Author: bugman
Date: Tue Oct 6 12:18:35 2009
New Revision: 9572
URL: http://svn.gna.org/viewcvs/relax?rev=9572&view=rev
Log:
Created the read_spin_data_file() generator function.
This is designed to replace quite a few inconsistent functions throughout the
generic function code
base. It reads a columnar formatted file with a spin per line.
Modified:
1.3/relax_io.py
Modified: 1.3/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/relax_io.py?rev=9572&r1=9571&r2=9572&view=diff
==============================================================================
--- 1.3/relax_io.py (original)
+++ 1.3/relax_io.py Tue Oct 6 12:18:35 2009
@@ -45,6 +45,7 @@
from sys import stdin, stdout, stderr
# relax module imports.
+from generic_fns.mol_res_spin import generate_spin_id_data_array
from relax_errors import RelaxError, RelaxFileError,
RelaxFileOverwriteError, RelaxMissingBinaryError, RelaxNoInPathError,
RelaxNonExecError
from relax_warnings import RelaxWarning
@@ -52,7 +53,7 @@
def delete(file_name, dir=None, fail=True):
"""Deleting the given file, taking into account missing compression
extensions.
-
+
@param file_name: The name of the file to delete.
@type file_name: str
@keyword dir: The directory containing the file.
@@ -460,6 +461,149 @@
return file_obj
+def read_spin_data_file(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.
+
+
+ @keyword id: The alignment tensor ID string.
+ @type id: str
+ @keyword file: The name of the file to open.
+ @type file: str
+ @keyword dir: The directory containing the file (defaults to
the current directory
+ if None).
+ @type dir: str or None
+ @keyword file_data: 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.
+ @type file_data: list of lists
+ @keyword spin_id_col: 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.
+ @type spin_id_col: int or None
+ @keyword mol_name_col: The column containing the molecule name
information. If supplied,
+ spin_id_col must be None.
+ @type mol_name_col: int or None
+ @keyword res_name_col: The column containing the residue name
information. If supplied,
+ spin_id_col must be None.
+ @type res_name_col: int or None
+ @keyword res_num_col: The column containing the residue number
information. If supplied,
+ spin_id_col must be None.
+ @type res_num_col: int or None
+ @keyword spin_name_col: The column containing the spin name information.
If supplied,
+ spin_id_col must be None.
+ @type spin_name_col: int or None
+ @keyword spin_num_col: The column containing the spin number
information. If supplied,
+ spin_id_col must be None.
+ @type spin_num_col: int or None
+ @keyword data_col: The column containing the data.
+ @type data_col: int or None
+ @keyword error_col: The column containing the errors.
+ @type error_col: int or None
+ @keyword sep: The column separator which, if None, defaults to
whitespace.
+ @type sep: str or None
+ @keyword spin_id: The spin ID string.
+ @type spin_id: None or str
+ @return: 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.
+ @rtype: str, list of [str, float], or list of [str,
float, float]
+ """
+
+ # Argument tests.
+ col_args = [spin_id_col, mol_name_col, res_name_col, res_num_col,
spin_name_col, spin_num_col, data_col, error_col]
+ col_arg_names = ['spin_id_col', 'mol_name_col', 'res_name_col',
'res_num_col', 'spin_name_col', 'spin_num_col', 'data_col', 'error_col']
+ for i in range(len(col_args)):
+ if col_args[i] == 0:
+ raise RelaxError, "The '%s' argument cannot be zero, column
numbering starts at one." % col_arg_names[i]
+ if spin_id_col and (mol_name_col or res_name_col or res_num_col or
spin_name_col or spin_num_col):
+ raise RelaxError, "If the 'spin_id_col' argument has been supplied,
then the mol_name_col, res_name_col, res_num_col, spin_name_col, and
spin_num_col must all be set to None."
+
+ # Minimum number of columns.
+ min_col_num = max(spin_id_col, mol_name_col, res_num_col, res_name_col,
spin_num_col, spin_name_col, data_col, error_col)
+
+ # Extract the data from the file.
+ if not file_data:
+ # Extract.
+ file_data = extract_data(file, dir)
+
+ # Strip the data of all comments and empty lines.
+ file_data = strip(file_data)
+
+ # Test the validity of the data.
+ if data_col or error_col:
+ missing = True
+ for i in xrange(len(file_data)):
+ # Skip missing data.
+ if len(file_data[i]) <= min_col_num:
+ continue
+ elif data_col and file_data[i][data_col-1] == 'None':
+ continue
+ elif error_col and file_data[i][error_col-1] == 'None':
+ continue
+
+ # Test that the data are numbers.
+ try:
+ if res_num_col:
+ int(file_data[i][res_num_col-1])
+ if spin_num_col:
+ int(file_data[i][spin_num_col-1])
+ if data_col:
+ float(file_data[i][data_col-1])
+ if error_col:
+ float(file_data[i][error_col-1])
+ except ValueError:
+ raise RelaxError("The data in the line " +
repr(file_data[i]) + " is invalid.")
+
+ # Right, data is OK and exists.
+ missing = False
+
+ # Hmmm, no data!
+ if missing:
+ raise RelaxError("No corresponding data could be found within
the file.")
+
+ # Yield the data, spin by spin.
+ for line in file_data:
+ # Skip missing data.
+ if len(line) <= min_col_num:
+ continue
+
+ # Generate the spin ID string.
+ if spin_id_col:
+ id = line[spin_id_col-1]
+ else:
+ id = generate_spin_id_data_array(data=line,
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col)
+
+ # Convert the data.
+ value = None
+ if data_col != None:
+ value = eval(line[data_col-1])
+ error = None
+ if error_col != None:
+ error = eval(line[error_col-1])
+
+ # Test the error value (cannot be 0.0).
+ if error == 0.0:
+ raise RelaxError("An invalid error value of zero has been
encountered.")
+
+ # Yield the data.
+ if data_col and error_col:
+ yield [id, value, error]
+ elif data_col:
+ yield [id, value]
+ elif error_col:
+ yield [id, error]
+ else:
+ yield id
+
+
def strip(data):
"""Function to remove all comment and empty lines from the file data
structure.
r9572 - /1.3/relax_io.py