# 3.3. Utils

## 3.3.1. GSGW

class `pymzml.utils.GSGW.``GSGW`(file=None, max_idx=10000, max_idx_len=8, max_offset_len=8, output_path='./test.dat.igzip', comp_str=-1)

  Generalized Gzip writer class with random access to indexed offsets.

  Keyword Arguments:
  | file (string) – Filename for the resulting file max_idx (int) – max number of indices which can be saved in this file max_idx_len (int) – maximal length of the index in bytes, must be between 1 and 255 max_offset_len (int) – maximal length of the offset in bytes output_path (str) – path to the output file

  `_allocate_index_bytes`()

    Allocate ‘self.max_index_num’ bytes of length ‘self.max_idx_len’ in the header for inserting the index later on.

  `_write_data`(data)

    Write data into file-stream.

    Parameters: | data (str) – uncompressed data

  `_write_gen_header`(Index=False, FLAGS=None)

    Write a valid gzip header with creation time, user defined flag fields and allocated index.

    Keyword Arguments:
    | Index (bool) – whether to or not to write an index into this header. FLAGS (list, optional) – list of flags (FTEXT, FHCRC, FEXTRA, FNAME) to set for this header.
    Returns: | offset – byte offset of the file pointer
    Return type: | int

  `_write_identifier`(identifier)

    Convert and write the identifier into output file.

    Parameters: | identifier (str or int) – identifier to write into index

  `_write_offset`(offset)

    Convert and write offset to output file.

    Parameters: | offset (int) – offset which will be formatted and written into file index

  `add_data`(data, identifier)

    Create a new gzip member with compressed ‘data’ indexed with ‘index’.

    Parameters: | data (str) – uncompressed data to write to file index (str or int) – unique index for the data

  `encoding`

    Returns the encoding used for this file

  `file_out`

    Output filehandler

  `write_index`()

    Only called after all the data is written, i.e. all calls to `add_data()` have been done.

    Seek back to the beginning of the file and write the index into the allocated comment bytes (see _write_gen_header(Index=True)).

## 3.3.2. GSGR

class `pymzml.utils.GSGR.``GSGR`(file=None)

  Generalized Gzip reader class which enables random access in files written with the `GSGW` class.

  Keyword Arguments:
  | file (str) – path to file to read

  `_check_magic_bytes`()

    Check if file is a gzip file.

  `_read_basic_header`()

    Read and save compression method, bitflags, changetime, compression speed and os.

  `_read_index`()

    Read and save offset dict from indexed gzip file

  `read`(size=-1)

    Read the content of the in File in binary mode

    Keyword Arguments:
    | size (int, optional) – number of bytes to read, -1 for everything
    Returns: | data – parsed bytes from input file
    Return type: | bytes

  `read_block`(index)

    Read and return the data block with the unique index index

    Parameters: | index (int or str) – identifier associated with a specific block
    Returns: | data – indexed text block as string
    Return type: | str

  `seek`(offset)

    Seek to byte offset in input file.

    Parameters: | offset (int) – byte offset to seek to in FileIn
    Returns: | None

Example:

    ..      class SQLiteDatabase(object):
    ..              """
    ..              Example implementation of a database Connector,
    ..              which can be used to make run accept paths to
    ..              sqlite db files.

Example:

    ..      def _open(self, path):
    ..              if path.endswith('.gz'):
    ..                      if self._indexed_gzip(path):
    ..                              self.file_handler = indexedGzip.IndexedGzip(path, self.encoding)
    ..                      else:
    ..                              self.file_handler = standardGzip.StandardGzip(path, self.encoding)
    ..              # Insert a new condition to enable your new fileclass
    ..              elif path.endswith('.db'):
    ..                      self.file_handler = utils.SQLiteConnector.SQLiteDatabase(path, self.encoding)
    ..              else:
    ..                      self.file_handler     = standardMzml.StandardMzml(path, self.encoding)
    ..              return self.file_handler