Mercurial > repos > eschen42 > mqppep_preproc
diff mqppep_mrgfltr.py @ 16:d9906288cc6a draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227"
| author | eschen42 |
|---|---|
| date | Tue, 05 Apr 2022 01:47:37 +0000 |
| parents | 42daf70d4ed4 |
| children | ba5f14c2a4af |
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--- a/mqppep_mrgfltr.py Sat Mar 26 02:26:38 2022 +0000 +++ b/mqppep_mrgfltr.py Tue Apr 05 01:47:37 2022 +0000 @@ -707,15 +707,13 @@ "dephosphorylated phosphopeptide not found in DephosphoPep_UniProtSeq_LUT", ) if ( - dephospho_pep - != PhosphoPep_UniProtSeq_LUT[(phospho_pep, DEPHOSPHOPEP)] + dephospho_pep != PhosphoPep_UniProtSeq_LUT[(phospho_pep, DEPHOSPHOPEP)] ): - raise PreconditionError( - dephospho_pep, - "dephosphorylated phosphopeptide does not match " - + "PhosphoPep_UniProtSeq_LUT[(phospho_pep,DEPHOSPHOPEP)] = " - + PhosphoPep_UniProtSeq_LUT[(phospho_pep, DEPHOSPHOPEP)], - ) + my_err_msg = "dephosphorylated phosphopeptide does not match " + my_err_msg += "PhosphoPep_UniProtSeq_LUT[(phospho_pep,DEPHOSPHOPEP)] = " + my_err_msg += PhosphoPep_UniProtSeq_LUT[(phospho_pep, DEPHOSPHOPEP)] + raise PreconditionError(dephospho_pep, my_err_msg) + result[SEQUENCE] = [dephospho_pep] result[UNIPROT_ID] = DephosphoPep_UniProtSeq_LUT[ (dephospho_pep, UNIPROT_ID) @@ -822,17 +820,13 @@ # add Sequence10 if psite < 10: # phospho_pep at N terminus seq10 = ( - str(UniProtSeq)[:psite] - + "p" - + str(UniProtSeq)[psite: psite + 11] + str(UniProtSeq)[:psite] + "p" + str(UniProtSeq)[psite: psite + 11] ) elif ( len(UniProtSeq) - psite < 11 ): # phospho_pep at C terminus seq10 = ( - str(UniProtSeq)[psite - 10: psite] - + "p" - + str(UniProtSeq)[psite:] + str(UniProtSeq)[psite - 10: psite] + "p" + str(UniProtSeq)[psite:] ) else: seq10 = str(UniProtSeq)[psite - 10: psite + 11]