NetphosParser
Parse NetPhos 3.1 results and filter against phospho-peptides
Usage
Create Instance
npp = NetphosParser()
Parse NetPhos 3.1 gff results:
npp.parse('netphos_results.txt')
Example NetPhos 3.1 gff results format:
##Type Protein A0A161I596
##Protein A0A161I596
##MAKPLTDQEKRKQISIRGIVGVENVAELKKGFNRHLHFTLVKDRNVATTRDYYFALAHTV
##RDHLVGRWIRTQQYYYEKDPKRTYYLSLEFYMGRTLQNTMINLGLQNACDEAIYQIGLDI
##EELEEMEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEYGIFNQKIKDGWQVEEA
##DDWLRHGNPWEKDRPEYMLPIHFYGRVEHHKTGVRWVDTQVVLAMPYDTPVPGYMNNTVN
##TMRLWSARAPNDFNLQDFNVGDYIEAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFV
##VAASLQDIIRRFKASGLGFKDRIRTGFDSFPEKVAIQLNDTHPALGIPELMRIFLDIEKL
##PWEKAWEITKKTFAYTNHTVLPEALERWPVDLVEKLLPRHLAIIYEINQRHLDRIAALYP
##KDLDRARRMSLIEEDGIKRINMAHLCIVGSHAVNGVAKIHSDIVKNQVFKDFNDMEPDKF
##QNKTNGITPRRWLLLCNPGLAELIAEKIGETYVKDLSQLTKLKKFVDDDVFIRDVSKVKE
##ENKLKFIQYLEKEYKMKLNPASMFDVHVKRIHEYKRQLLNCLHIITMYNRIRENPTKEFV
##PRTVIIGGKAAPGYHMAKMIIKVITAVGDIVNNDPLVGNKLKVIYLENYRVSLAEKVIPA
##TDLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENLFIFGMRVEEVA
##EMDKKGYNARDYYEKLPELKKAMDQIQNGFFSPTKPDLFKDIVNMLFNYDRFKVFADYEA
##YVKSQEKVSALYKNPKEWTKVVIKNIAASGMFSSDRTIKEYARDIWGVEPTDLKIAPPNE
##PRNVVDVKAAAPAAKG
##end-Protein
# seqname source feature start end score N/A ?
# ---------------------------------------------------------------------------
A0A161I596 netphos-3.1b phos-CKII 6 6 0.551 . . YES
A0A161I596 netphos-3.1b phos-unsp 15 15 0.981 . . YES
...
Read in phospho-peptides of interest and filter out NetPhos results that don't match any peptide
peptides = pd.read_csv('peptides.csv')
npp.filter(peptides)
Headers must be [uniprot,peptide] with # indicating phosphorylation of previous residue.
Example peptide format:
uniprot,orig_peptide,peptide
A0A2G9S9U7,_SSS[+80]VGS[+80]SSSVTASPAGR_.2,SSS#VGS#SSSVTASPAGR
Q98TT3,_SS[+80]IHNFM[+16]THPEFR_.3,SS#IHNFMTHPEFR
Q98TT3,_S[+80]SIHNFM[+16]THPEFR_.3,S#SIHNFMTHPEFR
A0A2G9S9U7,_SS[+80]S[+80]VGSSSSVTASPAGR_.2,SS#S#VGSSSSVTASPAGR
Output filtered results to pandas dataframe
npp.to_df()
Example output:
uniprot,orig_peptide,residue,residue_index,context,kinase,matching_peptides,score
A0A023UDJ8,_VINDNFGIVEGLMTT[+80]VHAYTATQK_.3,T,124,IVEGLMTTVHAYTAT,phos-PKC,VINDNFGIVEGLMTT#VHAYTATQK,0.683
A0A023UDJ8,_VINDNFGIVEGLMTT[+80]VHAYTATQK_.3,T,124,IVEGLMTTVHAYTAT,phos-cdc2,VINDNFGIVEGLMTT#VHAYTATQK,0.453
A0A023UDJ8,_VINDNFGIVEGLMTT[+80]VHAYTATQK_.3,T,124,IVEGLMTTVHAYTAT,phos-CaM-II,VINDNFGIVEGLMTT#VHAYTATQK,0.45
A0A023UDJ8,_VINDNFGIVEGLMTT[+80]VHAYTATQK_.3,T,124,IVEGLMTTVHAYTAT,phos-GSK3,VINDNFGIVEGLMTT#VHAYTATQK,0.438