small changes in peptide/protein search

pridepy.py

@@ -212,79 +212,6 @@ def get_files_by_project_accession(accession, filter, page_size, page, sort_dire
     project = Project()
     print(project.get_files_by_accession(accession, filter, page_size, page, sort_direction, sort_conditions))
 
-
-# @main.command()
-# @click.option('-pa', '--project_accession', required=False, help='projectAccession')
-# @click.option('-aa', '--assay_accession', required=False, help='assayAccession')
-# @click.option('-ra', '--reported_accession', required=False, help='reportedAccession')
-# @click.option('-ps', '--page_size', required=False, default=100, help='Number of results to fetch in a page')
-# @click.option('-p', '--page', required=False, default=0, help='Identifies which page of results to fetch')
-# @click.option('-sd', '--sort_direction', required=False, default='DESC', help='Sorting direction: ASC or DESC')
-# @click.option('-sc', '--sort_conditions', required=False, default='projectAccession',
-#               help='Field(s) for sorting the results on. Default for this '
-#                    'request is project_accession. More fields can be separated by '
-#                    'comma and passed. Example: submission_date,project_title')
-# def search_protein_evidences(project_accession, assay_accession, reported_accession, page_size, page,
-#                              sort_direction, sort_conditions):
-#     """
-#     search public pride protein evidences with keywords and filters
-#     :return:
-#     """
-#     protein = Protein()
-#     print(protein.protein_evidences(project_accession, assay_accession, reported_accession, page_size, page,
-#                                     sort_direction, sort_conditions))
-
-
-# @main.command()
-# @click.option('-usi', '--usi', required=False, help='usi, Provide multiple values separated by \n')
-# @click.option('-pa', '--project_accession', required=False, help='projectAccession')
-# @click.option('-aa', '--assay_accession', required=False, help='assayAccession')
-# @click.option('-pepSeq', '--peptide_sequence', required=False, help='peptideSequence')
-# @click.option('-modSeq', '--modified_sequence', required=False, help='peptideSequence')
-# @click.option('-rt', '--result_type', required=False, default='COMPACT', help='peptideSequence')
-# @click.option('-ps', '--page_size', required=False, default=100, help='Number of results to fetch in a page')
-# @click.option('-p', '--page', required=False, default=0, help='Identifies which page of results to fetch')
-# @click.option('-sd', '--sort_direction', required=False, default='DESC', help='Sorting direction: ASC or DESC')
-# @click.option('-sc', '--sort_conditions', required=False, default='projectAccession',
-#               help='Field(s) for sorting the results on. Default for this '
-#                    'request is project_accession. More fields can be separated by '
-#                    'comma and passed. Example: submission_date,project_title')
-# def search_spectra_evidences(usi, project_accession, assay_accession, peptide_sequence, modified_sequence,
-#                              result_type, page_size, page, sort_direction, sort_conditions):
-#     """
-#     search public pride spectra with keywords and filters
-#     :return:
-#     """
-#     spectra = Spectra()
-#     print(spectra.spectra_evidences(usi, project_accession, assay_accession, peptide_sequence, modified_sequence,
-#                                     result_type, page_size, page, sort_direction, sort_conditions))
-
-
-# @main.command()
-# @click.option('-pa', '--project_accession', required=False, help='projectAccession')
-# @click.option('-aa', '--assay_accession', required=False, help='assayAccession')
-# @click.option('-aa', '--protein_accession', required=False, help='proteinAccession')
-# @click.option('-aa', '--peptide_evidence_accession', required=False, help='peptideEvidenceAccession')
-# @click.option('-pepSeq', '--peptide_sequence', required=False, help='peptideSequence')
-# @click.option('-ps', '--page_size', required=False, default=100, help='Number of results to fetch in a page')
-# @click.option('-p', '--page', required=False, default=0, help='Identifies which page of results to fetch')
-# @click.option('-sd', '--sort_direction', required=False, default='DESC', help='Sorting direction: ASC or DESC')
-# @click.option('-sc', '--sort_conditions', required=False, default='projectAccession',
-#               help='Field(s) for sorting the results on. Default for this '
-#                    'request is project_accession. More fields can be separated by '
-#                    'comma and passed. Example: submission_date,project_title')
-# def search_peptide_evidences(project_accession, assay_accession, protein_accession, peptide_evidence_accession,
-#                              peptide_sequence, page_size, page, sort_direction, sort_conditions):
-#     """
-#     search public pride peptide evidences with keywords and filters
-#     :return:
-#     """
-#     peptide = Peptide()
-#     print(peptide.peptide_evidences(project_accession, assay_accession, protein_accession,
-#                                     peptide_evidence_accession, peptide_sequence,
-#                                     page_size, page, sort_direction, sort_conditions))
-
-
 @main.command()
 @click.option('-f', '--filter', required=False, help='Parameters to filter the search results. The structure of the '
                                                      'filter is: field1==value1, field2==value2. Example '