Hi Hannes, I didn't see this in time. Instead I looked at all the directories where configobj were installed (spectrast2tsv was giving me the same ImportError with configobj before I installed it). It was in 4 folders. 2 were very specific/esoteric, 1 already had msproteomicstoolslib, and 1 was C:\Python27\Lib\site-packages\ . I copied msproteomicstoolslib to that last directory and finally the script ran.
Unfortunately, even though the script ran, it did not generate any output file or even any output text (aside from the help lines that print at the beginning of the script). I will post another issue about that. Thanks, Steven On Thursday, October 19, 2017 at 7:25:37 AM UTC-7, Hannes Roest wrote: > > Hi Steven > > I have not seen that problem before, can you start Python from the command > line and try > > >>> import sys > >>> print (sys.path) > >>> from msproteomicstoolslib.data_structures.aminoacides import > Aminoacides > > Best > > Hannes > > On Wednesday, October 18, 2017 at 6:53:48 PM UTC-4, Steven Shuken wrote: >> >> Hello, >> >> I'm a grad student following the Aebersold protocol on SWATH library >> building: >> https://www.nature.com/nprot/journal/v10/n3/full/nprot.2015.015.html >> I'm on Step 37(B)(i) where the Anaconda script spectrast2rsv.py is run to >> extract the 6 most intense fragment ion peaks from each consensus spectrum >> to generate a SWATH library. >> >> When I run the script with the recommended options this happens: >> >> "C:\TPPdata>python C:\ProgramData\Anaconda2\Scripts\spectrast2tsv.py -1 >> 350,2000 >> -s b,y -x 1,2 -o 6 -n 6 -p 0.05 -d -e -w swaths.txt -k openswath -a >> SpecLib_cons >> _openswath.csv SpecLib_cons.sptxt >> Traceback (most recent call last): >> File "C:\ProgramData\Anaconda2\Scripts\spectrast2tsv.py", line 51, in >> <module> >> >> from msproteomicstoolslib.data_structures.aminoacides import >> Aminoacides >> >> ImportError: No module named >> msproteomicstoolslib.data_structures.aminoacides" >> >> In fact, I have installed msproteomicstools and msproteomicstoolslib >> (which contains data_structures\aminoacides.py, etc.) exists in >> C:\ProgramData\Anaconda2\Lib\site-packages\. (I am reminded of this fact >> every time I try to install msproteomicstools in a different location.) >> >> What am I missing? >> >> Thanks, >> Steven >> >> -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
