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How to use print_to_tty method in autotest

Best Python code snippet using autotest_python

gref.py

Source:gref.py

1#! /usr/bin/env python32# Search a FASTA or FASTQ file for a sequence that matches a pattern.  The3# pattern can be in the defline or the sequence letters.  Inspired by the 4# 'gref' script in the SEALS package.5# John Conery6# University of Oregon7# 2015-08-228# TBD: 2nd arg optional; if not supplied, read from stdin9import argparse10import os11import sys12import re13from FASTA import *14from FASTQ import *15# When searching a DNA file the script can use a regular expressions based on IUPAC16# ambiguity letter to match the sequence17iupac_map = {18	'A' : r'A',	 19	'C' : r'C',	 20	'G' : r'G',	 21	'T' : r'T',22	'R' : r'[AG]', 23	'Y' : r'[CT]',24	'S' : r'[GC]',25	'W' : r'[AT]',26	'K' : r'[GT]',27	'M' : r'[AC]',28	'B' : r'[CGT]',29	'D' : r'[AGT]',30	'H' : r'[ACT]',31	'V' : r'[ACG]',32	'N' : r'[ACGT]'33}34def iupac_regexp(pat):35    'Create a regular expression for a sequence, replacing IUPAC letters with groups'36    return ''.join(map(lambda ch: iupac_map[ch], pat))37    38complement = {39    'A' : 'T', 40    'T' : 'A', 41    'C' : 'G',42    'G' : 'C',43	'R' : r'[TC]', 44	'Y' : r'[GA]',45	'S' : r'[AT]',46	'W' : r'[GC]',47	'K' : r'[CA]',48	'M' : r'[TG]',49	'B' : r'.',50	'D' : r'.',51	'H' : r'.',52	'V' : r'.',53	'N' : r'.'54}55def reverse_complement(pat):56    return ''.join(map(lambda ch: complement[ch], reversed(pat)))57###58# Parse command line arguments...59def init_api():60    parser = argparse.ArgumentParser(61        description="""Find sequences that match a pattern in FASTA or FASTQ files.  If the --seq option62is used the program looks for the pattern in sequence characters, otherwise it looks for the pattern in63deflines.  Patterns are specified using PERL regular expression syntax.         64If the inputs are named files the program will infer the sequence type from the filename extension 65(.fa, .fn, or .fasta for FASTA files, .fastq for FASTQ files).  If the input is coming from stdin the 66sequence type must be defined with the --fasta or --fastq option.  67"""68)69    parser.add_argument('pattern', help='pattern to find')70    parser.add_argument('files', nargs='*', help='name(s) of sequence file(s)')71    parser.add_argument('-s', '--sequence', action='store_true', help='match sequence characters')72    parser.add_argument('-i', '--iupac', action='store_true', help='pattern contains IUPAC ambiguity letters')73    parser.add_argument('-v', action='store_true', help='print sequences that do not match the pattern')74    parser.add_argument('-r', '--reverse', action='store_true', help='use the reverse complement of the pattern')75    parser.add_argument('--fasta', action='store_true', help='input stream is in FASTA format')76    parser.add_argument('--fastq', action='store_true', help='input stream is in FASTQ format')77    return parser.parse_args()78reader_type = {79    '.fa'    : FASTAReader,80    '.fn'    : FASTAReader,81    '.fasta' : FASTAReader,82    '.fastq' : FASTQReader,83}84# The string %s inserted into this pattern will be printed in red (or the terminal's ANSI color #1)85ESC = chr(27)86highlight_region = ESC + '[1;31m' + '%s' + ESC + '[0m'87###88# Check the command line arguments89def validate(args):90    # if there are no file names we need either --fasta or --fastq91    if len(args.files) == 0:92        if bool(args.fasta) == bool(args.fastq):93            argparse.ArgumentParser.exit(1, 'specify either --fasta or --fastq when reading from stdin')94    # all file names need to end in a recognized extension95    for fn in args.files:96        if os.path.splitext(fn)[1] not in reader_type:97            argparse.ArgumentParser.exit(1, 'invalid filename extension: ' + fn)98###99# Process a single file100def scan_file(file, pattern, tty, args):101    for seq in file:102        src = seq.sequence() if args.sequence else seq.defline()103        match = re.search(pattern, src)104        if match is not None and not args.v:105            res = repr(seq)106            hit = match.group()107            if print_to_tty:108                res = re.sub(hit, highlight_region % hit, res) 109            print(res)110        elif match is None and args.v:111            print(repr(seq))112      113###114# Main program:115    116if __name__ == "__main__":117    args = init_api()118    validate(args)119    120    if args.iupac:121        pattern = iupac_regexp(args.pattern) 122    elif args.reverse:123        pattern = reverse_complement(args.pattern)124    else:125        pattern = args.pattern126        127    print_to_tty = os.isatty(sys.stdout.fileno())128    129    if len(args.files) == 0:130        reader = FASTAReader(sys.stdin) if args.fasta else FASTQReader(sys.stdin)131        scan_file(reader, pattern, print_to_tty, args)132    else:133        for fn in args.files:134            ext = os.path.splitext(fn)[1]135            cls = reader_type.get(ext)136            scan_file(cls(fn), pattern, print_to_tty, args)...

test_printer.py

Source:test_printer.py

...37]38@pytest.fixture39def printer():40    return ErrorPrinter(files=TEST_FILES, issues=TEST_ISSUES)41def test_print_to_tty(capfd, printer):42    expected_stdout = '\n'.join([43        'In /bad_file line 10:',44        'foo',45        '   ^-- WSC001: Bad line ending \'\\r\\n\'',46        '',47        'In /bad_file line 187:',48        'exit 0',49        '      ^-- WSC005: No newline at end of file',50        '',51        'In /bad_file line 188:',52        'echo \'foo--->bar\'  ',53        '                   ^-- WSC002: Tailing whitespace',54        ''55    ])56    printer.print_to_tty(False)57    out, err = capfd.readouterr()58    assert '' == err59    assert expected_stdout == out60def test_colored_print_to_tty(capfd, printer):61    bold = '\033[1m'62    yellow = '\033[33m'63    reset = '\033[0m'64    expected_stdout = '\n'.join([65        bold + 'In /bad_file line 10:' + reset,66        'foo',67        '   ' + yellow + '^-- WSC001: Bad line ending \'\\r\\n\'' + reset,68        '',69        bold + 'In /bad_file line 187:' + reset,70        'exit 0',71        '      ' + yellow + '^-- WSC005: No newline at end of file' + reset,72        '',73        bold + 'In /bad_file line 188:' + reset,74        'echo \'foo--->bar\'  ',75        '                   ' + yellow + '^-- WSC002: Tailing whitespace' + reset,76        ''77    ])78    printer.print_to_tty(True)79    out, err = capfd.readouterr()80    assert '' == err81    assert expected_stdout == out82def assert_equal_xml(generated_xml, expected_xml):83    """84    :type generated_xml: str85    :type expected_xml: str86    """87    __tracebackhide__ = True  # noqa88    differences = []89    def append_to_messages(message):90        """91        :type message: str92        """...

async-main.py

Source:async-main.py

...9parser.add_argument('--server', default=False, action='store_true')10parser.add_argument('--ip', default='127.0.0.1', type=str)11parser.add_argument('--port', default=5555, type=int)12args = parser.parse_args()13async def print_to_tty(reader: asyncio.StreamReader):14    while True:15        data = await reader.read(1024)16        if data:17            os.write(sys.stdout.fileno(), data)18        else:19            # cannot stop another coroutine20            # so just exit -_-21            sys.exit()22def blocking_io():23    return os.read(sys.stdin.fileno(), 1024)24        25async def read_from_tty(writer: asyncio.StreamWriter):26    loop = asyncio.get_running_loop()27    while True:28        with concurrent.futures.ThreadPoolExecutor() as pool:29            data = await loop.run_in_executor(30                pool, blocking_io)31            if data:32                writer.write(data)33                await writer.drain()34            else:35                writer.close()36                return37async def handle_netcat_reqeust(reader: asyncio.StreamReader, writer: asyncio.StreamWriter):38    await asyncio.gather(39        print_to_tty(reader),40        read_from_tty(writer),41    )42async def main():43    if args.server == True:44        server = await asyncio.start_server(handle_netcat_reqeust, args.ip, args.port)45        async with server:46            await server.serve_forever()47    else:48        reader, writer = await asyncio.open_connection(args.ip, args.port)49        await asyncio.gather(50            print_to_tty(reader),51            read_from_tty(writer),52        )...

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