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PyProphet / pyprophet

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
http://www.openswath.org
BSD 3-Clause "New" or "Revised" License
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pyprophet export ignores --out parameter #49

Closed hroest closed 3 years ago

hroest commented 5 years ago

E.g.

$ time pyprophet export --in ../olgas_K121026_013_SW_Wayne_R3_d00.new.osw   --max_rs_peakgroup_qvalue 1.0 --out test.csv
Info: Reading peak group-level results.
Info: Reading transition-level results.
Info: Reading protein identifiers.

real    0m33.396s
user    0m25.228s
sys     0m5.372s
(py27_bleeding) hr@hr-Precision-5520:~/openmsall/builds/openms_trunk2/t5$ ls -ltrh
total 188M
-rw-rw-r-- 1 hr hr 188M Feb 20 13:31 olgas_K121026_013_SW_Wayne_R3_d00.mzML.gz.tsv

no test.csv file is preduced, instead the file is named after the "run" filename with the full "mzML" and "gz" attached: schubert_chapter/raw/olgas_K121026_013_SW_Wayne_R3_d00.mzML.gz

grosenberger commented 5 years ago

I recently changed this to restore compatibility with the requant workflow that required separate files. A combined table can be obtained by setting --format=legacy_merged.

hroest commented 5 years ago

it is fine in general to have single files, but what was unexpected is that the filename will be "original mzML filename" + tsv and during mapping we did not expect that.