Author: bugman
Date: Fri Aug 16 19:42:56 2013
New Revision: 20616
URL: http://svn.gna.org/viewcvs/relax?rev=20616&view=rev
Log:
The NMRPipe seriesTab peak lists are now supported through the Peak_list
object.
Modified:
branches/peak_intensities/lib/software/nmrpipe.py
branches/peak_intensities/lib/spectrum/peak_list.py
branches/peak_intensities/pipe_control/spectrum.py
Modified: branches/peak_intensities/lib/software/nmrpipe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/peak_intensities/lib/software/nmrpipe.py?rev=20616&r1=20615&r2=20616&view=diff
==============================================================================
--- branches/peak_intensities/lib/software/nmrpipe.py (original)
+++ branches/peak_intensities/lib/software/nmrpipe.py Fri Aug 16 19:42:56 2013
@@ -31,19 +31,16 @@
from lib.io import open_write_file, strip
-def read_list_intensity_seriestab(file_data=None, int_col=None):
- """Return the peak intensity information from the NMRPipe SeriesTab peak
intensity file.
+def read_list_intensity_seriestab(peak_list=None, file_data=None,
int_col=None):
+ """Extract the intensity information from the NMRPipe SeriesTab peak
intensity file.
- The residue number, heteronucleus and proton names, and peak intensity
will be returned.
-
-
+ @keyword peak_list: The peak list object to place all data into.
+ @type peak_list: lib.spectrum.objects.Peak_list instance
@keyword file_data: The data extracted from the file converted into a
list of lists.
@type file_data: list of lists of str
@keyword int_col: The column which to multiply the peak intensity data
(used by the SeriesTab intensity file format).
@type int_col: int
@raises RelaxError: When the expected peak intensity is not a float.
- @return: The extracted data as a list of lists. The first
dimension corresponds to the spin. The second dimension consists of the
proton name, heteronucleus name, residue number, the intensity value, and the
original line of text.
- @rtype: list of lists of str, str, int, float, str
"""
# Set start variables.
@@ -93,78 +90,40 @@
# Remove the header.
file_data = file_data[header:]
- # Create an empty intensity list.
- intensity_list = [None]*len(spectra)
+ # Loop over the file data.
+ for line in file_data:
+ # Skip non-assigned peaks.
+ if line[ass_i] == '?-?':
+ continue
- # Create the whole empty data_all list, where entries will be replaced
later.
- # Format: H_name, X_name, spin_id, intensity, line.
- data_all = [[None, None, None, intensity_list, None]]*len(file_data)
+ # First split by the 2D separator.
+ assign2, assign1 = re.split('-', line[ass_i])
- # Define a current spectrum counter.
- i = 0
+ # The assignment of the first dimension.
+ row1 = re.split('([A-Z]+)', assign1)
+ name1 = row1[-2] + row1[-1]
- # Loop over the spectra.
- for spectrum in spectra:
- # Current intensity index.
- int_i = spectra_i[i]
+ # The assignment of the second dimension.
+ row2 = re.split('([A-Z]+)', assign2)
+ name2 = row2[-2] + row2[-1]
- # Define a current line counter.
- j = 0
+ # Get the residue number.
+ try:
+ res_num = int(row2[-3])
+ except:
+ raise RelaxError("Improperly formatted NMRPipe SeriesTab file.,
cannot process the assignment '%s'." % line[0])
- for line in file_data:
- # Skip non-assigned peaks.
- if line[ass_i] == '?-?':
- continue
+ # Get the intensities.
+ try:
+ # Loop over the spectra.
+ intensities = []
+ for i in range(len(spectra)):
+ # The intensity is given by column multiplication.
+ intensities.append(float(line[spectra_i[i]])*float(line[5]))
- # First split by the 2D separator.
- x_assign, h_assign = re.split('-', line[ass_i])
+ # Bad data.
+ except ValueError:
+ raise RelaxError("The peak intensity value %s from the line %s
is invalid." % (intensity, line))
- # The proton info.
- h_row = re.split('([A-Z]+)', h_assign)
- h_name = h_row[-2] + h_row[-1]
-
- # The heteronucleus info.
- x_row = re.split('([A-Z]+)', x_assign)
- x_name = x_row[-2] + x_row[-1]
-
- # Get the residue number.
- try:
- res_num = int(x_row[-3])
- except:
- raise RelaxError("Improperly formatted NMRPipe SeriesTab
file.")
-
- # Get the intensity.
- try:
- # The intensity is given by column multiplication.
- intensity = float(line[int_i])*float(line[5])
-
- # Extract the intensity_list
- intensity_list = data_all[j][3]
-
- # Replace the intensity.
- intensity_list[i] = intensity
-
- except ValueError:
- raise RelaxError("The peak intensity value %s from the line
%s is invalid."%(intensity,line))
-
- # Replace the data.
- # Format: H_name, X_name, spin_id, intensity, line.
- data_all[j] = [h_name, x_name, res_num, list(intensity_list),
line]
-
- # Add 1 to current line counter.
- j += 1
-
- # Add 1 to current spectrum counter.
- i += 1
-
- # Remove from data_all where empty list starts. They are created where
spins are
- # skipped for ID = '?-?'.
- for i in range(len(data_all)):
- spin = data_all[i]
- if spin[0] == None and spin[1] == None and spin[2] == None:
- # Replace the data
- data_all = data_all[:i]
- break
-
- # Return the data.
- return data_all
+ # Add the assignment to the peak list object.
+ peak_list.add(res_nums=[res_num, res_num], spin_names=[name1,
name2], intensity=intensities, intensity_name=spectra)
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=20616&r1=20615&r2=20616&view=diff
==============================================================================
--- branches/peak_intensities/lib/spectrum/peak_list.py (original)
+++ branches/peak_intensities/lib/spectrum/peak_list.py Fri Aug 16 19:42:56
2013
@@ -188,16 +188,7 @@
print("NMRPipe SeriesTab formatted data file.\n")
# Extract the data.
- nmrpipe.read_list_intensity_seriestab(peak_list=peak_list,
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(peak_list[0].intensity)
-
- # 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)
+ nmrpipe.read_list_intensity_seriestab(peak_list=peak_list,
file_data=file_data, int_col=int_col)
# Sparky.
elif format == 'sparky':
Modified: branches/peak_intensities/pipe_control/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/peak_intensities/pipe_control/spectrum.py?rev=20616&r1=20615&r2=20616&view=diff
==============================================================================
--- branches/peak_intensities/pipe_control/spectrum.py (original)
+++ branches/peak_intensities/pipe_control/spectrum.py Fri Aug 16 19:42:56
2013
@@ -507,7 +507,7 @@
# 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):
+ if spectrum_id != 'auto' and 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))
@@ -521,6 +521,10 @@
# Read the peak list data.
peak_list = 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)
+
+ # Automatic spectrum IDs.
+ if spectrum_id == 'auto':
+ spectrum_id = peak_list[0].intensity_name
# Loop over the assignments.
data = []
r20616 - in /branches/peak_intensities: lib/software/nmrpipe.py lib/spectrum/peak_list.py pipe_control/spectrum.py