libgunshotmatch.datafile

Represents a parsed datafile.

Classes:

Datafile(name, original_filename, …[, …])	Represents a single datafile in a project.
FileType(value)	Represents the input datafile types supported by PyMassSpec.
GCMSDataInfo(rt_range, time_step, …)	Represents information about a GCMS_data object returned by get_info_from_gcms_data().
Repeat(datafile, peaks[, qualified_peaks, …])	Represents a repeat sample in a project, constructed from a datafile.

Functions:

get_info_from_gcms_data(gcms_data)

Returns a information about the data in a pyms.GCMS.Class.GCMS_data object.

class Datafile(name, original_filename, original_filetype, description='', intensity_matrix=None, user=getpass.getuser(), device=socket.gethostname(), date_created=datetime.datetime.now(), date_modified=datetime.datetime.now(), version=1)

Represents a single datafile in a project.

Parameters

• name (str) – The name of the Datafile.

• original_filename (str) – The filename of the file the Datafile was created from.

• original_filetype (int) – The filetype of the file the Datafile was created from.

• description (str) – A description of the Datafile. Default ''.

• intensity_matrix (Optional[IntensityMatrix]) – PyMassSpec IntensityMatrix object. Default None.

• user (str) – The user who created the Repeat. Default taken from the currently logged-in us.

• device (str) – The device that created the Repeat. Default taken from the current device’s hostname.

• date_created (datetime) – The date and time the Repeat was created. Default is the current date and time.

• date_modified (datetime) – The date and time the Repeat was last modified. Default is the current date and time.

• version (int) – File format version . Default 1.

Attributes:

date_created	The date and time the Datafile was created.
date_modified	The date and time the Datafile was last modified.
description	A description of the Datafile.
device	The device that created the Datafile.
intensity_matrix	PyMassSpec IntensityMatrix object.
name	The name of the Datafile.
original_filename	The filename of the file the Datafile was created from.
original_filetype	The filetype of the file the Datafile was created from.
user	The user who created the Datafile.
version	File format version

Methods:

export(output_dir)	Export as a .gsmd file and return the output filename.
from_dict(d)	Construct a Datafile from a dictionary.
from_file(filename)	Parse a gsmd file.
load_gcms_data([filename])	Load GC-MS data from the datafile.
new(name, filename)	Construct a new Datafile from a file.
prepare_intensity_matrix(gcms_data[, …])	Build an IntensityMatrix for the datafile.
to_dict()	Returns a dictionary representation of this Datafile.

date_created

Type:    datetime

The date and time the Datafile was created.

date_modified

Type:    datetime

The date and time the Datafile was last modified.

description

Type:    str

A description of the Datafile.

device

Type:    str

The device that created the Datafile.

export(output_dir)

Export as a .gsmd file and return the output filename.

Parameters

output_dir (Union[str, Path, PathLike])

Return type

str

classmethod from_dict(d)

Construct a Datafile from a dictionary.

Parameters

d (Mapping[str, Any])

Return type

Datafile

classmethod from_file(filename)

Parse a gsmd file.

Parameters

filename (Union[str, Path, PathLike]) – The input filename.

Return type

Datafile

intensity_matrix

Type:    Optional[IntensityMatrix]

PyMassSpec IntensityMatrix object.

load_gcms_data(filename=None)

Load GC-MS data from the datafile.

Parameters

filename (Union[str, Path, PathLike, None]) – Alternative filename to load the data from. Useful if the file has moved since the Datafile was created. Default None.

Changed in version 0.4.0: Added the filename attribute.

Return type

GCMS_data

name

Type:    str

The name of the Datafile.

classmethod new(name, filename)

Construct a new Datafile from a file.

Parameters

• name (str) – The name of the Datafile

• filename (Union[str, Path, PathLike])

Return type

Datafile

original_filename

Type:    str

The filename of the file the Datafile was created from.

original_filetype

Type:    FileType

The filetype of the file the Datafile was created from.

prepare_intensity_matrix(gcms_data, savitzky_golay=True, tophat=True, tophat_structure_size='1.5m', crop_mass_range=None)

Build an IntensityMatrix for the datafile.

Parameters

• gcms_data (GCMS_data)

• savitzky_golay (Union[bool, SavitzkyGolayMethod]) – Whether to perform Savitzky-Golay smoothing. Default True.

• tophat (bool) – Whether to perform Tophat baseline correction. Default True.

• tophat_structure_size (str) – The structure size for Tophat baseline correction. Default '1.5m'.

• crop_mass_range (Optional[Tuple[float, float]]) – The range of masses to which the GC-MS data should be limited to. Default None.

Return type

IntensityMatrix

to_dict()

Returns a dictionary representation of this Datafile.

All keys are native, JSON-serializable, Python objects.

Return type

Dict[str, Any]

user

Type:    str

The user who created the Datafile.

version

Type:    int

File format version

enum FileType(value)

Bases: enum_tools.custom_enums.IntEnum

Represents the input datafile types supported by PyMassSpec.

Member Type

int

Valid values are as follows:

JDX = <FileType.JDX: 0>

MZML = <FileType.MZML: 1>

ANDI = <FileType.ANDI: 2>

namedtuple GCMSDataInfo(rt_range, time_step, time_step_stdev, n_scans, mz_range, num_mz_mean, num_mz_median)

Bases: NamedTuple

Represents information about a GCMS_data object returned by get_info_from_gcms_data().

Fields

0.  rt_range (Tuple[float, float]) – The minimum and maximum retention times.

1.  time_step (float) – The average time step between scans.

2.  time_step_stdev (float) – The standard deviation of the time steps between scans.

3.  n_scans (int) – The total number of scans.

4.  mz_range (Tuple[float, float]) – The minimum and maximum mass (m/z) values.

5.  num_mz_mean (float) – The mean average number of masses per scan.

6.  num_mz_median (float) – The median number of masses per scan.

class Repeat(datafile, peaks, qualified_peaks=None, user=getpass.getuser(), device=socket.gethostname(), date_created=datetime.datetime.now(), date_modified=datetime.datetime.now(), version=1)

Represents a repeat sample in a project, constructed from a datafile.

Parameters

• datafile (Datafile) – The Datafile for this repeat.

• peaks (List[Peak])

• qualified_peaks (Optional[List[QualifiedPeak]]) – Peaks containing identities from library search. This is usually populated after peak alignment. Default None.

• user (str) – The user who created the Repeat. Default taken from the currently logged-in user.

• device (str) – The device that created the Repeat. Default taken from the current device’s hostname.

• date_created (datetime) – The date and time the Repeat was created. Default is the current date and time.

• date_modified (datetime) – The date and time the Repeat was last modified. Default is the current date and time.

• version (int) – File format version . Default 1.

Attributes:

datafile	The Datafile for this repeat.
date_created	The date and time the Repeat was created.
date_modified	The date and time the Repeat was last modified.
device	The device that created the Repeat.
name	The name of the Datafile.
peaks
qualified_peaks	Peaks containing identities from library search.
user	The user who created the Repeat.
version	File format version

Methods:

export(output_dir)	Export as a .gsmr file and return the output filename.
from_dict(d)	Construct a Repeat from a dictionary.
from_file(filename)	Parse a gsmr file.
to_dict()	Returns a dictionary representation of this Repeat.

datafile

Type:    Datafile

The Datafile for this repeat.

date_created

Type:    datetime

The date and time the Repeat was created.

date_modified

Type:    datetime

The date and time the Repeat was last modified.

device

Type:    str

The device that created the Repeat.

export(output_dir)

Export as a .gsmr file and return the output filename.

New in version 0.4.0.

Parameters

output_dir (Union[str, Path, PathLike])

Return type

str

classmethod from_dict(d)

Construct a Repeat from a dictionary.

Parameters

d (Mapping[str, Any])

Return type

Repeat

classmethod from_file(filename)

Parse a gsmr file.

Parameters

filename (Union[str, Path, PathLike]) – The input filename.

Return type

Repeat

New in version 0.4.0.

property name

The name of the Datafile.

Return type

str

New in version 0.4.0.

peaks

Type:    PeakList

qualified_peaks

Type:    Optional[List[QualifiedPeak]]

Peaks containing identities from library search. This is usually populated after peak alignment.

to_dict()

Returns a dictionary representation of this Repeat.

All keys are native, JSON-serializable, Python objects.

Return type

Dict[str, Any]

user

Type:    str

The user who created the Repeat.

version

Type:    int

File format version

get_info_from_gcms_data(gcms_data)

Returns a information about the data in a pyms.GCMS.Class.GCMS_data object.

Parameters

gcms_data (GCMS_data)

Return type

GCMSDataInfo