems a binary file. Aborted.")

    if s.find("\x00") != -1:
        sys.exit("azcat: file seems a binary file. Aborted.")

    # confirm if file size is larger than 1MB
    if os.path.getsize(filepath) > 1024*1024:
        if input("file size is big; do you continue? [Y/n]: ") == "n":
            sys.exit("aborted.")

    # if the number of lines is over 50, pipe to a pager
    if s.count("\n") > 50:
        p = Popen(["less", "-R", "-"], stdin=PIPE)
        try:
            out = p.stdin
            pretty_print(filepath, out)
            p.stdin = sys.stdin
            p.wait()
        except IOError: # this will raised after the pager existed
            pass
    else:
        out = sys.stdout.buffer
        pretty_print(filepath, out)

# 需要导入模块: from subprocess import Popen [as 别名]
# 或者: from subprocess.Popen import stdin [as 别名]
def main (args):
    s = load_file(args["file"])

    # if the number of lines is over 50, pipe to a pager
    if s.count("\n") > 50:
        p = Popen(["less", "-R", "-"], stdin=PIPE)
        try:
            pretty_print(args["file"], s, p.stdin, args["with_formatter"])
            p.stdin = sys.stdin
            p.wait()
        except IOError: # this will raised after the pager existed
            pass
    else:
        out = sys.stdout.buffer
        pretty_print(args["file"], s, out, args["with_formatter"])

# 需要导入模块: from subprocess import Popen [as 别名]
# 或者: from subprocess.Popen import stdin [as 别名]
def nopen_keep_parent_stdin(f, mode="r"):

    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=sys.stdin,
                  stderr=sys.stderr if mode == "r" else PIPE,
                  shell=True, bufsize=-1, # use system default for buffering
                  preexec_fn=toolshed.files.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(sys.stdin)
            if mode != "r":
                p.stderr = io.TextIOWrapper(p.stderr)

        if mode and mode[0] == "r":
            return toolshed.files.process_iter(p, f[1:])
        return p
    else:
        return toolshed.files.nopen(f,mode)

# 需要导入模块: from subprocess import Popen [as 别名]
# 或者: from subprocess.Popen import stdin [as 别名]
def bwamips(fastqs, ref_fasta, mips, num_cores, umi_length, picard):

    tmp_sam_name = mktemp(suffix=".sam.gz")
    name = get_base_name(*fastqs)
    sam_gz = bwa_mem(fastqs, name, ref_fasta, tmp_sam_name, num_cores, umi_length)
    if op.exists("{picard}/FixMateInformation.jar".format(picard=picard)):
        jar = "{picard}/FixMateInformation.jar"
    else:
        jar = "{picard}/picard.jar FixMateInformation"

    out = Popen("java -jar -Xmx2G {jar} \
            SO=coordinate I=/dev/stdin O=/dev/stdout && sleep 4".format(jar=jar.format(picard=picard)),
            stderr=sys.stderr,
            stdout=sys.stdout, stdin=PIPE, shell=True)
    if sys.version_info[0] > 2:
        import io
        out.stdin = io.TextIOWrapper(out.stdin)

    dedup_sam(dearm_sam(sam_gz, mips), get_umi if umi_length > 0 else None,
              out.stdin, mips)
    out.stdin.flush()
    out.stdin.close()
    sys.stdout.flush()
    out.wait()

# 需要导入模块: from subprocess import Popen [as 别名]
# 或者: from subprocess.Popen import stdin [as 别名]
def main (args):
    # GNU global
    if args["t"] is not None:
        try:
            output = check_output(["global", "-x", args["t"]]).decode("utf-8")
            if output == "":
                sys.exit("azcat: symbol ``{0}'' not found".format(args["t"]))
            line, file = list(filter(lambda x: x != "", output.split(" ")))[1:3]
            line = int(line)
        except Exception as e:
            sys.exit("azcat: error occurred in global(1)")
    # normal
    else:
        file = args["file"]
        line = 1

    s = load_file(file)

    # get the height of a terminal
    try:
        height = int(check_output(["stty", "size"], stderr="/dev/stderr").decode("utf-8").split()[0])
    except:
        height = 50 # failed to get the height so use 50 instead

    # if the number of lines is larger than height of the terminal, pipe to a pager
    if s.count("\n") > height:
        p = Popen(["less", "-R", "+{0}g".format(line)], stdin=PIPE)
        try:
            pretty_print(file, s, p.stdin, args["with_formatter"], ext=args.get("f"))
            p.stdin = sys.stdin
            p.wait()
        except IOError: # this will raised after the pager existed
            pass
    else:
        out = sys.stdout.buffer
        pretty_print(file, s, out, args["with_formatter"], ext=args.get("f"))

# 需要导入模块: from subprocess import Popen [as 别名]
# 或者: from subprocess.Popen import stdin [as 别名]
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
                  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)