Author: tlinnet
Date: Wed Sep 3 22:50:48 2014
New Revision: 25610
URL: http://svn.gna.org/viewcvs/relax?rev=25610&view=rev
Log:
Added function to search a dir for NMRPipe fourier transformed files, call
showApod on them, extract RMSD and write to file.
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=25610&r1=25609&r2=25610&view=diff
==============================================================================
--- trunk/lib/spectrum/nmrpipe.py (original)
+++ trunk/lib/spectrum/nmrpipe.py Wed Sep 3 22:50:48 2014
@@ -25,12 +25,15 @@
# Python module imports.
import re
+from glob import glob
+from os import sep
+from os.path import abspath
from warnings import warn
# relax module imports.
import dep_check
from lib.errors import RelaxError
-from lib.io import file_root, get_file_path, open_write_file, write_data
+from lib.io import file_root, get_file_path, open_write_file, sort_filenames,
write_data
from lib.warnings import RelaxWarning
# Check subprocess is available.
@@ -251,6 +254,7 @@
return rmsd
if not found:
+ print(show_apod_lines)
raise RelaxError("Could not find the line: 'REMARK Automated Noise Std
Dev in Processed Data:', from the output of showApod.")
@@ -304,3 +308,43 @@
# Return path to file.
return wfile_path
+
+def show_apod_rmsd_dir_to_files(file_ext='.ft2', dir=None,
path_to_command='showApod', outdir=None, force=False):
+ """Searches 'dir' for files with extension 'file_ext'. Extract showApod
'Noise Std Dev' from showApod, and write to file with same filename and ending
'.rmsd'.
+
+ @keyword file_ext: The extension for files which is NMRPipe
fourier transformed file.
+ @type file_ext: str
+ @keyword dir: The directory where the files 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 files. 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: list of filepaths
+ """
+
+ # First get correct dir, no matter if dir is specified with or without
system folder separator.
+ dir_files = abspath(dir)
+
+ # Define glop pattern.
+ glob_pat = '*%s' % file_ext
+
+ # Get a list of files which math the file extension.
+ file_list = glob(dir_files + sep + glob_pat)
+
+ # Now sort into Alphanumeric order.
+ file_list_sorted = sort_filenames(filenames=file_list, rev=False)
+
+ # Loop over the files.
+ rmsd_files = []
+ for ft_file in file_list_sorted:
+ # Write rmsd to file, and get file path to file.
+ rmsd_file = show_apod_rmsd_to_file(file_name=ft_file,
path_to_command=path_to_command, outdir=outdir, force=force)
+
+ # Collect file path.
+ rmsd_files.append(rmsd_file)
+
+ return rmsd_files
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