PATH issuse with pyprophet

[sjr24]

Greetings,

cmd prompt was set to directory with .osw files. The following command was run

C:\Users\Shawn\Desktop\DIA2018\Tutorial4_OpenSWATH>pyprophet merge --out=training.osw --subsample_ratio=0.33 *.osw

The error listed below was produced by the above command.

Usage: pyprophet merge [OPTIONS] [INFILES]...

Error: Invalid value for "infiles": Path "*.osw" does not exist.

Adding the path the command "C:\Users\Shawn\Desktop\DIA2018\Tutorial4_OpenSWATH*.osw" did not work either.

Any suggestions?

Thanks, Shawn

[grosenberger]

I'm unfortunately not sure about wildcards on Windows and there might be differences between the command line and PowerShell. Does it work if you use the full filenames?

[sjr24]

George, Using the full file names allowed the files to be recognized, but the following error occurred. This error occurred in Power Shell and the Command prompt.

PS C:\Users\srice\Desktop\DIA2018\Tutorial4_OpenSWATH> C:\Anaconda3\Scripts\pyprophet merge --out=training.osw --subsample_ratio=0.33 collinsb_I180316_001_SW-A.osw collinsb_I180316_002_SW-B.osw Traceback (most recent call last): File "c:\anaconda3\lib\runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "c:\anaconda3\lib\runpy.py", line 85, in _run_code exec(code, run_globals) File "C:\Anaconda3\Scripts\pyprophet.exe__main.py", line 9, in File "c:\anaconda3\lib\site-packages\click\core.py", line 722, in call__ return self.main(args, kwargs) File "c:\anaconda3\lib\site-packages\click\core.py", line 697, in main rv = self.invoke(ctx) File "c:\anaconda3\lib\site-packages\click\core.py", line 1092, in invoke rv.append(sub_ctx.command.invoke(sub_ctx)) File "c:\anaconda3\lib\site-packages\click\core.py", line 895, in invoke return ctx.invoke(self.callback, ctx.params) File "c:\anaconda3\lib\site-packages\click\core.py", line 535, in invoke return callback(args, **kwargs) File "c:\anaconda3\lib\site-packages\pyprophet\main.py", line 191, in merge merge_osw(infiles, outfile, subsample_ratio, test) File "c:\anaconda3\lib\site-packages\pyprophet\levels_contexts.py", line 217, in merge_osw ''') sqlite3.OperationalError: no such table: RUN

Any ideas?

Thanks, Shawn

From: George Rosenberger [mailto:notifications@github.com] Sent: Thursday, September 27, 2018 10:36 AM To: PyProphet/pyprophet pyprophet@noreply.github.com Cc: Rice, Shawn srice@pennstatehealth.psu.edu; Author author@noreply.github.com Subject: Re: [PyProphet/pyprophet] PATH issuse with pyprophet (#33)

I'm unfortunately not sure about wildcards on Windows and there might be differences between the command line and PowerShell. Does it work if you use the full filenames?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/PyProphet/pyprophet/issues/33#issuecomment-425116986, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Alh9PhZS2pJPgkDk7a1oV7blrddQ7JCcks5ufOJigaJpZM4W50Mg.

[grosenberger]

Hi Shawn,

Are you using OpenSWATH 2.3? This version unfortunately is not yet fully compatible with the new PyProphet. Version 2.4 will be released over the next few weeks or you could also use the development version or nightly builds. On Windows, it might be a better to use the Docker image that we provide which contains all compatible versions of the tools.

[sjr24]

George, I am, indeed, using OpenSWATH v2.3. I will play around with the docker.

Thanks, Shawn

From: George Rosenberger [mailto:notifications@github.com] Sent: Thursday, September 27, 2018 2:14 PM To: PyProphet/pyprophet pyprophet@noreply.github.com Cc: Rice, Shawn srice@pennstatehealth.psu.edu; Author author@noreply.github.com Subject: Re: [PyProphet/pyprophet] PATH issuse with pyprophet (#33)

Hi Shawn,

Are you using OpenSWATH 2.3? This version unfortunately is not yet fully compatible with the new PyProphet. Version 2.4 will be released over the next few weeks or you could also use the development version or nightly builds. On Windows, it might be a better to use the Docker image that we provide which contains all compatible versions of the tools.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/PyProphet/pyprophet/issues/33#issuecomment-425191813, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Alh9Plls9K9tyWuoP29_5eBB9c36y1dnks5ufRVegaJpZM4W50Mg.

[ghost]

Hi George,

I hope this is the correct place to post the following, and apologies Shawn if you have since sorted this and moved on. I was having the same issue (before realising PyProphet wasn't supported by OpenMS 2.3), and have since decided to install the latest OpenMS nightly version. However, when running PyProphet this time, I now get the following (in Command prompt and Power Shell):

C:\Jess\OpenSWATH\CAF\v42>pyprophet merge --out=training.osw --subsample_ratio=0 .33 20180727_SWATH_CAFref_HpH*.osw

usage: pyprophet [options] input_file or pyprophet --help or pyprophet --version

parameters:

--apply_scorer                               default: None  [name of *_score

r.bin file of existing classifier] --apply_weights default: None [name of *_weigh ts.txt file of existing LDA weights] --compute.probabilities default: False [Compute approxi mate binned probability values] --d_score.cutoff default: -1000.0 [Filter output such that only results with a d_score higher than this value are reported] --delim.in default: 'tab' [you can eg use 'tab' or ','] --delim.out default: 'tab' [you can eg use 'tab' or ','] --export.mayu default: False [export input fi les for MAYU] --final_statistics.fdr_all_pg default: False [use all peak gr oups for score & q-value calculation] --final_statistics.lambda default: 0.4 --ignore.invalid_score_columns default: False [ignore score co lumns which only contain NaN or infinity values] --is_test default: 0 [switches random ness off] --num_processes default: 1 [-1 means 'all a vailable cpus'] --semi_supervised_learner.initial_fdr default: 0.15 --semi_supervised_learner.initial_lambda default: 0.4 --semi_supervised_learner.iteration_fdr default: 0.02 --semi_supervised_learner.iteration_lambda default: 0.4 --semi_supervised_learner.num_iter default: 5 --target.dir default: None --target.overwrite default: 0 --xeval.fraction default: 0.5 --xeval.num_iter default: 5

Traceback (most recent call last): File "c:\programdata\anaconda2\lib\runpy.py", line 174, in _run_module_as_main

"__main__", fname, loader, pkg_name)

File "c:\programdata\anaconda2\lib\runpy.py", line 72, in _run_code exec code in run_globals File "C:\ProgramData\Anaconda2\Scripts\pyprophet.exe__main__.py", line 9, in

File "c:\programdata\anaconda2\lib\site-packages\pyprophet\main.py", line 61, in main _main(sys.argv[1:]) File "c:\programdata\anaconda2\lib\site-packages\pyprophet\main.py", line 87, in _main raise Exception("duplicate input file argument") Exception: duplicate input file argument Any advise would be greatly appreciated! If not, as you've recommended above, I will have a go with Docker, but thought it was worth asking about this anyway! Best, Jess

[grosenberger]

Hi Jess,

It seems that you are using the latest version of PyProphet on PyPI. The commands only work with the GitHub version at the moment though.

OpenMS 2.4 was released a few days ago and I will release a compatible PyProphet version (same as current GitHub version) on PyPI within the next days.

Best regards, George

[grosenberger]

Ok, PyProphet 2.0.1 is now available from PyPI: https://pypi.org/project/pyprophet/2.0.1/

This version should be fully compatible with OpenMS 2.4: https://github.com/OpenMS/OpenMS/releases/tag/Release2.4.0

[ghost]

Great! Thanks so much for the quick reply - I look forward to trying it out. Jess