Python sys.stdin() Examples

def _fopen(fname, mode):
    """
    Extend file open function, to support 
        1) "-", which means stdin/stdout
        2) "$cmd |" which means pipe.stdout
    """
    if mode not in ["w", "r", "wb", "rb"]:
        raise ValueError("Unknown open mode: {mode}".format(mode=mode))
    if not fname:
        return None
    fname = fname.rstrip()
    if fname == "-":
        if mode in ["w", "wb"]:
            return sys.stdout.buffer if mode == "wb" else sys.stdout
        else:
            return sys.stdin.buffer if mode == "rb" else sys.stdin
    elif fname[-1] == "|":
        pin = pipe_fopen(fname[:-1], mode, background=(mode == "rb"))
        return pin if mode == "rb" else TextIOWrapper(pin)
    else:
        if mode in ["r", "rb"] and not os.path.exists(fname):
            raise FileNotFoundError(
                "Could not find common file: {}".format(fname))
        return open(fname, mode) 

def main():
    if len(sys.argv) > 2:
        Fatal('usage: %s [containers.yaml]' % sys.argv[0])

    if len(sys.argv) == 2:
        with open(sys.argv[1], 'r') as fp:
            config = yaml.load(fp)
    else:
        config = yaml.load(sys.stdin)

    syslog.openlog(PROGNAME)
    LogInfo('processing container manifest')

    CheckVersion(config)

    all_volumes = LoadVolumes(config.get('volumes', []))
    user_containers = LoadUserContainers(config.get('containers', []),
                                         all_volumes)
    CheckGroupWideConflicts(user_containers)

    if user_containers:
        infra_containers = LoadInfraContainers(user_containers)
        RunContainers(infra_containers + user_containers) 

def supervisor_events(stdin, stdout):
    """
    An event stream from Supervisor.
    """

    while True:
        stdout.write('READY\n')
        stdout.flush()

        line = stdin.readline()
        headers = get_headers(line)

        payload = stdin.read(int(headers['len']))
        event_headers, event_data = eventdata(payload)

        yield event_headers, event_data

        stdout.write('RESULT 2\nOK')
        stdout.flush() 

def add_command_args(parser):
    group = parser.add_mutually_exclusive_group()
    group.add_argument("--watch", action="store_true", help="Monitor submitted job, stream log until job completes")
    group.add_argument("--wait", action="store_true",
                       help="Block on job. Exit with code 0 if job succeeded, 1 if failed")
    group = parser.add_mutually_exclusive_group()
    group.add_argument("--command", nargs="+", help="Run these commands as the job (using " + BOLD("bash -c") + ")")
    group.add_argument("--execute", type=argparse.FileType("rb"), metavar="EXECUTABLE",
                       help="Read this executable file and run it as the job")
    group.add_argument("--wdl", type=argparse.FileType("rb"), metavar="WDL_WORKFLOW",
                       help="Read this WDL workflow file and run it as the job")
    parser.add_argument("--wdl-input", type=argparse.FileType("r"), metavar="WDL_INPUT_JSON", default=sys.stdin,
                        help="With --wdl, use this JSON file as the WDL job input (default: stdin)")
    parser.add_argument("--environment", nargs="+", metavar="NAME=VALUE",
                        type=lambda x: dict(zip(["name", "value"], x.split("=", 1))), default=[])
    parser.add_argument("--staging-s3-bucket", help=argparse.SUPPRESS) 

def _sender(conn,stdin):
    # Warning: when the parent dies we are seeing continual
    # newlines, so we only access so many before stopping
    counter = 0

    while True:
        try:
            line = stdin.readline().strip()

            if line == "":
                counter += 1
                if counter > 100:
                    break
                continue
            counter = 0

            conn.send(line)

            sendLogger.debug(line)

        except:
            pass 

def build(args):
    words={}

    for line in sys.stdin:
        line=line.strip()
        if not line or line.startswith("#"):
            continue
        cols=line.split("\t")
        word=(cols[FORM], cols[UPOS], cols[XPOS], cols[FEATS], cols[LEMMA])
        if word not in words:
            words[word]=0
        words[word]+=1

    for word, count in sorted(words.items(), key=lambda x: x[1], reverse=True):

        if count>args.cutoff:
            w="\t".join(word)
            if len(w.strip().split("\t"))!=5: # make sure there is no empty columns
                print("Skipping weird line", w, file=sys.stderr)
                continue
            print(w)
        else:
            break 

def hciCallback(self, record):
                hcipkt, orig_len, inc_len, flags, drops, recvtime = record

                dummy = "\x00\x00\x00"      # TODO: Figure out purpose of these fields
                direction = p8(flags & 0x01)
                packet = dummy + direction + hcipkt.getRaw()
                length = len(packet)
                ts_sec =  recvtime.second #+ timestamp.minute*60 + timestamp.hour*60*60 #FIXME timestamp not set
                ts_usec = recvtime.microsecond
                pcap_packet = struct.pack('@ I I I I', ts_sec, ts_usec, length, length) + packet
                try:
                    self.wireshark_process.stdin.write(pcap_packet)
                    self.wireshark_process.stdin.flush()
                    log.debug("HciMonitorController._callback: done")
                except IOError as e:
                    log.warn("HciMonitorController._callback: broken pipe. terminate.")
                    self.killMonitor() 

def lmpCallback(self, lmp_packet, sendByOwnDevice, src, dest, timestamp):
                eth_header = dest + src + "\xff\xf0"
                meta_data  = "\x00"*6 if sendByOwnDevice else "\x01\x00\x00\x00\x00\x00"
                packet_header = "\x19\x00\x00" + p8(len(lmp_packet)<<3 | 7)

                packet = eth_header + meta_data + packet_header + lmp_packet
                packet += "\x00\x00" # CRC
                length = len(packet)
                ts_sec =  timestamp.second + timestamp.minute*60 + timestamp.hour*60*60
                ts_usec = timestamp.microsecond
                pcap_packet = struct.pack('@ I I I I', ts_sec, ts_usec, length, length) + packet
                try:
                    self.wireshark_process.stdin.write(pcap_packet)
                    self.wireshark_process.stdin.flush()
                    log.debug("LmpMonitorController._callback: done")
                except IOError as e:
                    log.warn("LmpMonitorController._callback: broken pipe. terminate.")
                    self.killMonitor() 

def main():
    # Initialize the logger
    logging.basicConfig()

    # Intialize from our arguments
    insightfinder = InsightfinderStore(*sys.argv[1:])

    current_chunk = 0

    # Get all the inputs
    for line in sys.stdin:
        if insightfinder.filter_string not in line:
            continue
        map_size = len(bytearray(json.dumps(insightfinder.metrics_map)))
        if map_size >= insightfinder.flush_kb * 1000:
            insightfinder.logger.debug("Flushing chunk number: " + str(current_chunk))
            insightfinder.send_metrics()
            current_chunk += 1
        insightfinder.append(line.strip())
    insightfinder.logger.debug("Flushing chunk number: " + str(current_chunk))
    insightfinder.send_metrics()
    insightfinder.save_grouping()
    insightfinder.logger.debug("Finished sending all chunks to InsightFinder") 

def __call__(self, string):
            # the special argument "-" means sys.std{in,out}
            if string == '-':
                if 'r' in self._mode:
                    return sys.stdin
                elif 'w' in self._mode:
                    return sys.stdout
                else:
                    msg = _('argument "-" with mode %r') % self._mode
                    raise ValueError(msg)

            # all other arguments are used as file names
            try:
                return open(string, self._mode, self._bufsize, self._encoding, self._errors)
            except OSError as e:
                message = _("can't open '%s': %s")
                raise ArgumentTypeError(message % (string, e)) 

def _token_to_filenames(token):
        if token[0] == '!':
            pattern = token[1:]
            filenames = glob.glob(pattern)
            if not filenames:
                raise RuntimeError('No filenames matched "%s" pattern' % pattern)
        elif token[0] == '@':
            filelist_name = sys.stdin if token == '@-' else token[1:]
            with open(filelist_name) as filelist:
                filenames = [line.rstrip('\n') for line in filelist]
            directory = os.path.dirname(token[1:])
            if directory != '.':
                filenames = [f if f[0] != '/' else directory + '/' + f for f in filenames]
        else:
            filenames = [token]
        return filenames 

def next_filehandle(self):
        """Go to the next file and retrun its filehandle or None (meaning no more files)."""
        filename = self.next_filename()
        if filename is None:
            fhandle = None
        elif filename == '-':
            fhandle = io.TextIOWrapper(sys.stdin.buffer, encoding=self.encoding)
        elif filename == '<filehandle_input>':
            fhandle = self.filehandle
        else:
            filename_extension = filename.split('.')[-1]
            if filename_extension == 'gz':
                myopen = gzip.open
            elif filename_extension == 'xz':
                myopen = lzma.open
            elif filename_extension == 'bz2':
                myopen = bz2.open
            else:
                myopen = open
            fhandle = myopen(filename, 'rt', encoding=self.encoding)
        self.filehandle = fhandle
        return fhandle 

def description_of(lines, name='stdin'):
    """
    Return a string describing the probable encoding of a file or
    list of strings.

    :param lines: The lines to get the encoding of.
    :type lines: Iterable of bytes
    :param name: Name of file or collection of lines
    :type name: str
    """
    u = UniversalDetector()
    for line in lines:
        u.feed(line)
    u.close()
    result = u.result
    if result['encoding']:
        return '{0}: {1} with confidence {2}'.format(name, result['encoding'],
                                                     result['confidence'])
    else:
        return '{0}: no result'.format(name) 

def redirect_output(self, statement):
        if statement.parsed.pipeTo:
            self.kept_state = Statekeeper(self, ('stdout',))
            self.kept_sys = Statekeeper(sys, ('stdout',))
            self.redirect = subprocess.Popen(statement.parsed.pipeTo, shell=True, stdout=subprocess.PIPE, stdin=subprocess.PIPE)
            sys.stdout = self.stdout = self.redirect.stdin
        elif statement.parsed.output:
            if (not statement.parsed.outputTo) and (not can_clip):
                raise EnvironmentError('Cannot redirect to paste buffer; install ``xclip`` and re-run to enable')
            self.kept_state = Statekeeper(self, ('stdout',))
            self.kept_sys = Statekeeper(sys, ('stdout',))
            if statement.parsed.outputTo:
                mode = 'w'
                if statement.parsed.output == 2 * self.redirector:
                    mode = 'a'
                sys.stdout = self.stdout = open(os.path.expanduser(statement.parsed.outputTo), mode)
            else:
                sys.stdout = self.stdout = tempfile.TemporaryFile(mode="w+")
                if statement.parsed.output == '>>':
                    self.stdout.write(get_paste_buffer()) 

def do_py(self, arg):
        '''
        py <command>: Executes a Python command.
        py: Enters interactive Python mode.
        End with ``Ctrl-D`` (Unix) / ``Ctrl-Z`` (Windows), ``quit()``, ``exit()``.
        Non-python commands can be issued with ``cmd("your command")``.
        Run python code from external files with ``run("filename.py")``
        '''
        self.pystate['self'] = self
        arg = arg.parsed.raw[2:].strip()
        localvars = (self.locals_in_py and self.pystate) or {}
        interp = InteractiveConsole(locals=localvars)
        interp.runcode('import sys, os;sys.path.insert(0, os.getcwd())')
        if arg.strip():
            interp.runcode(arg)
        else:
            def quit():
                raise EmbeddedConsoleExit
            def onecmd_plus_hooks(arg):
                return self.onecmd_plus_hooks(arg + '\n')
            def run(arg):
                try:
                    file = open(arg)
                    interp.runcode(file.read())
                    file.close()
                except IOError as e:
                    self.perror(e)
            self.pystate['quit'] = quit
            self.pystate['exit'] = quit
            self.pystate['cmd'] = onecmd_plus_hooks
            self.pystate['run'] = run
            try:
                cprt = 'Type "help", "copyright", "credits" or "license" for more information.'
                keepstate = Statekeeper(sys, ('stdin','stdout'))
                sys.stdout = self.stdout
                sys.stdin = self.stdin
                interp.interact(banner= "Python %s on %s\n%s\n(%s)\n%s" %
                       (sys.version, sys.platform, cprt, self.__class__.__name__, self.do_py.__doc__))
            except EmbeddedConsoleExit:
                pass
            keepstate.restore() 

def do_load(self, arg=None):
        """Runs script of command(s) from a file or URL."""
        if arg is None:
            targetname = self.default_file_name
        else:
            arg = arg.split(None, 1)
            targetname, args = arg[0], (arg[1:] or [''])[0].strip()
        try:
            target = self.read_file_or_url(targetname)
        except IOError as e:
            self.perror('Problem accessing script from %s: \n%s' % (targetname, e))
            return
        keepstate = Statekeeper(self, ('stdin','use_rawinput','prompt',
                                       'continuation_prompt','current_script_dir'))
        self.stdin = target
        self.use_rawinput = False
        self.prompt = self.continuation_prompt = ''
        self.current_script_dir = os.path.split(targetname)[0]
        stop = self._cmdloop()
        self.stdin.close()
        keepstate.restore()
        self.lastcmd = ''
        return stop and (stop != self._STOP_SCRIPT_NO_EXIT) 

def in_idle():
    """
    @rtype: C{boolean}
    @return: true if this function is run within idle.  Tkinter
    programs that are run in idle should never call L{Tk.mainloop}; so
    this function should be used to gate all calls to C{Tk.mainloop}.

    @warning: This function works by checking C{sys.stdin}.  If the
    user has modified C{sys.stdin}, then it may return incorrect
    results.
    """
    import sys, types
    return (type(sys.stdin) == types.InstanceType and \
            sys.stdin.__class__.__name__ == 'PyShell')

##//////////////////////////////////////////////////////
##  Test code.
##////////////////////////////////////////////////////// 

def in_idle():
    """
    Return True if this function is run within idle.  Tkinter
    programs that are run in idle should never call ``Tk.mainloop``; so
    this function should be used to gate all calls to ``Tk.mainloop``.

    :warning: This function works by checking ``sys.stdin``.  If the
        user has modified ``sys.stdin``, then it may return incorrect
        results.
    :rtype: bool
    """
    import sys
    return sys.stdin.__class__.__name__ in ('PyShell', 'RPCProxy')

##########################################################################
# PRETTY PRINTING
########################################################################## 

def interact(self):
        """
        Interact with the socket. This will send all keyboard input to the
        socket and input from the socket to the console until an EOF occurs.
        """

        sockets = [sys.stdin, self.channel]
        while True:
            ready = select.select(sockets, [], [])[0]

            if sys.stdin in ready:
                line = sys.stdin.readline().encode('latin1')
                if not line:
                    break
                self.write(line)

            if self.channel in ready:
                self.read(1, echo=True) 

def ask_password(profile, interactive):
    """
    Prompt for profile password
    """
    if not PY3:
        profile = profile.encode(SYS_ENCODING)

    passmsg = "\nMaster Password for profile {0}: ".format(profile)

    if sys.stdin.isatty() and interactive:
        passwd = getpass(passmsg)

    else:
        # Ability to read the password from stdin (echo "pass" | ./firefox_...)
        if sys.stdin in select.select([sys.stdin], [], [], 0)[0]:
            passwd = sys.stdin.readline().rstrip("\n")
        else:
            LOG.warning("Master Password not provided, continuing with blank password")
            passwd = ""

    return py2_decode(passwd) 

def process(self, argv=sys.argv, ifile=sys.stdin, ofile=sys.stdout):
        """ Process data.

        :param argv: Command line arguments.
        :type argv: list or tuple

        :param ifile: Input data file.
        :type ifile: file

        :param ofile: Output data file.
        :type ofile: file

        :return: :const:`None`
        :rtype: NoneType

        """
        if len(argv) > 1:
            self._process_protocol_v1(argv, ifile, ofile)
        else:
            self._process_protocol_v2(argv, ifile, ofile) 

def process(self, argv=sys.argv, ifile=sys.stdin, ofile=sys.stdout):
        """ Process data.

        :param argv: Command line arguments.
        :type argv: list or tuple

        :param ifile: Input data file.
        :type ifile: file

        :param ofile: Output data file.
        :type ofile: file

        :return: :const:`None`
        :rtype: NoneType

        """
        if len(argv) > 1:
            self._process_protocol_v1(argv, ifile, ofile)
        else:
            self._process_protocol_v2(argv, ifile, ofile) 

def main():
    """
    Main application loop.
    """

    env = os.environ

    try:
        host = env['SYSLOG_SERVER']
        port = int(env['SYSLOG_PORT'])
        socktype = socket.SOCK_DGRAM if env['SYSLOG_PROTO'] == 'udp' \
            else socket.SOCK_STREAM
    except KeyError:
        sys.exit("SYSLOG_SERVER, SYSLOG_PORT and SYSLOG_PROTO are required.")

    handler = SysLogHandler(
        address=(host, port),
        socktype=socktype,
    )
    handler.setFormatter(PalletFormatter())

    for event_headers, event_data in supervisor_events(sys.stdin, sys.stdout):
        event = logging.LogRecord(
            name=event_headers['processname'],
            level=logging.INFO,
            pathname=None,
            lineno=0,
            msg=event_data,
            args=(),
            exc_info=None,
        )
        event.process = int(event_headers['pid'])
        handler.handle(event) 

def __init__(self):  # type: () -> None
        super(StandardInputStream, self).__init__(sys.stdin) 

def main():
    config = read_config(sys.stdin, os.environ)
    tags = build_tags(config)

    for tag in tags:
        print(tag) 

def _fclose(fname, fd):
    """
    Extend file close function, to support
        1) "-", which means stdin/stdout
        2) "$cmd |" which means pipe.stdout
        3) None type
    """
    if fname != "-" and fd and fname[-1] != "|":
        fd.close() 

def parse_scps(scp_path,
               value_processor=lambda x: x,
               num_tokens=2,
               restrict=True):
    """
    Parse kaldi's script(.scp) file with supported for stdin
    WARN: last line of scripts could not be None and with "\n" end
    """
    scp_dict = dict()
    line = 0
    with ext_open(scp_path, "r") as f:
        for raw_line in f:
            scp_tokens = raw_line.strip().split()
            line += 1
            if scp_tokens[-1] == "|":
                key, value = scp_tokens[0], " ".join(scp_tokens[1:])
            else:
                token_len = len(scp_tokens)
                if num_tokens >= 2 and token_len != num_tokens or restrict and token_len < 2:
                    raise RuntimeError(f"For {scp_path}, format error " +
                                       f"in line[{line:d}]: {raw_line}")
                if num_tokens == 2:
                    key, value = scp_tokens
                else:
                    key, value = scp_tokens[0], scp_tokens[1:]
            if key in scp_dict:
                raise ValueError(
                    f"Duplicate key \'{key}\' exists in {scp_path}")
            scp_dict[key] = value_processor(value)
    return scp_dict 

def convert(csv, json, **kwargs):
    '''Convert csv to json.

    csv:  filename or file-like object
    json: filename  or file-like object


    if csv is '-' or None:
        stdin is used for input
    if json is '-' or None:
        stdout is used for output
    '''

    csv_local, json_local = None, None
    try:
        if csv == '-' or csv is None:
            csv = sys.stdin
        elif isinstance(csv, str):
            csv = csv_local = open(csv, 'r')

        if json == '-' or json is None:
            json = sys.stdout
        elif isinstance(json, str):
            json = json_local = open(json, 'w')

        data = load_csv(csv, **kwargs)
        save_json(data, json, **kwargs)
    finally:
        if csv_local is not None:
            csv_local.close()
        if json_local is not None:
            json_local.close() 

def anonymize_sequences(
		self, mapping, input_stream=sys.stdin, output_stream=sys.stdout,
		sequence_prefix='', file_format="fasta"):
		"""
			Anonymize sequences and write a mapping file

			@attention: only 'fasta' and 'fastq' supported

			@param mapping: output stream for sequence id mapping
			@type mapping: file | io.FileIO | StringIO.StringIO
			@param input_stream: Input stream of fasta format data
			@type input_stream: file | io.FileIO | StringIO.StringIO
			@param output_stream: Output stream of anonymous fasta format data
			@type output_stream: file | io.FileIO | StringIO.StringIO
			@param sequence_prefix: Prefix of the anonymous sequence id.
			@type sequence_prefix: basestring
			@param file_format: Fasta format of input and output. Either 'fasta' or 'fastq'.
			@type file_format: basestring

			@return: None
			@rtype: None
		"""
		assert self.is_stream(input_stream)
		assert self.is_stream(output_stream)
		assert self.is_stream(mapping)
		assert isinstance(sequence_prefix, basestring)
		assert isinstance(file_format, basestring)
		file_format = file_format.lower()
		assert file_format in self._legal_formats

		sequence_counter = 0
		for seq_record in SeqIO.parse(input_stream, file_format):
			anonymous_id = "{pre}{ct}".format(pre=sequence_prefix, ct=sequence_counter)
			map_line = "{oldid}\t{newid}\n".format(oldid=seq_record.id, newid=anonymous_id)
			mapping.write(map_line)
			seq_record.id = anonymous_id
			seq_record.description = ''
			output_stream.write(seq_record.format(file_format))
			sequence_counter += 1 

def findPlasmids(outPlasmidFilePath):
    """
        Read sequence descriptions from a DBK files (stdin), output sequence ids (record.id) if the corresponding
        description contain "plasmid".
        Plasmids can be also within the sequences!
    """
    # append to a file if it already exists
    if os.path.isfile(outPlasmidFilePath):
        outFileMode = 'a'
    else:
        outFileMode = 'w'
    outBuffer = csv.OutFileBuffer(outPlasmidFilePath, bufferText=False, fileOpenMode=outFileMode)

    recordCount = 0
    plasmidCount = 0

    for record in SeqIO.parse(sys.stdin, "genbank"):
        recordCount += 1

        if string.find(record.description, 'plasmid') != -1:
            outBuffer.writeText(str(str(record.id) + '\n'))
            plasmidCount += 1

    outBuffer.close()
    print 'file, records, plasmids:', outPlasmidFilePath, recordCount, plasmidCount
    #for feature in record.features:
    #    if feature.type == "source":