InspectOutfile

class pyopenms.InspectOutfile

Bases: object

Cython implementation of _InspectOutfile

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1InspectOutfile.html

__init__()

Cython signature: void InspectOutfile() This class serves to read in an Inspect outfile and write an idXML file
Cython signature: void InspectOutfile(InspectOutfile &)

Methods

`__init__`	Cython signature: void InspectOutfile()
`compressTrieDB`	Cython signature: void compressTrieDB(const String & database_filename, const String & index_filename, libcpp_vector[size_t] & wanted_records, const String & snd_database_filename, const String & snd_index_filename, bool append) Generates a trie database from another one, using the wanted records only
`generateTrieDB`	Cython signature: void generateTrieDB(const String & source_database_filename, const String & database_filename, const String & index_filename, bool append, const String species) Generates a trie database from a given one (the type of database is determined by getLabels)
`getACAndACType`	Cython signature: void getACAndACType(String line, String & accession, String & accession_type) Retrieve the accession type and accession number from a protein description line
`getExperiment`	Cython signature: void getExperiment(MSExperiment & exp, String & type_, const String & in_filename) Get the experiment from a file
`getLabels`	Cython signature: void getLabels(const String & source_database_filename, String & ac_label, String & sequence_start_label, String & sequence_end_label, String & comment_label, String & species_label) Retrieve the labels of a given database (at the moment FASTA and Swissprot)
`getSearchEngineAndVersion`	Cython signature: bool getSearchEngineAndVersion(const String & cmd_output, ProteinIdentification & protein_identification) Get the search engine and its version from the output of the InsPecT executable without parameters.
`getSequences`	Cython signature: libcpp_vector[size_t] getSequences(const String & database_filename, libcpp_map[size_t,size_t] & wanted_records, libcpp_vector[String] & sequences) Retrieve sequences from a trie database
`getWantedRecords`	Cython signature: libcpp_vector[size_t] getWantedRecords(const String & result_filename, double p_value_threshold)
`load`	Cython signature: libcpp_vector[size_t] load(const String & result_filename, libcpp_vector[PeptideIdentification] & peptide_identifications, ProteinIdentification & protein_identification, double p_value_threshold, const String & database_filename)
`readOutHeader`	Cython signature: void readOutHeader(const String & filename, const String & header_line, int & spectrum_file_column, int & scan_column, int & peptide_column, int & protein_column, int & charge_column, int & MQ_score_column, int & p_value_column, int & record_number_column, int & DB_file_pos_column, int & spec_file_pos_column, size_t & number_of_columns) Read the header of an inspect output file and retrieve various information

compressTrieDB(): Cython signature: void compressTrieDB(const String & database_filename, const String & index_filename, libcpp_vector[size_t] & wanted_records, const String & snd_database_filename, const String & snd_index_filename, bool append) Generates a trie database from another one, using the wanted records only

generateTrieDB(): Cython signature: void generateTrieDB(const String & source_database_filename, const String & database_filename, const String & index_filename, bool append, const String species) Generates a trie database from a given one (the type of database is determined by getLabels)

getACAndACType(): Cython signature: void getACAndACType(String line, String & accession, String & accession_type) Retrieve the accession type and accession number from a protein description line

getExperiment(): Cython signature: void getExperiment(MSExperiment & exp, String & type_, const String & in_filename) Get the experiment from a file

getLabels(): Cython signature: void getLabels(const String & source_database_filename, String & ac_label, String & sequence_start_label, String & sequence_end_label, String & comment_label, String & species_label) Retrieve the labels of a given database (at the moment FASTA and Swissprot)

getSearchEngineAndVersion(): Cython signature: bool getSearchEngineAndVersion(const String & cmd_output, ProteinIdentification & protein_identification) Get the search engine and its version from the output of the InsPecT executable without parameters. Returns true on success, false otherwise

getSequences(): Cython signature: libcpp_vector[size_t] getSequences(const String & database_filename, libcpp_map[size_t,size_t] & wanted_records, libcpp_vector[String] & sequences) Retrieve sequences from a trie database

getWantedRecords()

Cython signature: libcpp_vector[size_t] getWantedRecords(const String & result_filename, double p_value_threshold)

Parameters

result_filename – The filename of the results file
p_value_threshold – Only identifications exceeding this threshold are read

Raises

Exception: FileNotFound is thrown if the given file could not be found

Raises

Exception: FileEmpty is thrown if the given file is empty

load()

Cython signature: libcpp_vector[size_t] load(const String & result_filename, libcpp_vector[PeptideIdentification] & peptide_identifications, ProteinIdentification & protein_identification, double p_value_threshold, const String & database_filename)

Parameters

result_filename – Input parameter which is the file name of the input file
peptide_identifications – Output parameter which holds the peptide identifications from the given file
protein_identification – Output parameter which holds the protein identifications from the given file

:param p_value_threshold :param database_filename :raises:

Exception: FileNotFound is thrown if the given file could not be found

Raises: Exception: ParseError is thrown if the given file could not be parsed
Raises: Exception: FileEmpty is thrown if the given file is empty

readOutHeader(): Cython signature: void readOutHeader(const String & filename, const String & header_line, int & spectrum_file_column, int & scan_column, int & peptide_column, int & protein_column, int & charge_column, int & MQ_score_column, int & p_value_column, int & record_number_column, int & DB_file_pos_column, int & spec_file_pos_column, size_t & number_of_columns) Read the header of an inspect output file and retrieve various information