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I am working with rel-3-07-01 and I am running into a problem with the -K/--protein-name-separator parameter. When used only the first protein in the list of proteins that a PSM matches to shows up.
Specifically, when I run: percolator -U -m tab_sep.out QE3_RP180_4ug_Exp13_r2_t3.pin
the output for an example PSM looks like: QE3_RP180_4ug_Exp13_r2_t3_76331_2_1 2.78719 0.00356664 4.73844e-08 R.CTEECPFGALDDDEK.G bin_049_000000000018_14 bin_050_000000000187_2 bin_064_000000000037_3
Whereas when I run: percolator -U -K , -m comma_sep.out QE3_RP180_4ug_Exp13_r2_t3.pin
The same PSM looks like: QE3_RP180_4ug_Exp13_r2_t3_76331_2_1 2.78719 0.00356664 4.73844e-08 R.CTEECPFGALDDDEK.G bin_049_000000000018_14
when instead I would expect a comma separated list of protein IDs.
This issue is slightly different from similar issues that have arisen before, e.g. #343, in that the protein name column is not completely empty.
I have tested all of the 3.6 releases and the same problem occurs in all of them. I am running Ubuntu and have tried both the standalone executable version (percolator-noxml-ubuntu-portable.zip) and the deb version (percolator-noxml-v3-07-linux-amd64.deb). I have also tried both -K and --protein-name-separator as well as several different separator characters.
The text was updated successfully, but these errors were encountered:
Hello,
I am working with rel-3-07-01 and I am running into a problem with the
-K/--protein-name-separatorparameter. When used only the first protein in the list of proteins that a PSM matches to shows up.Specifically, when I run:
percolator -U -m tab_sep.out QE3_RP180_4ug_Exp13_r2_t3.pinthe output for an example PSM looks like:
QE3_RP180_4ug_Exp13_r2_t3_76331_2_1 2.78719 0.00356664 4.73844e-08 R.CTEECPFGALDDDEK.G bin_049_000000000018_14 bin_050_000000000187_2 bin_064_000000000037_3Whereas when I run:
percolator -U -K , -m comma_sep.out QE3_RP180_4ug_Exp13_r2_t3.pinThe same PSM looks like:
QE3_RP180_4ug_Exp13_r2_t3_76331_2_1 2.78719 0.00356664 4.73844e-08 R.CTEECPFGALDDDEK.G bin_049_000000000018_14when instead I would expect a comma separated list of protein IDs.
This issue is slightly different from similar issues that have arisen before, e.g. #343, in that the protein name column is not completely empty.
I have tested all of the 3.6 releases and the same problem occurs in all of them. I am running Ubuntu and have tried both the standalone executable version (percolator-noxml-ubuntu-portable.zip) and the deb version (percolator-noxml-v3-07-linux-amd64.deb). I have also tried both
-Kand--protein-name-separatoras well as several different separator characters.The text was updated successfully, but these errors were encountered: