Author: tlinnet
Date: Wed Sep 3 22:50:33 2014
New Revision: 25603
URL: http://svn.gna.org/viewcvs/relax?rev=25603&view=rev
Log:
To the lib function of spectrum.nmrpipe, added function to call the
NMRPipe program showApod, to get the output from the program.
Modified:
trunk/lib/spectrum/nmrpipe.py
Modified: trunk/lib/spectrum/nmrpipe.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/nmrpipe.py?rev=25603&r1=25602&r2=25603&view=diff
==============================================================================
--- trunk/lib/spectrum/nmrpipe.py (original)
+++ trunk/lib/spectrum/nmrpipe.py Wed Sep 3 22:50:33 2014
@@ -28,8 +28,14 @@
from warnings import warn
# relax module imports.
+import dep_check
from lib.errors import RelaxError
+from lib.io import get_file_path
from lib.warnings import RelaxWarning
+
+# Check subprocess is available.
+if dep_check.subprocess_module:
+ import subprocess
def read_seriestab(peak_list=None, file_data=None, int_col=None):
@@ -185,3 +191,35 @@
# Add the assignment to the peak list object.
peak_list.add(res_nums=[res_num1, res_num2],
res_names=[res_name1, res_name2], spin_names=[name1, name2], shifts=[w1,
w2], intensity=intensities, intensity_name=spectra)
+
+
+def show_apod_extract(file_name=None, dir=None,
path_to_command='showApod'):
+ """Extract showApod information for spectrum fourier transformed
with NMRPipe.
+
+ @keyword file: The filename of the NMRPipe fourier
transformed file.
+ @type file: str
+ @keyword dir: The directory where the file is located.
+ @type dir: str
+ @keyword path_to_command: If showApod not in PATH, then specify
absolute path as: /path/to/showApod
+ @type dir: str
+ @return: The output from showApod as list of
lines.
+ @rtype: list of lines
+ """
+
+ # Get the file path.
+ file_path = get_file_path(file_name=file_name, dir=dir)
+
+ if dep_check.subprocess_module:
+ # Call function.
+ Temp=subprocess.Popen([path_to_command, file_path],
stdout=subprocess.PIPE)
+
+ # Communicate with program, and get outout and exitcode.
+ (output, errput) = Temp.communicate()
+
+ # Wait for finish and get return code.
+ return_value = Temp.wait()
+
+ return output.splitlines()
+
+ else:
+ raise RelaxError("python module 'subprocess' not found. Cannot
call showApod.")
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