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
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: bytes | str | String, index_filename: bytes | str | String, wanted_records: List[int], snd_database_filename: bytes | str | String, snd_index_filename: bytes | str | String, append: bool) None #
Generates a trie database from another one, using the wanted records only
- generateTrieDB(self, source_database_filename: bytes | str | String, database_filename: bytes | str | String, index_filename: bytes | str | String, append: bool, species: bytes | str | String) None #
Generates a trie database from a given one (the type of database is determined by getLabels)
- getACAndACType(self, line: 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: bytes | str | String) None #
Get the experiment from a file
- getLabels(self, source_database_filename: 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: 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: bytes | str | String, wanted_records: Dict[int, int], sequences: List[bytes]) List[int] #
Retrieve sequences from a trie database
- getWantedRecords(self, result_filename: 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: bytes | str | String, peptide_identifications: List[PeptideIdentification], protein_identification: ProteinIdentification, p_value_threshold: float, database_filename: 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: bytes | str | String, header_line: 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