Author: bugman
Date: Thu Nov 22 12:36:59 2007
New Revision: 3818
URL: http://svn.gna.org/viewcvs/relax?rev=3818&view=rev
Log:
Started to implement the read, sequence_exists, and valid_sequence functions.
Modified:
1.3/generic_fns/sequence.py
Modified: 1.3/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/sequence.py?rev=3818&r1=3817&r2=3818&view=diff
==============================================================================
--- 1.3/generic_fns/sequence.py (original)
+++ 1.3/generic_fns/sequence.py Thu Nov 22 12:36:59 2007
@@ -23,9 +23,130 @@
# relax module imports.
from data import Data as relax_data_store
from relax_errors import RelaxError, RelaxFileEmptyError,
RelaxNoPdbChainError, RelaxNoPipeError, RelaxNoSequenceError,
RelaxSequenceError
-
-
-# The relax data storage object.
+from relax_io import extract_data
+
+
+
+def read(file=None, dir=None, mol_name_col=None, res_num_col=0,
res_name_col=1, spin_num_col=None, spin_name_col=None, sep=None):
+ """Function for reading sequence data."""
+
+ # Test if sequence data already exists.
+ if sequence_exists():
+ raise RelaxSequenceError
+
+ # Extract the data from the file.
+ file_data = extract_data(file, dir)
+
+ # Count the number of header lines.
+ header_lines = 0
+ for i in xrange(len(file_data)):
+ try:
+ int(file_data[i][num_col])
+ except:
+ header_lines = header_lines + 1
+ else:
+ break
+
+ # Remove the header.
+ file_data = file_data[header_lines:]
+
+ # Strip data.
+ file_data = strip(file_data)
+
+ # Do nothing if the file does not exist.
+ if not file_data:
+ raise RelaxFileEmptyError
+
+ # Alias the current data pipe.
+ cdp = relax_data_store[relax_data_store.current_pipe]
+
+ # Test if the sequence data is valid.
+ # Add the run to 'relax_data_store.res'.
+ relax_data_store.res.add_list(run)
+
+ # Fill the array 'relax_data_store.res[run]' with data containers and
place sequence data into the array.
+ for i in xrange(len(file_data)):
+ # Append a data container.
+ relax_data_store.res[run].add_item()
+
+ # Insert the data.
+ relax_data_store.res[run][i].num = int(file_data[i][num_col])
+ relax_data_store.res[run][i].name = file_data[i][name_col]
+ relax_data_store.res[run][i].select = 1
+
+
+def sequence_exists():
+ """Function for determining if sequence data already exists in the
current data pipe.
+
+ @return: The answer to the question.
+ @rtype: Boolean
+ """
+
+ # Dummy return
+ return False
+
+
+def valid_sequence(data):
+ """Function for testing if the sequence data is valid.
+
+ The only function this performs is to raise a RelaxError if the data is
invalid.
+
+
+ @param data: The sequence data.
+ @type data: list of lists.
+ """
+
+ # Loop over the data.
+ for i in xrange(len(file_data)):
+ # Molecule name data.
+ if mol_name_col != None:
+ try:
+ file_data[i][mol_name_col]
+ except IndexError:
+ raise RelaxInvalidSeqError, file_data[i]
+
+ # Residue number data.
+ if res_num_col != None:
+ # No data in column.
+ try:
+ file_data[i][res_num_col]
+ except IndexError:
+ raise RelaxInvalidSeqError, file_data[i]
+
+ # Bad data in column.
+ try:
+ int(file_data[i][res_num_col])
+ except ValueError:
+ raise RelaxInvalidSeqError, file_data[i]
+
+ # Residue name data.
+ if res_name_col != None:
+ try:
+ file_data[i][res_name_col]
+ except IndexError:
+ raise RelaxInvalidSeqError, file_data[i]
+
+ # Spin number data.
+ if spin_num_col != None:
+ # No data in column.
+ try:
+ file_data[i][spin_num_col]
+ except IndexError:
+ raise RelaxInvalidSeqError, file_data[i]
+
+ # Bad data in column.
+ try:
+ int(file_data[i][spin_num_col])
+ except ValueError:
+ raise RelaxInvalidSeqError, file_data[i]
+
+ # Spin name data.
+ if spin_name_col != None:
+ try:
+ file_data[i][spin_name_col]
+ except IndexError:
+ raise RelaxInvalidSeqError, file_data[i]
+
@@ -181,61 +302,6 @@
relax_data_store.res[run][i].select = 1
- def read(self, run=None, file=None, dir=None, num_col=0, name_col=1,
sep=None):
- """Function for reading sequence data."""
-
- # Test if the run exists.
- if not run in relax_data_store.run_names:
- raise RelaxNoPipeError, run
-
- # Test if the sequence data has already been read.
- if relax_data_store.res.has_key(run):
- raise RelaxSequenceError, run
-
- # Extract the data from the file.
- file_data = self.relax.IO.extract_data(file, dir)
-
- # Count the number of header lines.
- header_lines = 0
- for i in xrange(len(file_data)):
- try:
- int(file_data[i][num_col])
- except:
- header_lines = header_lines + 1
- else:
- break
-
- # Remove the header.
- file_data = file_data[header_lines:]
-
- # Strip data.
- file_data = self.relax.IO.strip(file_data)
-
- # Do nothing if the file does not exist.
- if not file_data:
- raise RelaxFileEmptyError
-
- # Test if the sequence data is valid.
- for i in xrange(len(file_data)):
- try:
- int(file_data[i][num_col])
- except ValueError:
- raise RelaxError, "Sequence data is invalid."
-
- # Add the run to 'relax_data_store.res'.
- relax_data_store.res.add_list(run)
-
- # Fill the array 'relax_data_store.res[run]' with data containers
and place sequence data into the array.
- for i in xrange(len(file_data)):
- # Append a data container.
- relax_data_store.res[run].add_item()
-
- # Insert the data.
- relax_data_store.res[run][i].num = int(file_data[i][num_col])
- relax_data_store.res[run][i].name = file_data[i][name_col]
- relax_data_store.res[run][i].select = 1
-
-
def sort(self, run=None):
"""Function for sorting the sequence by residue number."""
r3818 - /1.3/generic_fns/sequence.py