Python Path.replace Examples

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def main(args):
    """Main script"""
    pdb_parser = PDBParser()

    pdb_name = Path(args.pdb).stem
    # deal with FoldX repaired PDBs
    if pdb_name.endswith('_Repair'):
        pdb_name = pdb_name.replace('_Repair', '')

    structure = pdb_parser.get_structure(pdb_name, args.pdb)

    sections = import_sections(args.yaml, pdb_name)

    variants = []
    if sections is not None:
        for section in sections:
            filter_region = 'region' in section
            for residue in structure[0][section['chain']]:
                if not residue.id[0] == ' ':
                    continue  # Filter HETATMs

                position = int(residue.id[1])
                amino_acid = seq1(residue.get_resname())

                if not amino_acid in AA_ALPHABET:
                    # Filter non-standard AAs, required when processing
                    # foldx repaired PDBs as they turn HETATMs to regular ATOMs
                    # for regular proteins
                    continue

                if (filter_region and (position > section['region'][1]
                                       or position < section['region'][0])):
                    continue

                variants.extend([
                    f"{amino_acid}{section['chain']}{position}{x}"
                    for x in AA_ALPHABET if not x == amino_acid
                ])
    else:
        for chain in structure[0]:
            for residue in chain:
                if not residue.id[0] == ' ':
                    continue  # Filter HETATMs

                position = int(residue.id[1])
                amino_acid = seq1(residue.get_resname())

                if not amino_acid in AA_ALPHABET:
                    continue

                variants.extend([
                    f"{amino_acid}{chain.id}{position}{x}" for x in AA_ALPHABET
                    if not x == amino_acid
                ])

    print(*variants, sep=';\n', end=';\n', file=sys.stdout)

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Python Path.replace Examples

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def clean_template(template, removals=None, cfmt=cfmt):
    if removals is None:
        removals = ['temp', 'dx', 'dy']
    d = cfmt.format(template, defaultdict(str))

    for r in removals:
        d = d.replace('[{}=]'.format(r), '')
    z = re.sub(r"__+", "_", d)
    z = z.replace('_.', '.')
    e = z.replace('[', '')
    e = e.replace(']', '')
    e = e.replace('(', '')
    e = e.replace(')', '')
    f = Path(e).as_posix()
    f = f.replace('/_', '/')
    return f

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Python Path.replace Examples

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def update(generated_folder, destination_folder, global_conf, local_conf):
    """Update data from generated to final folder"""
    wrapper_files_or_dirs = merge_options(global_conf, local_conf, "wrapper_filesOrDirs") or []
    delete_files_or_dirs = merge_options(global_conf, local_conf, "delete_filesOrDirs") or []
    generated_relative_base_directory = local_conf.get('generated_relative_base_directory') or \
        global_conf.get('generated_relative_base_directory')

    client_generated_path = Path(generated_folder)
    if generated_relative_base_directory:
        client_generated_path = next(client_generated_path.glob(generated_relative_base_directory))

    for wrapper_file_or_dir in wrapper_files_or_dirs:
        for file_path in Path(destination_folder).glob(wrapper_file_or_dir):
            relative_file_path = file_path.relative_to(destination_folder)
            file_path_dest = client_generated_path.joinpath(str(relative_file_path))
            file_path.replace(file_path_dest)

    for delete_file_or_dir in delete_files_or_dirs:
        for file_path in client_generated_path.glob(delete_file_or_dir):
            if file_path.is_file():
                file_path.unlink()
            else:
                shutil.rmtree(str(file_path))

    shutil.rmtree(destination_folder)
    client_generated_path.replace(destination_folder)

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Python Path.replace Examples

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def validate_io_streams(input_file: pathlib.Path, output_file: pathlib.Path) -> bool:
    """
    Ensure I/O paths are valid and clean for program
    :param input_file: Input file (JSON)
    :param output_file: Output file (SQLite)
    :return: Good to continue status
    """
    if not input_file.is_file():
        LOGGER.fatal("Input file {} does not exist.".format(input_file))
        return False

    output_file.parent.mkdir(exist_ok=True)
    if output_file.is_file():
        LOGGER.warning("Output file {} exists already, moving it.".format(output_file))
        output_file.replace(output_file.parent.joinpath(output_file.name + ".old"))

    return True

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Python Path.replace Examples

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def _extract_to_folder(db_archive_path, db_folder):
        with tarfile.open(db_archive_path) as tar_archive:
            for member in tar_archive.getmembers():
                if not member.isreg():
                    continue
                # Will skip the dirs to extract only file objects

                tar_archive.extract(member, db_folder)
                # The files are extract to a subfolder (with a date in the name)
                # We want to move these into the main folder above this.
                targetname = Path(member.name).name
                if targetname != member.name:
                    curr_file = Path(db_folder).joinpath(member.name)
                    extr_folder = Path(db_folder).joinpath(member.name).parent
                    curr_file.replace(Path(db_folder).joinpath(targetname))
                    # if the folder is empty, remove it
                    if not list(extr_folder.glob("*")):
                        extr_folder.rmdir()

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def _transform_mobile_v1_2_to_pprf_2_0(rec_dir: str):
    _generate_pprf_2_0_info_file(rec_dir)

    # rename info.csv file to info.mobile.csv
    info_csv = Path(rec_dir) / "info.csv"
    new_path = info_csv.with_name("info.mobile.csv")
    info_csv.replace(new_path)

    recording = PupilRecording(rec_dir)

    # patch world.intrinsics
    # NOTE: could still be worldless at this point
    update_utils._try_patch_world_instrinsics_file(
        rec_dir,
        recording.files().mobile().world().videos())

    _rename_mobile_files(recording)
    _rewrite_timestamps(recording)

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Python Path.replace Examples

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def _fmt(path):
     text = Path(path).read_text().strip()
     # Remove repositories tag, as it's a detail that's always the same
     text = re.sub(r" +<repositories>.*?</repositories>.*?\n  <o",
                   "  <o",
                   text,
                   flags=re.S | re.M)
     text = text.replace("\n\n", "\n")
     return text

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Python Path.replace Examples

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def move_file(self, source, destination, overwrite=False):
        """Move file from source path to destination path,
        optionally overwriting the destination.

        :param source:      source file path for moving
        :param destination: path to move to
        :param overwrite:   replace destination file if it already exists
        """
        src = Path(source)
        dst = Path(destination)

        if not src.is_file():
            raise FileNotFoundError(f"Source {src} is not a file")
        if dst.exists() and not overwrite:
            raise FileExistsError(f"Destination {dst} already exists")

        src.replace(dst)
        self.logger.info("Moved file: %s -> %s", src, dst)

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def postdownloading_callback(self, input_kwargs, *args):
        r = args[-1]
        url = args[-2]
        if not r:
            print("Error: No response\n")
            return
        song_id = get_song_id(url)
        if r.error:
            print(f"Error: {r.error}", file=sys.stderr)
            if any(err in r.error for err in errors):
                print(f"Error: Beatmap not found: {url}\n", file=sys.stderr)
            if any(rerr in r.error for rerr in retry_errors):
                print(f"{url}\nAdded retry after queue end\n")
                if input_kwargs and "proxies" in input_kwargs:
                    proxy = re.search(r"//([^/]*)/",
                                      input_kwargs["proxies"]["http"]).group(1)
                    if proxy in self._proxy.proxies:
                        self._proxy.proxies.remove(proxy)
                    if len(self._proxy.proxies) < 2:
                        print("No valid proxies, exiting\n")
                        del self._proxy
                return self.retry_download(url)
            return

        if r.url == 'https://osu.ppy.sh/p/error':
            print("Error: Osu site internal error", file=sys.stderr)
            return Path(r.out_file).unlink()

        try:
            old_filename = Path(r.out_file).resolve(strict=True)
            name = r.info._headers[6][1].split('"')[1::2][0]
            name = re.sub(r'[^\w_.)( -]', '', name)
            name = old_filename.parent.joinpath(name)
            old_filename.replace(name)
        except Exception as e:
            print(f"Error: Failed to rename beatmap: {url}\n{e}",
                  file=sys.stderr)
            pass
        else:
            if self.auto_start:
                os.startfile(name)
            print(f"Successfully downloaded: {name.stem}")
            del old_filename, name
        del r, song_id

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def compile_tex(tex_file, tex_compiler, output_format):
    """Compiles a tex_file into a .dvi or a .xdv or a .pdf

    Parameters
    ----------
    tex_file : :class:`str`
        File name of TeX file to be typeset.
    tex_compiler : :class:`str`
        String containing the compiler to be used, e.g. ``pdflatex`` or ``lualatex``
    output_format : :class:`str`
        String containing the output format generated by the compiler, e.g. ``.dvi`` or ``.pdf``

    Returns
    -------
    :class:`str`
        Path to generated output file in desired format (DVI, XDV or PDF).
    """
    result = tex_file.replace(".tex", output_format)
    result = Path(result).as_posix()
    tex_file = Path(tex_file).as_posix()
    tex_dir = Path(config.get_dir("tex_dir")).as_posix()
    if not os.path.exists(result):
        command = tex_compilation_command(tex_compiler, output_format,
                                          tex_file, tex_dir)
        exit_code = os.system(command)
        if exit_code != 0:
            log_file = tex_file.replace(".tex", ".log")
            if not Path(log_file).exists():
                raise RuntimeError(
                    f"{tex_compiler} failed but did not produce a log file. "
                    "Check your LaTeX installation.")
            with open(log_file, "r") as f:
                log = f.readlines()
                log_error_pos = [
                    ind for (ind, line) in enumerate(log)
                    if line.startswith("!")
                ]
                if log_error_pos:
                    logger.error(
                        f"LaTeX compilation error! {tex_compiler} reports:")
                    for lineno in log_error_pos:
                        # search for a line starting with "l." in the next
                        # few lines past the error; otherwise just print some lines.
                        printed_lines = 1
                        for _ in range(10):
                            if log[lineno + printed_lines].startswith("l."):
                                break
                            printed_lines += 1

                        for line in log[lineno:lineno + printed_lines + 1]:
                            logger.error(line)

            raise ValueError(f"{tex_compiler} error converting to"
                             f" {output_format[1:]}. See log output above or"
                             f" the log file: {log_file}")
    return result

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def _make_pt_vrt(self, layer_name, out_dir):
        """
        Make a vrt file for station point ratios in summary CSV for a 
        specific layer or field name. Save to out_dir. Used for gdal_grid 
        interpolation commands of scatter point data.
        """
        if not Path(out_dir).is_dir():
            os.makedirs(out_dir)
        # old method
        #summary_file = Path(self.summary_csv_path).name
        
        point_data = Path(self.summary_csv_path).name.replace(
                '.csv', '_tmp.csv')

        # make tmp point data csv for given layer, drop missing values
        df = pd.read_csv(self.summary_csv_path)
        df = df[['STATION_LAT', 'STATION_LON', layer_name]]
        df = df[df[layer_name] != -999]
        tmp_out_path = str(Path(self.summary_csv_path).parent / point_data)
        df.to_csv(tmp_out_path, index=False)

        # if out_dir adjust summary CSV path by prepending parent dirs 
        tmp = copy(Path(out_dir))
        n_parent_dirs = 0
        while len(Path(tmp).parents) > 0:    
            if tmp.name == self.summary_csv_path.parent.name:
                break
            tmp = Path(tmp).parent
            n_parent_dirs+=1
        
        path_to_data = str(
            Path(
                '..{}'.format(os.sep)*n_parent_dirs
            ).joinpath(point_data)
        )
        
        out_file = '{}.vrt'.format(layer_name) # keep it simple just layer name

        # VRT format for reading CSV point data
        root = ET.Element('OGRVRTDataSource')
        OGRVRTLayer = ET.SubElement(root, 'OGRVRTLayer', 
                                    name=point_data.replace('.csv', ''))
        # set all fields, SRS WGS84, point geom
        ET.SubElement(OGRVRTLayer, 'SrcDataSource').text = path_to_data
        ET.SubElement(OGRVRTLayer, 'LayerSRS').text = 'epsg:4326'
        ET.SubElement(OGRVRTLayer, 'GeometryType').text = 'wkbPoint'
        ET.SubElement(OGRVRTLayer, 'GeometryField', encoding='PointFromColumns',
                     x='STATION_LON', y='STATION_LAT', z=layer_name)
        
        tree = ET.ElementTree(root)
        # indent xml, save to out_dir
        out_xml_str = _prettify(root)
        
        out_path = os.path.join(out_dir, out_file)
        with open(out_path, 'w') as outf:
            outf.write(out_xml_str)

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