when running pept2go (maybe others) and selecting the go term fields, if there are no go terms the fields aren't outputted. I would expect there to be 2 comma's to indicate the empty fields. See the last line in this example:
peptide,total_protein_count,go_term,go_protein_count
AAAINTIAHSTGAAK,46,GO:0051287 GO:0050661 GO:0006006 GO:0016620 GO:0004365 ,46 46 46 27 20
AAAINTIPHSTGAAK,50,GO:0051287 GO:0050661 GO:0006006 GO:0016620 GO:0004365 ,50 50 50 28 22
AAALNIVPNSTGAAK,85,GO:0051287 GO:0016620 GO:0050661 GO:0006006 GO:0004365 ,83 83 83 83 1
AAAMSMIPTSTGAAK,460,GO:0051287 GO:0050661 GO:0006006 GO:0016620 GO:0004365 GO:0043891 GO:0047100 GO:0005737,402 402 402 372 65 16 1 1
AAANESFGYNEDEIVSSDIVGMR,56,GO:0051287 GO:0016620 GO:0050661 GO:0006006 ,56 56 56 56
AAANYLDIPLYR,123,GO:0000287 GO:0004634 GO:0000015 GO:0006096 GO:0005576 GO:0009986 ,123 123 123 123 118 118
AAAVNIVPNSTGAAK,383,GO:0016620 GO:0051287 GO:0050661 GO:0006006 ,381 375 375 375
AADAAAAIGEGLQAFCIPGSVADHR,0
when running pept2go (maybe others) and selecting the go term fields, if there are no go terms the fields aren't outputted. I would expect there to be 2 comma's to indicate the empty fields. See the last line in this example: