Author: bugman
Date: Fri Aug 16 17:18:21 2013
New Revision: 20600
URL: http://svn.gna.org/viewcvs/relax?rev=20600&view=rev
Log:
Started to shift the spectrum.read_intensities user function backend to use
lib.spectrum.peak_list.
Modified:
branches/peak_intensities/lib/spectrum/peak_list.py
branches/peak_intensities/pipe_control/spectrum.py
Modified: branches/peak_intensities/lib/spectrum/peak_list.py
URL:
http://svn.gna.org/viewcvs/relax/branches/peak_intensities/lib/spectrum/peak_list.py?rev=20600&r1=20599&r2=20600&view=diff
==============================================================================
--- branches/peak_intensities/lib/spectrum/peak_list.py (original)
+++ branches/peak_intensities/lib/spectrum/peak_list.py Fri Aug 16 17:18:21
2013
@@ -142,23 +142,15 @@
return data
-def read(file=None, dir=None, spectrum_id=None, heteronuc=None, proton=None,
int_col=None, int_method=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,
sep=None, spin_id=None, ncproc=None, verbose=True):
+def read_peak_list(file=None, dir=None, int_col=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, sep=None, spin_id=None):
"""Read the peak intensity data.
@keyword file: The name of the file containing the peak
intensities.
@type file: str
@keyword dir: The directory where the file is located.
@type dir: str
- @keyword spectrum_id: The spectrum identification string.
- @type spectrum_id: str or list of str
- @keyword heteronuc: The name of the heteronucleus as specified in
the peak intensity file.
- @type heteronuc: str
- @keyword proton: The name of the proton as specified in the peak
intensity file.
- @type proton: str
- @keyword int_col: The column containing the peak intensity data
(used by the generic intensity file format).
- @type int_col: int
- @keyword int_method: The integration method, one of 'height', 'point
sum' or 'other'.
- @type int_method: str
+ @keyword int_col: The column containing the peak intensity data.
If set to None, no intensity data will be returned.
+ @type int_col: None or int
@keyword spin_id_col: The column containing the spin ID strings (used
by the generic intensity file format). 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 (used by the generic intensity file format). If supplied,
spin_id_col must be None.
@@ -173,28 +165,9 @@
@type spin_num_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 used to restrict data loading
to a subset of all spins. If 'auto' is provided for a NMRPipe seriesTab
formatted file, the ID's are auto generated in form of Z_Ai.
+ @keyword spin_id: The spin ID string used to restrict data loading
to a subset of all spins.
@type spin_id: None or str
- @keyword ncproc: The Bruker ncproc binary intensity scaling
factor.
- @type ncproc: int or None
- @keyword verbose: A flag which if True will cause all relaxation
data loaded to be printed out.
- @type verbose: bool
"""
-
- # Check the file name.
- if file == None:
- raise RelaxError("The file name must be supplied.")
-
- # Test that the intensity measures are identical.
- if hasattr(cdp, 'int_method') and cdp.int_method != int_method:
- raise RelaxError("The '%s' measure of peak intensities does not
match '%s' of the previously loaded spectra." % (int_method, cdp.int_method))
-
- # Check the intensity measure.
- if not int_method in ['height', 'point sum', 'other']:
- raise RelaxError("The intensity measure '%s' is not one of 'height',
'point sum', 'other'." % int_method)
-
- # Set the peak intensity measure.
- cdp.int_method = int_method
# Extract the data from the file.
file_data = extract_data(file, dir, sep=sep)
@@ -207,14 +180,6 @@
# Print out.
print("Generic formatted data file.\n")
- # Checks.
- if isinstance(spectrum_id, list) and not isinstance(int_col, list):
- raise RelaxError("If a list of spectrum IDs is supplied, the
intensity column argument must also be a list of equal length.")
- if not isinstance(spectrum_id, list) and isinstance(int_col, list):
- raise RelaxError("If a list of intensity columns is supplied,
the spectrum ID argument must also be a list of equal length.")
- if isinstance(spectrum_id, list) and len(spectrum_id) !=
len(int_col):
- raise RelaxError("The spectrum ID list %s has a different number
of elements to the intensity column list %s." % (spectrum_id, int_col))
-
# Extract the data.
intensity_data = intensity_generic(file_data=file_data,
spin_id_col=spin_id_col, 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, data_col=int_col, sep=sep, spin_id=spin_id)
@@ -226,21 +191,13 @@
# Extract the data.
intensity_data = nmrview.read_list_intensity(file_data=file_data)
- # Convert the residue number to a spin ID.
- for i in range(len(intensity_data)):
- # Generate the spin_id.
- spin_id = generate_spin_id_unique(res_num=intensity_data[i][2],
spin_name=intensity_data[i][1])
-
- # Replace the data.
- intensity_data[i][2] = spin_id
-
# NMRPipe SeriesTab.
elif format == 'seriestab':
# Print out.
print("NMRPipe SeriesTab formatted data file.\n")
# Extract the data.
- intensity_data =
nmrpipe.read_list_intensity_seriestab(file_data=file_data, int_col=int_col)
+ intensity_data =
nmrpipe.read_list_intensity_seriestab(file_data=file_data, int_col=int_col,
int_col_labels=int_col_labels)
# Extract the expected number of spectrum ID's.
nr_int_col = len(intensity_data[0][3])
@@ -251,14 +208,6 @@
for i in range(nr_int_col):
spectrum_id.append('Z_A%s'%i)
- # Convert the residue number to a spin ID.
- for i in range(len(intensity_data)):
- # Generate the spin_id.
- spin_id = generate_spin_id_unique(res_num=intensity_data[i][2],
spin_name=intensity_data[i][1])
-
- # Replace the data.
- intensity_data[i][2] = spin_id
-
# Sparky.
elif format == 'sparky':
# Print out.
@@ -267,109 +216,13 @@
# Extract the data.
intensity_data = sparky.read_list_intensity(file_data=file_data,
int_col=int_col)
- # Convert the residue number to a spin ID.
- for i in range(len(intensity_data)):
- # Generate the spin_id.
- spin_id = generate_spin_id_unique(res_num=intensity_data[i][2],
spin_name=intensity_data[i][1])
-
- # Replace the data.
- intensity_data[i][2] = spin_id
-
# XEasy.
elif format == 'xeasy':
# Print out.
print("XEasy formatted data file.\n")
# Extract the data.
- intensity_data = xeasy.read_list_intensity(file_data=file_data,
proton=proton, heteronuc=heteronuc, int_col=int_col)
-
- # Convert the residue number to a spin ID.
- for i in range(len(intensity_data)):
- # Generate the spin_id.
- spin_id = generate_spin_id_unique(res_num=intensity_data[i][2],
spin_name=intensity_data[i][1])
-
- # Replace the data.
- intensity_data[i][2] = spin_id
-
- # Loop over the peak intensity data.
- data = []
- data_flag = False
-
- for i in range(len(intensity_data)):
- # Extract the data.
- H_name, X_name, spin_id, intensity, line = intensity_data[i]
-
- # Convert the intensity data and spectrum IDs to lists if needed.
- if not isinstance(intensity, list):
- intensity = [intensity]
- if not isinstance(spectrum_id, list):
- spectrum_id = [spectrum_id]
-
- # Checks for matching length of spectrum IDs and intensities columns.
- if len(spectrum_id) != len(intensity):
- raise RelaxError("The spectrum ID list %s has a different number
of elements to the intensity column list %s." % (spectrum_id, nr_int_col))
-
- # Loop over the data.
- for i in range(len(intensity)):
- # Sanity check.
- if intensity[i] == 0.0:
- warn(RelaxWarning("A peak intensity of zero has been
encountered for the spin '%s' - this could be fatal later on." % spin_id))
-
- # Skip data.
- if (X_name and X_name != heteronuc) or (H_name and H_name !=
proton):
- warn(RelaxWarning("Proton and heteronucleus names do not
match, skipping the data %s." % line))
- continue
-
- # Get the spin container.
- spin = return_spin(spin_id)
- if not spin:
- warn(RelaxNoSpinWarning(spin_id))
- continue
-
- # Skip deselected spins.
- if not spin.select:
- continue
-
- # Initialise.
- if not hasattr(spin, 'intensities'):
- spin.intensities = {}
-
- # Intensity scaling.
- if ncproc != None:
- intensity[i] = intensity[i] / float(2**ncproc)
-
- # Add the data.
- spin.intensities[spectrum_id[i]] = intensity[i]
-
- # Switch the flag.
- data_flag = True
-
- # Append the data for printing out.
- data.append([spin_id, repr(intensity[i])])
-
- # Add the spectrum id (and ncproc) to the relax data store.
- spectrum_ids = spectrum_id
- if isinstance(spectrum_id, str):
- spectrum_ids = [spectrum_id]
- if not hasattr(cdp, 'spectrum_ids'):
- cdp.spectrum_ids = []
- if ncproc != None:
- cdp.ncproc = {}
- for i in range(len(spectrum_ids)):
- if not spectrum_ids[i] in cdp.spectrum_ids:
- cdp.spectrum_ids.append(spectrum_ids[i])
- if ncproc != None:
- cdp.ncproc[spectrum_ids[i]] = ncproc
-
- # No data.
- if not data_flag:
- # Delete all the data.
- delete(spectrum_id)
-
- # Raise the error.
- raise RelaxError("No data could be loaded from the peak list")
-
- # Print out.
- if verbose:
- print("\nThe following intensities have been loaded into the relax
data store:\n")
- write_data(out=sys.stdout, headings=["Spin_ID", "Intensity"],
data=data)
+ intensity_data = xeasy.read_list_intensity(file_data=file_data,
int_col=int_col)
+
+ # Return the data.
+ return mol_names, res_names, res_nums, spin_names, spin_nums,
Modified: branches/peak_intensities/pipe_control/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/peak_intensities/pipe_control/spectrum.py?rev=20600&r1=20599&r2=20600&view=diff
==============================================================================
--- branches/peak_intensities/pipe_control/spectrum.py (original)
+++ branches/peak_intensities/pipe_control/spectrum.py Fri Aug 16 17:18:21
2013
@@ -32,9 +32,9 @@
# relax module imports.
from lib.errors import RelaxError, RelaxImplementError,
RelaxNoSequenceError, RelaxNoSpectraError
-from lib.io import extract_data, write_data
+from lib.io import write_data
from lib.software import nmrpipe, nmrview, sparky, xeasy
-from lib.spectrum.peak_list import autodetect_format, intensity_generic
+from lib.spectrum.peak_list import read_peak_list
from lib.warnings import RelaxWarning, RelaxNoSpinWarning
from pipe_control import pipes
from pipe_control.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_unique, return_spin, spin_loop
@@ -504,6 +504,14 @@
if hasattr(cdp, 'int_method') and cdp.int_method != int_method:
raise RelaxError("The '%s' measure of peak intensities does not
match '%s' of the previously loaded spectra." % (int_method, cdp.int_method))
+ # Intensity column checks.
+ if isinstance(spectrum_id, list) and not isinstance(int_col, list):
+ raise RelaxError("If a list of spectrum IDs is supplied, the
intensity column argument must also be a list of equal length.")
+ if not isinstance(spectrum_id, list) and isinstance(int_col, list):
+ raise RelaxError("If a list of intensity columns is supplied, the
spectrum ID argument must also be a list of equal length.")
+ if isinstance(spectrum_id, list) and len(spectrum_id) != len(int_col):
+ raise RelaxError("The spectrum ID list %s has a different number of
elements to the intensity column list %s." % (spectrum_id, int_col))
+
# Check the intensity measure.
if not int_method in ['height', 'point sum', 'other']:
raise RelaxError("The intensity measure '%s' is not one of 'height',
'point sum', 'other'." % int_method)
@@ -511,100 +519,17 @@
# Set the peak intensity measure.
cdp.int_method = int_method
- # Extract the data from the file.
- file_data = extract_data(file, dir, sep=sep)
-
- # Automatic format detection.
- format = autodetect_format(file_data)
-
- # Generic.
- if format == 'generic':
- # Print out.
- print("Generic formatted data file.\n")
-
- # Checks.
- if isinstance(spectrum_id, list) and not isinstance(int_col, list):
- raise RelaxError("If a list of spectrum IDs is supplied, the
intensity column argument must also be a list of equal length.")
- if not isinstance(spectrum_id, list) and isinstance(int_col, list):
- raise RelaxError("If a list of intensity columns is supplied,
the spectrum ID argument must also be a list of equal length.")
- if isinstance(spectrum_id, list) and len(spectrum_id) !=
len(int_col):
- raise RelaxError("The spectrum ID list %s has a different number
of elements to the intensity column list %s." % (spectrum_id, int_col))
-
- # Extract the data.
- intensity_data = intensity_generic(file_data=file_data,
spin_id_col=spin_id_col, 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, data_col=int_col, sep=sep, spin_id=spin_id)
-
- # NMRView.
- elif format == 'nmrview':
- # Print out.
- print("NMRView formatted data file.\n")
-
- # Extract the data.
- intensity_data = nmrview.read_list_intensity(file_data=file_data)
-
- # Convert the residue number to a spin ID.
- for i in range(len(intensity_data)):
- # Generate the spin_id.
- spin_id = generate_spin_id_unique(res_num=intensity_data[i][2],
spin_name=intensity_data[i][1])
-
- # Replace the data.
- intensity_data[i][2] = spin_id
-
- # NMRPipe SeriesTab.
- elif format == 'seriestab':
- # Print out.
- print("NMRPipe SeriesTab formatted data file.\n")
-
- # Extract the data.
- intensity_data =
nmrpipe.read_list_intensity_seriestab(file_data=file_data, int_col=int_col)
-
- # Extract the expected number of spectrum ID's.
- nr_int_col = len(intensity_data[0][3])
-
- # Make it possible to autogenerate spectrum ID's, if
spectrum_id='auto'.
- if not isinstance(spectrum_id, list) and spectrum_id.lower() ==
'auto':
- spectrum_id = []
- for i in range(nr_int_col):
- spectrum_id.append('Z_A%s'%i)
-
- # Convert the residue number to a spin ID.
- for i in range(len(intensity_data)):
- # Generate the spin_id.
- spin_id = generate_spin_id_unique(res_num=intensity_data[i][2],
spin_name=intensity_data[i][1])
-
- # Replace the data.
- intensity_data[i][2] = spin_id
-
- # Sparky.
- elif format == 'sparky':
- # Print out.
- print("Sparky formatted data file.\n")
-
- # Extract the data.
- intensity_data = sparky.read_list_intensity(file_data=file_data,
int_col=int_col)
-
- # Convert the residue number to a spin ID.
- for i in range(len(intensity_data)):
- # Generate the spin_id.
- spin_id = generate_spin_id_unique(res_num=intensity_data[i][2],
spin_name=intensity_data[i][1])
-
- # Replace the data.
- intensity_data[i][2] = spin_id
-
- # XEasy.
- elif format == 'xeasy':
- # Print out.
- print("XEasy formatted data file.\n")
-
- # Extract the data.
- intensity_data = xeasy.read_list_intensity(file_data=file_data,
proton=proton, heteronuc=heteronuc, int_col=int_col)
-
- # Convert the residue number to a spin ID.
- for i in range(len(intensity_data)):
- # Generate the spin_id.
- spin_id = generate_spin_id_unique(res_num=intensity_data[i][2],
spin_name=intensity_data[i][1])
-
- # Replace the data.
- intensity_data[i][2] = spin_id
+ # Read the peak list data.
+ x = read_peak_list(file=file, dir=dir, int_col=int_col,
spin_id_col=spin_id_col, 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, sep=sep, spin_id=spin_id)
+ print x
+
+ # Convert the residue number to a spin ID.
+ for i in range(len(intensity_data)):
+ # Generate the spin_id.
+ spin_id = generate_spin_id_unique(res_num=intensity_data[i][2],
spin_name=intensity_data[i][1])
+
+ # Replace the data.
+ intensity_data[i][2] = spin_id
# Loop over the peak intensity data.
data = []
r20600 - in /branches/peak_intensities: lib/spectrum/peak_list.py pipe_control/spectrum.py