API¶

Python wrapper around the ThermoRawFileParser command line interface.

class pyrawr.ThermoRawFileParser(executable='thermorawfileparser', docker_image=None)¶

Wrapper around ThermoRawFileParser CLI.

Parameters

executable (str) – ThermoRawFileParser shell command. For example, thermorawfileparser or mono ThermoRawFileParser.exe.
docker_image (str, optional) – Docker image with ThermoRawFileParser. Requires the docker run CLI command.

version_requirement¶

ThermoRawFile semver version requirement.

Type: str

installed_version¶

Installed ThermoRawFileParser version.

Type: str

Examples

>>> from pyrawr import ThermoRawFileParser
>>> trfp = ThermoRawFileParser(
...     executable="thermorawfileparser",
...     docker_image="quay.io/biocontainers/thermorawfileparser:1.3.3--ha8f3691_1"
... )
>>> trfp.parse("OR4_110719_OB_PAR14_sSCX_fr10.raw")

>>> trfp.metadata("OR4_110719_OB_PAR14_sSCX_fr10.raw")
{'FileProperties': [{'accession': 'NCIT:C47922', 'cvLabel': 'NCIT' ... }]}

>>> trfp.query("OR4_110719_OB_PAR14_sSCX_fr10.raw", "508,680")
[{'mzs': [204.8467254638672,
262.4529113769531,
309.53961181640625,
...

>>> trfp.xic(
...     "OR4_110719_OB_PAR14_sSCX_fr10.raw",
...     [{"mz":488.5384, "tolerance":10, "tolerance_unit":"ppm"}],
... )
{'OutputMeta': {'base64': False, 'timeunit': 'minutes'},
'Content': [{'Meta': {'MzStart': 488.53351461600005,
    'MzEnd': 488.543285384,
    'RtStart': 0.007536666666666666,
    'RtEnd': 179.99577166666666},
'RetentionTimes': [0.007536666666666666,
    0.022771666666666666,
    0.036936666666666666,
    ...

parse(input_file, output_format=None, options=None)¶

Parse raw file to one of the supported output formats.

Parameters

input_file (str) – Path to input file.
output_format (str, optional) – Output format. One of mgf, mzml, indexed_mzml, parquet, or scan_info.
options (List) – List of other CLI options to pass to ThermoRawFileParser. See ThermoRawFileParser docs for more info.

metadata(input_file)¶

Get raw file metadata as Python dictionary.

Parameters: input_file (str) – Path to input file.
Returns: metadata – Dictionary containing raw file metadata.
Return type: dict

query(input_file, scans, options=None)¶

Retrieve specific spectra by scan number in ProXI format.

Parameters

input_file (str) – Path to input file.
scans (str) – Scan numbers, e.g. 1-5, 20, 25-30.
options (list) – List of other CLI options to pass to ThermoRawFileParser. See ThermoRawFileParser docs for more info.

Returns

spectra – List of spectra in ProXI format.

Return type

list

xic(input_file, query, base64=False)¶

Retrieve one or more chromatograms based on a query.

Parameters

input_file (str) – Path to input file.
query (list) – List of query dictionaries. See ThermoRawFileParser docs for more info.
base64 (boolean, optional) – Encode the content of the xic vectors as base 64.

Returns

xic – Dictionary containing XICs.

Return type

dict

exception pyrawr.ThermoRawFileParserError¶: General ThermoRawFileParser error.

exception pyrawr.ThermoRawFileParserInstallationError¶: Could not find ThermoRawFileParser CLI.

exception pyrawr.ThermoRawFileParserRunError¶: Error running ThermoRawFileParser.