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
+
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