Hi Troels,
This also looks good, but needs a whitespace fix for the '=' sign.
For the RelaxError, I would also capitalise the P in Python, as Python
is always with a capitial P and this is the start of a sentence. It
is also better to use a single sentence for the RelaxError when
possible:
RelaxError: Python module 'subprocess' not found, cannot call showApod.
I would suggest also changing the logic at the start to be:
"""
if not dep_check.subprocess_module:
raise RelaxError("Python...
"""
Then you don't need to indent the rest and the code is hence simpler.
You could also add a check of 'if not dep_check.showApod:" to give a
RelaxError when showApod is not available.
Cheers,
Edward
On 3 September 2014 22:50, <[email protected]> wrote:
> 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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