InspectOutfile

class pyopenms.InspectOutfile

Bases: object

Cython implementation of _InspectOutfile

Original C++ documentation is available here

__init__()

Overload:

__init__(self) → None

This class serves to read in an Inspect outfile and write an idXML file

Overload:

__init__(self, in_0: InspectOutfile) → None

Methods

`__init__`	Overload:
`compressTrieDB`(self, database_filename, ...)	Generates a trie database from another one, using the wanted records only
`generateTrieDB`(self, ...)	Generates a trie database from a given one (the type of database is determined by getLabels)
`getACAndACType`(self, line, accession, ...)	Retrieve the accession type and accession number from a protein description line
`getExperiment`(self, exp, type_, in_filename)	Get the experiment from a file
`getLabels`(self, source_database_filename, ...)	Retrieve the labels of a given database (at the moment FASTA and Swissprot)
`getSearchEngineAndVersion`(self, cmd_output, ...)	Get the search engine and its version from the output of the InsPecT executable without parameters.
`getSequences`(self, database_filename, ...)	Retrieve sequences from a trie database
`getWantedRecords`(self, result_filename, ...)	Loads only results which exceeds a given p-value threshold
`load`(self, result_filename, ...)	Load the results of an Inspect search
`readOutHeader`(self, filename, header_line, ...)	Read the header of an inspect output file and retrieve various information

compressTrieDB(self, database_filename: Union[bytes, str, String], index_filename: Union[bytes, str, String], wanted_records: List[int], snd_database_filename: Union[bytes, str, String], snd_index_filename: Union[bytes, str, String], append: bool) → None: Generates a trie database from another one, using the wanted records only

generateTrieDB(self, source_database_filename: Union[bytes, str, String], database_filename: Union[bytes, str, String], index_filename: Union[bytes, str, String], append: bool, species: Union[bytes, str, String]) → None: Generates a trie database from a given one (the type of database is determined by getLabels)

getACAndACType(self, line: Union[bytes, str, String], accession: String, accession_type: String) → None: Retrieve the accession type and accession number from a protein description line

getExperiment(self, exp: MSExperiment, type_: String, in_filename: Union[bytes, str, String]) → None: Get the experiment from a file

getLabels(self, source_database_filename: Union[bytes, str, String], ac_label: String, sequence_start_label: String, sequence_end_label: String, comment_label: String, species_label: String) → None: Retrieve the labels of a given database (at the moment FASTA and Swissprot)

getSearchEngineAndVersion(self, cmd_output: Union[bytes, str, String], protein_identification: ProteinIdentification) → bool: Get the search engine and its version from the output of the InsPecT executable without parameters. Returns true on success, false otherwise

getSequences(self, database_filename: Union[bytes, str, String], wanted_records: Dict[int, int], sequences: List[bytes]) → List[int]: Retrieve sequences from a trie database

getWantedRecords(self, result_filename: Union[bytes, str, String], p_value_threshold: float) → List[int]

Loads only results which exceeds a given 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(self, result_filename: Union[bytes, str, String], peptide_identifications: List[PeptideIdentification], protein_identification: ProteinIdentification, p_value_threshold: float, database_filename: Union[bytes, str, String]) → List[int]

Load the results of an Inspect search

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
p_value_threshold –
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(self, filename: Union[bytes, str, String], header_line: Union[bytes, str, String], 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: int, number_of_columns: int) → None: Read the header of an inspect output file and retrieve various information