Crash due to dependency on qvality in v0.1.0

[MatthewThe]

Triqler 0.1.0 has a dependency on an external program (qvality), this causes execution to fail if this program is not present:

$ python -m triqler --fold_change_eval 0.8 iPRG2016.tsv
The process cannot access the file because it is being used by another
process.
Traceback (most recent call last):
  File "C:\Python27\lib\runpy.py", line 162, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "C:\Python27\lib\runpy.py", line 72, in _run_code
    exec code in run_globals
  File "C:\Python27\lib\site-packages\triqler\__main__.py", line 8, in
<module>
    main()
  File "C:\Python27\lib\site-packages\triqler\triqler.py", line 28, in main
    runTriqler(params, args.in_file, args.out_file)
  File "C:\Python27\lib\site-packages\triqler\triqler.py", line 79, in
runTriqle                                                                r
    peptQuantRows = convertTriqlerInputToPeptQuantRows(triqlerInputFile,
peptQua                                                               
ntRowFile, params)
  File "C:\Python27\lib\site-packages\triqler\triqler.py", line 89, in
convertTr                                                               
iqlerInputToPeptQuantRows
    peptQuantRowMap, getPEPFromScore, params['fileList'],
params['groupLabels'],                                                                
params['groups'] = getPeptQuantRowMap(triqlerInputFile,
params['decoyPattern'])
  File "C:\Python27\lib\site-packages\triqler\triqler.py", line 124, in
getPeptQ                                                               
uantRowMap
    _, peps = qvality.getQvaluesFromScores(targetScores, decoyScores,
includePEP                                                               
s = True, includeDecoys = True, tdcInput = True)
  File "C:\Python27\lib\site-packages\triqler\qvality.py", line 245, in
getQvalu                                                               
esFromScores
    qvals, peps = parseQvalues(qvalFile, includePEPs = includePEPs)
  File "C:\Python27\lib\site-packages\triqler\qvality.py", line 271, in
parseQva                                                                lues
    next(reader)
StopIteration

There is already code available to get rid of this dependency, but this was not used yet.

[percolator]

Was this error triggered by a real user, or is this your own observation?

…

On Wed, Jun 20, 2018 at 3:30 PM, MatthewThe ***@***.***> wrote: Triqler 0.1.0 has a dependency on an external program (qvality), this causes execution to fail if this program is not present: $ python -m triqler --fold_change_eval 0.8 iPRG2016.tsv The process cannot access the file because it is being used by another process. Traceback (most recent call last): File "C:\Python27\lib\runpy.py", line 162, in _run_module_as_main "__main__", fname, loader, pkg_name) File "C:\Python27\lib\runpy.py", line 72, in _run_code exec code in run_globals File "C:\Python27\lib\site-packages\triqler\__main__.py", line 8, in <module> main() File "C:\Python27\lib\site-packages\triqler\triqler.py", line 28, in main runTriqler(params, args.in_file, args.out_file) File "C:\Python27\lib\site-packages\triqler\triqler.py", line 79, in runTriqle r peptQuantRows = convertTriqlerInputToPeptQuantRows(triqlerInputFile, peptQua ntRowFile, params) File "C:\Python27\lib\site-packages\triqler\triqler.py", line 89, in convertTr iqlerInputToPeptQuantRows peptQuantRowMap, getPEPFromScore, params['fileList'], params['groupLabels'], params['groups'] = getPeptQuantRowMap(triqlerInputFile, params['decoyPattern']) File "C:\Python27\lib\site-packages\triqler\triqler.py", line 124, in getPeptQ uantRowMap _, peps = qvality.getQvaluesFromScores(targetScores, decoyScores, includePEP s = True, includeDecoys = True, tdcInput = True) File "C:\Python27\lib\site-packages\triqler\qvality.py", line 245, in getQvalu esFromScores qvals, peps = parseQvalues(qvalFile, includePEPs = includePEPs) File "C:\Python27\lib\site-packages\triqler\qvality.py", line 271, in parseQva lues next(reader) StopIteration There is already code available to get rid of this dependency, but this was not used yet. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAF1AJtFN-OZ19uFcRE390MfWNJR5LiVks5t-k6NgaJpZM4UvRwC> .

-- ======================== Lukas Käll http://kaell.org Royal Institute of Technology - KTH Science for Life Laboratory School of Biotechnology Box 1031, 171 65 Solna, Sweden +46 8 790 9852 or +46 76 9425179

[jjGG]

I did report this.. Best regards Jonas Grossmann sent from a mobile device ;) sorry for typos and unwanted auto corrections

…

Am 20.06.2018 um 18:57 schrieb Lukas Käll ***@***.***>: Was this error triggered by a real user, or is this your own observation? On Wed, Jun 20, 2018 at 3:30 PM, MatthewThe ***@***.***> wrote: > Triqler 0.1.0 has a dependency on an external program (qvality), this > causes execution to fail if this program is not present: > > $ python -m triqler --fold_change_eval 0.8 iPRG2016.tsv > The process cannot access the file because it is being used by another > process. > Traceback (most recent call last): > File "C:\Python27\lib\runpy.py", line 162, in _run_module_as_main > "__main__", fname, loader, pkg_name) > File "C:\Python27\lib\runpy.py", line 72, in _run_code > exec code in run_globals > File "C:\Python27\lib\site-packages\triqler\__main__.py", line 8, in > <module> > main() > File "C:\Python27\lib\site-packages\triqler\triqler.py", line 28, in main > runTriqler(params, args.in_file, args.out_file) > File "C:\Python27\lib\site-packages\triqler\triqler.py", line 79, in > runTriqle r > peptQuantRows = convertTriqlerInputToPeptQuantRows(triqlerInputFile, > peptQua > ntRowFile, params) > File "C:\Python27\lib\site-packages\triqler\triqler.py", line 89, in > convertTr > iqlerInputToPeptQuantRows > peptQuantRowMap, getPEPFromScore, params['fileList'], > params['groupLabels'], > params['groups'] = getPeptQuantRowMap(triqlerInputFile, > params['decoyPattern']) > File "C:\Python27\lib\site-packages\triqler\triqler.py", line 124, in > getPeptQ > uantRowMap > _, peps = qvality.getQvaluesFromScores(targetScores, decoyScores, > includePEP > s = True, includeDecoys = True, tdcInput = True) > File "C:\Python27\lib\site-packages\triqler\qvality.py", line 245, in > getQvalu > esFromScores > qvals, peps = parseQvalues(qvalFile, includePEPs = includePEPs) > File "C:\Python27\lib\site-packages\triqler\qvality.py", line 271, in > parseQva lues > next(reader) > StopIteration > > There is already code available to get rid of this dependency, but this > was not used yet. > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#1>, or mute > the thread > <https://github.com/notifications/unsubscribe-auth/AAF1AJtFN-OZ19uFcRE390MfWNJR5LiVks5t-k6NgaJpZM4UvRwC> > . > -- ======================== Lukas Käll http://kaell.org Royal Institute of Technology - KTH Science for Life Laboratory School of Biotechnology Box 1031, 171 65 Solna, Sweden +46 8 790 9852 or +46 76 9425179 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.