Package: curtainutils
CurtainUtilsA utility package for converting different MS output files into a format usable by Curtain (https://curtain.proteo.info) and CurtainPTM (https://curtainptm.proteo.info)InstallationThe package can be installed using the following command.pip install curtainutilsConvert MSFragger PTM single site output to CurtainPTM inputThis script should be used to convert a differential analysis file that contains the index column and peptide column. The index column should also be the original index column output by MS-Fragger that contains both the Accession ID as well as position of the PTM within the protein sequence.Usage:msf-curtainptm-f<MSFraggerPTMsinglesiteoutputfile>-i<indexcolumnwithsiteinformation>-o<outputfile>-p<peptidecolumn>-a<fastafile>Convert DIA-NN PTM output to CurtainPTM inputThis script should be used to convert a differential analysis file that contains the following column "Modified.Sequence", "Precursor.Id", "Protein.Group" from the pr report file by combining the file with the Report file which contains the column "PTM.Site.Confidence".diann-curtainptm-p<differentialanalysisfile>-r<reportfile>-o<outputfile>-m<modification_of_interestsfromtheModified.Sequencecolumn>Convert Spectronaut output to Curtain inputThis script should be used to convert a differential analysis file that contains the "PTM_collapse_key" and "PEP.StrippedSequence" columns from the original Spectronaut output.spn-curtainptm-f<differentialanalysisfile>-o<outputfile>Submit data to a Curtain serverUsage example:fromcurtainutils.clientimportCurtainClientde_file=r"differential-file-path"raw_file=r"raw-file-path"fc_col="foldchange-column-name"transform_fc=Falsetransform_significant=Falsereverse_fc=Falsep_col="significance-column-name"comp_col=""# Leave empty if no comparison column is usedcomp_select=[]# Leave empty if no comparison column is usedprimary_id_de_col="primary-id-column-name-in-differential-file"primary_id_raw_col="primary-id-column-name-in-raw-file"sample_cols=["4Hr-AGB1.01","4Hr-AGB1.02","4Hr-AGB1.03","4Hr-AGB1.04","4Hr-AGB1.05","24Hr-AGB1.01","24Hr-AGB1.02","24Hr-AGB1.03","24Hr-AGB1.04","24Hr-AGB1.05","4Hr-Cis.01","4Hr-Cis.02","4Hr-Cis.03","24Hr-Cis.01","24Hr-Cis.02","24Hr-Cis.03"]c=CurtainClient("curtain-backend-url")payload=c.create_curtain_session_payload(de_file,raw_file,fc_col,transform_fc,transform_significant,reverse_fc,p_col,comp_col,comp_select,primary_id_de_col,primary_id_raw_col,sample_cols)package={"enable":"True","description":payload["settings"]["description"],"curtain_type":"TP",}result=c.post_curtain_session(package,payload)print(result)Submit data to a CurtainPTM serverfromcurtainutils.clientimportCurtainClientde_file=r"differential-file-path"raw_file=r"raw-file-path"fc_col="foldchange-column-name"transform_fc=Falsetransform_significant=Falsereverse_fc=Falsep_col="significance-column-name"comp_col=""# Leave empty if no comparison column is usedcomp_select=[]# Leave empty if no comparison column is usedprimary_id_de_col="primary-id-column-name-in-differential-file"primary_id_raw_col="primary-id-column-name-in-raw-file"sample_cols=[]peptide_col="peptide-sequence-column-name"acc_col="protein-accession-column-name"position_col="position-in-protein-column-name"position_in_peptide_col="position-in-peptide-column-name"sequence_window_col="sequence-window-column-name"score_col="score-column-name"c=CurtainClient("curtain-backend-url")payload=c.create_curtain_ptm_session_payload(de_file,raw_file,fc_col,transform_fc,transform_significant,reverse_fc,p_col,comp_col,comp_select,primary_id_de_col,primary_id_raw_col,sample_cols,peptide_col,acc_col,position_col,position_in_peptide_col,sequence_window_col,score_col)package={"enable":"True","description":payload["settings"]["description"],"curtain_type":"PTM",}result=c.post_curtain_session(package,payload)