Table of Contents - protk-1.4.4 Documentation
Pages
- Makefile
- ExecutePipeline.trf
- FeatureFinderCentroided.ini
- FeatureFinderIsotopeWavelet.ini
- apt-get_packages.yaml
- brew_packages.yaml
- galaxyenv.sh
- predefined_db.crap.yaml
- predefined_db.sphuman.yaml
- predefined_db.swissprot_annotation.yaml
- predefined_db.swissprot_fasta_annotation.yaml
- tandem-style.css
- tandem-style.xsl
- tandem_gpm_defaults.xml
- tandem_isb_kscore_defaults.xml
- tandem_isb_native_defaults.xml
- tandem_params.xml
- taxonomy_template.xml
- template_pep.xml
- template_prot.xml
- unimod.xml
- uniprot_accessions.loc
- uniprot_accessions_table
- uniprot_input_accessions.loc
- yum_packages.yaml
- manage_db_rakefile.rake
- setup_rakefile.rake
Classes and Modules
- Bio
- Bio::GFF
- Bio::GFF::GFF3
- Bio::GFF::GFF3::Record
- Bio::SPTR
- CommandRunner
- Constants
- ConvertUtil
- Decoymaker
- FastaDB
- FastaDatabase
- GFFDB
- GalaxyStager
- GalaxyUtil
- GffToProteinDBTool
- IndistinguishablePeptide
- ManageDBTool
- MascotUtil
- MzIdentMLDoc
- MzMLParser
- OMSSAUtil
- Object
- OpenMSDefaults
- PSM
- PepXML
- PepXMLWriter
- Peptide
- PeptideEvidence
- PeptideMod
- PeptideNotInProteinError
- PlasmoDB
- ProphetTool
- ProtXMLToGFFTool
- ProtXMLToGFFTool::CDSInfo
- ProtXMLWriter
- Protein
- ProteinGroup
- ProteinSummary
- ProteinToGenomeMapper
- ProtkError
- Randomize
- SearchTool
- SetupTool
- Sniffer
- SpectrumQuery
- String
- SwissprotDatabase
- TandemSearchTool
- Tool
- UniprotMapper
Methods
- ::add_retention_times — OMSSAUtil
- ::create — FastaDB
- ::create — GFFDB
- ::decode_galaxy_string! — GalaxyUtil
- ::default_output_path — Tool
- ::ensure_mzml_indexed — ConvertUtil
- ::extension_from_filename — Tool
- ::find — MzIdentMLDoc
- ::for_galaxy? — GalaxyUtil
- ::from_data — PeptideMod
- ::from_mzid — Peptide
- ::from_mzid — Protein
- ::from_mzid — ProteinGroup
- ::from_mzid — ProteinSummary
- ::from_mzid — PeptideEvidence
- ::from_mzid — PSM
- ::from_mzid — SpectrumQuery
- ::from_protxml — Peptide
- ::from_protxml — IndistinguishablePeptide
- ::from_protxml — PeptideMod
- ::from_protxml — Protein
- ::from_sequence — Peptide
- ::index_mgf_times — MascotUtil
- ::index_mzml — ConvertUtil
- ::input_basename — MascotUtil
- ::is_mgf_format — Sniffer
- ::is_mzml_format — Sniffer
- ::make_decoys — Decoymaker
- ::make_decoys — Randomize
- ::new — CommandRunner
- ::new — Constants
- ::new — ProtkError
- ::new — FastaDB
- ::new — GalaxyStager
- ::new — GffToProteinDBTool
- ::new — GFFDB
- ::new — ManageDBTool
- ::new — MzIdentMLDoc
- ::new — MzMLParser
- ::new — OpenMSDefaults
- ::new — Peptide
- ::new — PeptideMod
- ::new — PepXML
- ::new — PepXMLWriter
- ::new — PlasmoDB
- ::new — ProphetTool
- ::new — Protein
- ::new — ProteinGroup
- ::new — ProteinSummary
- ::new — ProtXMLToGFFTool
- ::new — ProtXMLWriter
- ::new — PeptideEvidence
- ::new — PSM
- ::new — SearchTool
- ::new — SpectrumQuery
- ::new — SwissprotDatabase
- ::new — TandemSearchTool
- ::new — FastaDatabase
- ::new — Tool
- ::new — UniprotMapper
- ::remove_charge_from_title_string — MascotUtil
- ::replace_references — GalaxyStager
- ::sniff_format — Sniffer
- ::stage_fasta — GalaxyUtil
- ::stage_pepxml — GalaxyUtil
- ::unindexed_mzml? — ConvertUtil
- ::xinteract_code_for_enzyme — ProphetTool
- #<=> — Bio::GFF::GFF3::Record
- #accessions — Bio::SPTR
- #add — ManageDBTool
- #add_boolean_option — Tool
- #add_default_to_help — Tool
- #add_putative_nterm_to_gff — ProtXMLToGFFTool
- #add_value_option — Tool
- #all_database_names — ManageDBTool
- #altnames — Bio::SPTR
- #analysis_software — MzIdentMLDoc
- #append_dataset_derivation — ProtXMLWriter
- #append_header — ProtXMLWriter
- #append_option — TandemSearchTool
- #append_protein_group — ProtXMLWriter
- #append_spectrum_query — PepXMLWriter
- #as_pepxml — PeptideEvidence
- #as_pepxml — PSM
- #as_pepxml — SpectrumQuery
- #as_protxml — Peptide
- #as_protxml — Protein
- #as_protxml — ProteinGroup
- #as_protxml — ProteinSummary
- #bin — Constants
- #blast_root — Constants
- #blastdbcmd — Constants
- #cd — Bio::SPTR
- #cds_info_from_fasta — ProtXMLToGFFTool
- #check_options — Tool
- #coords_in_protein — Peptide
- #current_database_for_name — Constants
- #database_downloads — Constants
- #database_info — Tool
- #dbexist? — Constants
- #dbsequence_cache — MzIdentMLDoc
- #dbsequences — MzIdentMLDoc
- #disease — Bio::SPTR
- #domain — Bio::SPTR
- #ensembl — Bio::SPTR
- #ensembl_link — Bio::SPTR
- #enzymes — MzIdentMLDoc
- #extract_db — PepXML
- #extract_engine — PepXML
- #extract_enzyme — PepXML
- #feature_dump — Bio::SPTR
- #fetch — FastaDB
- #find — MzIdentMLDoc
- #find_runs — PepXML
- #fragment_coords_from_protein_coords — ProtXMLToGFFTool
- #function — Bio::SPTR
- #generate_fragment_gffs_for_coords — ProtXMLToGFFTool
- #generate_gff_for_peptide_mapped_to_protein — ProtXMLToGFFTool
- #generate_parameter_doc — TandemSearchTool
- #generate_protein_gff — ProtXMLToGFFTool
- #get_best_psm_for_peptide — MzIdentMLDoc
- #get_by_id — FastaDB
- #get_by_id — GFFDB
- #get_cds_by_parent_id — GFFDB
- #get_cterm_coords_for_peptide — ProtXMLToGFFTool
- #get_cvParam — MzIdentMLDoc
- #get_dbsequence — MzIdentMLDoc
- #get_dna_sequence — ProtXMLToGFFTool
- #get_entry_for_name — PlasmoDB
- #get_entry_for_name — SwissprotDatabase
- #get_fasta_record — ProtXMLToGFFTool
- #get_lines_matching — GffToProteinDBTool
- #get_nterm_peptide_for_peptide — ProtXMLToGFFTool
- #get_path_for_executable — Constants
- #get_peptide_coordinates — ProtXMLToGFFTool
- #get_peptide_coordinates_from_transcript_info — ProtXMLToGFFTool
- #get_peptide_coordinates_sixframe — ProtXMLToGFFTool
- #get_peptide_evidence_from_psm — MzIdentMLDoc
- #get_peptides_for_protein — MzIdentMLDoc
- #get_predefined_definition — ManageDBTool
- #get_protein_probability — MzIdentMLDoc
- #get_proteins_for_group — MzIdentMLDoc
- #get_sequence_for_peptide — MzIdentMLDoc
- #get_sequence_for_psm — MzIdentMLDoc
- #get_start_codon_coords_for_peptide — ProtXMLToGFFTool
- #gff_record_for_peptide_fragment — Peptide
- #gff_records_for_coords_in_protein — Peptide
- #go_entries — Bio::SPTR
- #go_terms — Bio::SPTR
- #import_fasta_database — Constants
- #initialize_loggers — Constants
- #install — SetupTool
- #intact — Bio::SPTR
- #intact_link — Bio::SPTR
- #ipi — Bio::SPTR
- #is_new_genome_location — ProtXMLToGFFTool
- #is_valid_type — PepXML
- #jobid_prefix — Tool
- #jobid_prefix= — Tool
- #length — Bio::GFF::GFF3::Record
- #location — Bio::SPTR
- #log — Constants
- #log_file — Constants
- #make_index — FastaDB
- #make_index — GFFDB
- #makeblastdb — Constants
- #map — UniprotMapper
- #mascot2xml — Constants
- #method_missing — Constants
- #method_missing — Tool
- #modifications_from_sequence — Peptide
- #mods_to_gff3_records — Peptide
- #msgfplus_root — Constants
- #msgfplusjar — Constants
- #ncbi_taxon_id — Bio::SPTR
- #next_runid — MzMLParser
- #next_spectrum — MzMLParser
- #nextbio — Bio::SPTR
- #nextbio_link — Bio::SPTR
- #num_transmem — Bio::SPTR
- #omssa_root — Constants
- #openms_root — Constants
- #overlap — ProtXMLToGFFTool::CDSInfo
- #params_doc — TandemSearchTool
- #path_for_builtin_database — Constants
- #peptide_evidence — MzIdentMLDoc
- #peptide_gff_is_duplicate — ProtXMLToGFFTool
- #peptide_is_in_sixframe — ProtXMLToGFFTool
- #peptide_nodes — ProtXMLToGFFTool
- #peptides — MzIdentMLDoc
- #predefined_databases_help — ManageDBTool
- #predefined_names — ManageDBTool
- #pride — Bio::SPTR
- #pride_link — Bio::SPTR
- #protein_database_root — Constants
- #protein_groups — MzIdentMLDoc
- #protein_names — ProtXMLToGFFTool
- #proteins — MzIdentMLDoc
- #psms — MzIdentMLDoc
- #pwiz_root — Constants
- #rakefile_path — ManageDBTool
- #recname — Bio::SPTR
- #ref_dump — Bio::SPTR
- #replace_references — GalaxyStager
- #representative_peptides — Protein
- #restore_references — GalaxyStager
- #run — Tool
- #run_batch — CommandRunner
- #run_local — CommandRunner
- #run_local — Constants
- #safely_get_drentry_for_key — Bio::SPTR
- #save — PepXMLWriter
- #save — ProtXMLWriter
- #search_databases — MzIdentMLDoc
- #seq_dump — Bio::SPTR
- #set_option — TandemSearchTool
- #signalp — Bio::SPTR
- #similarity — Bio::SPTR
- #source_files — MzIdentMLDoc
- #species_dump — Bio::SPTR
- #spectrum_as_hash — MzMLParser
- #spectrum_queries — MzIdentMLDoc
- #start_new_gene — GffToProteinDBTool
- #subunit — Bio::SPTR
- #supported_options — Tool
- #tandem_bin — Constants
- #tandem_keys_in_params_file — TandemSearchTool
- #tandem_root — Constants
- #taxon_from_taxonomy_file — TandemSearchTool
- #taxonomy_doc — TandemSearchTool
- #tissues — Bio::SPTR
- #to_bool — String
- #to_gff3_records — Peptide
- #tpp_root — Constants
- #type_from_base_name — PepXML
- #type_from_summary_attributes — PepXML
- #uniprot_link — Bio::SPTR
- #update_user_config — Constants
- #xtandem_modification_motif? — String