Module io

Classes

DummyFileObject

SplitIO

Functions

delete(file_name, dir=None, fail=True)
Deleting the given file, taking into account missing compression extensions.

(int, str) determine_compression(file_path)
Function for determining the compression type, and for also testing if the file exists.

list of lists of str extract_data(file=None, dir=None, file_data=None, sep=None)
Return all data in the file as a list of lines where each line is a list of line elements.

str file_root(file_path)
Return the root file name, striped of path and extension details.

str get_file_path(file_name=None, dir=None)
Generate and expand the full file path.

io_streams_restore(verbosity=1)
Restore all IO streams to the Python defaults.

io_streams_log(file_name=None, dir=None, verbosity=1)
Turn on logging, sending both STDOUT and STDERR streams to a file.

io_streams_tee(file_name=None, dir=None, compress_type=0, verbosity=1)
Turn on teeing to split both STDOUT and STDERR streams and sending second part to a file.

mkdir_nofail(dir=None, verbosity=1)
Create the given directory, or exit without raising an error if the directory exists.

file object open_read_file(file_name=None, dir=None, verbosity=1)
Open the file 'file' and return all the data.

writable file object (if return_path, then a tuple of the writable file and the full file path) open_write_file(file_name=None, dir=None, force=False, compress_type=0, verbosity=1, return_path=False)
Function for opening a file for writing and creating directories if necessary.

str, list of [str, float], or list of [str, float, float] read_spin_data(file=None, dir=None, file_data=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, data_col=None, error_col=None, sep=None, spin_id=None)
Generator function for reading the spin specific data from file.

list of lists of str strip(data, comments=True)
Remove all comment and empty lines from the file data structure.

test_binary(binary)
Function for testing that the binary string corresponds to a valid executable file.

write_data(out=None, headings=None, data=None, sep=None)
Write out a table of the data to the given file handle.

write_spin_data(file, dir=None, sep=None, spin_ids=None, mol_names=None, res_nums=None, res_names=None, spin_nums=None, spin_names=None, force=False, data=None, data_name=None, error=None, error_name=None, float_format='%20.15g')
Generator function for reading the spin specific data from file.

Variables

__package__ = None
hash(x)

Imports: dep_check, devnull, F_OK, X_OK, access, altsep, getenv, makedirs, pathsep, remove, sep, expanduser, basename, splitext, isfile, search, sys, stdin, stdout, stderr, warn, bz2_open, gz_open, pipe_control, is_filetype, is_float, RelaxError, RelaxFileError, RelaxFileOverwriteError, RelaxInvalidSeqError, RelaxMissingBinaryError, RelaxNoInPathError, RelaxNonExecError, spin_id_to_data_list, RelaxWarning, RelaxFileEmptyWarning

Function Details

delete(file_name, dir=None, fail=True)

Deleting the given file, taking into account missing compression extensions.

Parameters:

• file_name (str) - The name of the file to delete.
• dir (None or str) - The directory containing the file.
• fail (bool) - A flag which if True will cause RelaxFileError to be raised.

Raises:

• RelaxFileError - If the file does not exist, and fail is set to true.

determine_compression(file_path)

Function for determining the compression type, and for also testing if the file exists.

Parameters:

• file_path (str) - The full file path of the file.

Returns: (int, str)

A tuple of the compression type and full path of the file (including its extension). A value of 0 corresponds to no compression. Bzip2 compression corresponds to a value of 1. Gzip compression corresponds to a value of 2.

extract_data(file=None, dir=None, file_data=None, sep=None)

Return all data in the file as a list of lines where each line is a list of line elements.

Parameters:

• file (str or file object) - The file to extract the data from.
• dir (str or None) - The path where the file is located. If None and the file argument is a string, then the current directory is assumed.
• file_data (list of str) - If the file data has already been extracted from the file, it can be passed into this function using this argument. If data is supplied here, then the file_name and dir args are ignored.
• sep (str) - The character separating the columns in the file data. If None, then whitespace is assumed.

Returns: list of lists of str

The file data.

file_root(file_path)

Return the root file name, striped of path and extension details.

Parameters:

• file_path (str) - The full path to the file.

Returns: str

The file root (with all directories and the extension stripped away).

get_file_path(file_name=None, dir=None)

Generate and expand the full file path.

Parameters:

• file_name (str) - The name of the file to extract the data from.
• dir (str) - The path where the file is located. If None, then the current directory is assumed.

Returns: str

The full file path.

io_streams_restore(verbosity=1)

Restore all IO streams to the Python defaults.

Parameters:

• verbosity (int) - The verbosity level.

io_streams_log(file_name=None, dir=None, verbosity=1)

Turn on logging, sending both STDOUT and STDERR streams to a file.

Parameters:

• file_name (str) - The name of the file.
• dir (str) - The path where the file is located. If None, then the current directory is assumed.
• verbosity (int) - The verbosity level.

io_streams_tee(file_name=None, dir=None, compress_type=0, verbosity=1)

Turn on teeing to split both STDOUT and STDERR streams and sending second part to a file.

Parameters:

• file_name (str) - The name of the file.
• dir (str) - The path where the file is located. If None, then the current directory is assumed.
• compress_type (int) - The compression type. The integer values correspond to the compression type: 0, no compression; 1, Bzip2 compression; 2, Gzip compression.
• verbosity (int) - The verbosity level.

mkdir_nofail(dir=None, verbosity=1)

Create the given directory, or exit without raising an error if the directory exists.

Parameters:

• dir (str) - The directory to create.
• verbosity (int) - The verbosity level.

open_read_file(file_name=None, dir=None, verbosity=1)

Open the file 'file' and return all the data.

Parameters:

• file_name (str) - The name of the file to extract the data from.
• dir (str) - The path where the file is located. If None, then the current directory is assumed.
• verbosity (int) - The verbosity level.

Returns: file object

The open file object.

open_write_file(file_name=None, dir=None, force=False, compress_type=0, verbosity=1, return_path=False)

Function for opening a file for writing and creating directories if necessary.

Parameters:

• file_name (str) - The name of the file to extract the data from.
• dir (str) - The path where the file is located. If None, then the current directory is assumed.
• force (bool) - Boolean argument which if True causes the file to be overwritten if it already exists.
• compress_type (int) - The compression type. The integer values correspond to the compression type: 0, no compression; 1, Bzip2 compression; 2, Gzip compression.
• verbosity (int) - The verbosity level.
• return_path (bool) - If True, the function will return a tuple of the file object and the full file path.

Returns: writable file object (if return_path, then a tuple of the writable file and the full file path)

The open, writable file object and, if the return_path is True, then the full file path is returned as well.

read_spin_data(file=None, dir=None, file_data=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, data_col=None, error_col=None, sep=None, spin_id=None)

Generator function for reading the spin specific data from file.

Description

This function reads a columnar formatted file where each line corresponds to a spin system. Spin identification is either through a spin ID string or through columns containing the molecule name, residue name and number, and/or spin name and number.

Parameters:

• file (str) - The name of the file to open.
• dir (str or None) - The directory containing the file (defaults to the current directory if None).
• file_data (list of lists) - An alternative to opening a file, if the data already exists in the correct format. The format is a list of lists where the first index corresponds to the row and the second the column.
• spin_id_col (int or None) - The column containing the spin ID strings. If supplied, the mol_name_col, res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be none.
• mol_name_col (int or None) - The column containing the molecule name information. If supplied, spin_id_col must be None.
• res_name_col (int or None) - The column containing the residue name information. If supplied, spin_id_col must be None.
• res_num_col (int or None) - The column containing the residue number information. If supplied, spin_id_col must be None.
• spin_name_col (int or None) - The column containing the spin name information. If supplied, spin_id_col must be None.
• spin_num_col (int or None) - The column containing the spin number information. If supplied, spin_id_col must be None.
• data_col (int or None) - The column containing the data.
• error_col (int or None) - The column containing the errors.
• sep (str or None) - The column separator which, if None, defaults to whitespace.
• spin_id (None or str) - The spin ID string used to restrict data loading to a subset of all spins.

Returns: str, list of [str, float], or list of [str, float, float]

A list of the spin specific data is yielded. The format is a list consisting of the spin ID string, the data value (if data_col is give), and the error value (if error_col is given). If both data_col and error_col are None, then the spin ID string is simply yielded.

strip(data, comments=True)

Remove all comment and empty lines from the file data structure.

Parameters:

• data (list of lists of str) - The file data to clean up.
• comments (bool) - A flag which if True will cause comments to be deleted.

Returns: list of lists of str

The input data with the empty and comment lines removed.

test_binary(binary)

Function for testing that the binary string corresponds to a valid executable file.

Parameters:

• binary (str) - The name or path of the binary executable file.

write_data(out=None, headings=None, data=None, sep=None)

Write out a table of the data to the given file handle.

Parameters:

• out (file handle) - The file handle to write to.
• headings (list of str or None) - The optional headings to print out.
• data (list of list of str) - The data to print out.
• sep (str or None) - The column separator which, if None, defaults to whitespace.

write_spin_data(file, dir=None, sep=None, spin_ids=None, mol_names=None, res_nums=None, res_names=None, spin_nums=None, spin_names=None, force=False, data=None, data_name=None, error=None, error_name=None, float_format='%20.15g')

Generator function for reading the spin specific data from file.

Description

This function writes a columnar formatted file where each line corresponds to a spin system. Spin identification is either through a spin ID string or through columns containing the molecule name, residue name and number, and/or spin name and number.

Parameters:

• file (str or file object) - The name of the file to write the data to (or alternatively an already opened file object).
• dir (str or None) - The directory to place the file into (defaults to the current directory if None and the file argument is not a file object).
• sep (str or None) - The column separator which, if None, defaults to whitespace.
• spin_ids (None or list of str) - The list of spin ID strings.
• mol_names (None or list of str) - The list of molecule names.
• res_nums (None or list of int) - The list of residue numbers.
• res_names (None or list of str) - The list of residue names.
• spin_nums (None or list of int) - The list of spin numbers.
• spin_names (None or list of str) - The list of spin names.
• force (bool) - A flag which if True will cause an existing file to be overwritten.
• data (list or list of lists) - A list of the data to write out. The first dimension corresponds to the spins. A second dimension can also be given if multiple data sets across multiple columns are desired.
• data_name (str or list of str) - A name corresponding to the data argument. If the data argument is a list of lists, then this must also be a list with the same length as the second dimension of the data arg.
• error (list or list of lists) - A list of the errors to write out. The first dimension corresponds to the spins. A second dimension can also be given if multiple data sets across multiple columns are desired. These will be inter-dispersed between the data columns, if the data is given. If the data arg is not None, then this must have the same dimensions as that object.
• error_name (str or list of str) - A name corresponding to the error argument. If the error argument is a list of lists, then this must also be a list with the same length at the second dimension of the error arg.
• float_format (str) - A float formatting string to use for the data and error whenever a float is found.