r25607 - /trunk/lib/spectrum/nmrpipe.py -- September 03, 2014 - 22:50

Author: tlinnet
Date: Wed Sep  3 22:50:41 2014
New Revision: 25607

URL: http://svn.gna.org/viewcvs/relax?rev=25607&view=rev
Log:
Added function to write 'Noise Std Dev' from showApod to file, and fix 
documentation.

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=25607&r1=25606&r2=25607&view=diff
==============================================================================
--- trunk/lib/spectrum/nmrpipe.py       (original)
+++ trunk/lib/spectrum/nmrpipe.py       Wed Sep  3 22:50:41 2014
@@ -30,7 +30,7 @@
 # relax module imports.
 import dep_check
 from lib.errors import RelaxError
-from lib.io import get_file_path
+from lib.io import file_root, get_file_path, open_write_file, write_data
 from lib.warnings import RelaxWarning
 
 # Check subprocess is available.
@@ -201,7 +201,7 @@
     @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
+    @type path_to_command:      str
     @return:                    The output from showApod as list of lines.
     @rtype:                     list of lines
     """
@@ -233,7 +233,7 @@
     @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
+    @type path_to_command:      str
     @return:                    The Noise Std Dev from line: 'REMARK 
Automated Noise Std Dev in Processed Data'
     @rtype:                     float
     """
@@ -253,3 +253,54 @@
     if not found:
         raise RelaxError("Could not find the line: 'REMARK Automated Noise 
Std Dev in Processed Data:', from the output of showApod.")
 
+
+def show_apod_rmsd_to_file(file_name=None, dir=None, 
path_to_command='showApod', outdir=None, force=False):
+    """Extract showApod 'Noise Std Dev' from showApod, and write to file 
with same filename and ending '.rmsd'
+
+    @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
+    @keyword outdir:            The directory where to write the file.  If 
'None', then write in same directory.
+    @type outdir:               str
+    @param force:               Boolean argument which if True causes the 
file to be overwritten if it already exists.
+    @type force:                bool
+    @return:                    Write the 'Noise Std Dev' from showApod to a 
file with same file filename, with ending '.rmsd'.
+    @rtype:                     filepath
+    """
+
+    # Call extract function.
+    apod_rmsd = show_apod_rmsd(file_name=file_name, dir=dir, 
path_to_command=path_to_command)
+
+    # Get the filename striped of extension details.
+    file_name_root = file_root(file_name)
+
+    # Define extension.
+    extension = ".rmsd"
+
+    # Define file name for writing.
+    file_name_out = file_name_root + extension
+
+    # Define folder to write to.
+    if outdir == None:
+        write_outdir = dir
+    else:
+        write_outdir = outdir
+
+    # Open file for writing,
+    wfile, wfile_path = open_write_file(file_name=file_name_out, 
dir=write_outdir, force=force, verbosity=1, return_path=True)
+
+    # Write to file.
+    out_write_data = [['%s'%apod_rmsd]]
+
+    # Write data
+    write_data(out=wfile, headings=None, data=out_write_data, sep=None)
+
+    # Close file.
+    wfile.close()
+
+    # Return path to file.
+    return wfile_path
+