How to use get_open_func method in autotest

Best Python code snippet using autotest_python

misc.py

Source:misc.py

...16    """17    Returns the names and sequences for the given fasta file as a list of tuples (name, seq).18    """19    fasta_seqs = []20    with get_open_func(filename)(filename, 'rt') as fasta_file:21        name = ''22        sequence = ''23        for line in fasta_file:24            line = line.strip()25            if not line:26                continue27            if line[0] == '>':  # Header line = start of new contig28                if name:29                    fasta_seqs.append((name.split()[0], sequence.upper()))30                    sequence = ''31                name = line[1:]32            else:33                sequence += line34        if name:35            fasta_seqs.append((name.split()[0], sequence.upper()))36    return fasta_seqs37def get_compression_type(filename):38    """39    Attempts to guess the compression (if any) on a file using the first few bytes.40    http://stackoverflow.com/questions/1304456241    """42    magic_dict = {'gz': (b'\x1f', b'\x8b', b'\x08'),43                  'bz2': (b'\x42', b'\x5a', b'\x68'),44                  'zip': (b'\x50', b'\x4b', b'\x03', b'\x04')}45    max_len = max(len(x) for x in magic_dict)46    unknown_file = open(filename, 'rb')47    file_start = unknown_file.read(max_len)48    unknown_file.close()49    compression_type = 'plain'50    for file_type, magic_bytes in magic_dict.items():51        if file_start.startswith(magic_bytes):52            compression_type = file_type53    if compression_type == 'bz2':54        sys.exit('Error: cannot use bzip2 format - use gzip instead')55    if compression_type == 'zip':56        sys.exit('Error: cannot use zip format - use gzip instead')57    return compression_type58def get_open_func(filename):59    if get_compression_type(filename) == 'gz':60        return gzip.open61    else:  # plain text62        return open63REV_COMP_DICT = {'A': 'T', 'T': 'A', 'G': 'C', 'C': 'G', 'a': 't', 't': 'a', 'g': 'c', 'c': 'g',64                 'R': 'Y', 'Y': 'R', 'S': 'S', 'W': 'W', 'K': 'M', 'M': 'K', 'B': 'V', 'V': 'B',65                 'D': 'H', 'H': 'D', 'N': 'N', 'r': 'y', 'y': 'r', 's': 's', 'w': 'w', 'k': 'm',66                 'm': 'k', 'b': 'v', 'v': 'b', 'd': 'h', 'h': 'd', 'n': 'n', '.': '.', '-': '-',67                 '?': '?'}68def complement_base(base):69    try:70        return REV_COMP_DICT[base]71    except KeyError:72        return 'N'...

find_unclassified.py

Source:find_unclassified.py

...25    return args26def main():27    args = get_arguments()28    unclassified_reads = set()29    with get_open_func(args.cent_1)(args.cent_1, 'rt') as cent_1_file:30        for line in cent_1_file:31            parts = line.strip().split('\t')32            read_name, classification = parts[0], parts[1]33            if read_name == 'readID' or classification == 'unclassified':34                # include the header as well as unclassified reads35                unclassified_reads.add(read_name)36    with get_open_func(args.cent_2)(args.cent_2, 'rt') as cent_2_file:37        for line in cent_2_file:38            line = line.strip()39            parts = line.split('\t')40            read_name = parts[0]41            if read_name in unclassified_reads:42                print(line)43def get_compression_type(filename):44    """45    Attempts to guess the compression (if any) on a file using the first few bytes.46    http://stackoverflow.com/questions/1304456247    """48    magic_dict = {'gz': (b'\x1f', b'\x8b', b'\x08'),49                  'bz2': (b'\x42', b'\x5a', b'\x68'),50                  'zip': (b'\x50', b'\x4b', b'\x03', b'\x04')}51    max_len = max(len(x) for x in magic_dict)52    unknown_file = open(filename, 'rb')53    file_start = unknown_file.read(max_len)54    unknown_file.close()55    compression_type = 'plain'56    for file_type, magic_bytes in magic_dict.items():57        if file_start.startswith(magic_bytes):58            compression_type = file_type59    if compression_type == 'bz2':60        sys.exit('Error: cannot use bzip2 format - use gzip instead')61    if compression_type == 'zip':62        sys.exit('Error: cannot use zip format - use gzip instead')63    return compression_type64def get_open_func(filename):65    if get_compression_type(filename) == 'gz':66        return gzip.open67    else:  # plain text68        return open69if __name__ == '__main__':...

racon_utils.py

Source:racon_utils.py

...39    elif first_char == "@":40        return "FASTQ"41    else:42        raise ValueError("<E> get_sequence_file_type: File is neither FASTA or FASTQ")43def get_open_func(filename: str):44    """test which open function to use"""45    if get_compression_type(filename) == "gz":46        return gzip.open47    else:  # plain text48        return open49def iterate_fasta(filename: str) -> []:50    """iterate fasta file"""51    if get_sequence_file_type(filename) != "FASTA":52        log("<E> iterate_fasta: Error: {} is not FASTA format".format(filename))53        raise StopIteration54    with get_open_func(filename)(filename, "rt") as fasta:55        for line in fasta:56            line = line.strip()57            if len(line) == 0:58                continue59            if not line.startswith(">"):60                continue61            name = line[1:].split()[0]62            sequence = next(fasta).strip()63            yield name, sequence64def iterate_fastq(filename: str) -> []:65    """iterate fastq file"""66    if get_sequence_file_type(filename) != "FASTQ":67        log("<E> iterate_fastq: Error: {} is not FASTQ format".format(filename))68        raise StopIteration69    with get_open_func(filename)(filename, "rt") as fastq:70        for line in fastq:71            line = line.strip()72            if len(line) == 0:73                continue74            if not line.startswith("@"):75                continue76            name = line[1:].split()[0]77            sequence = next(fastq).strip()78            _ = next(fastq)79            qualities = next(fastq).strip()...

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