gunshotmatch-reports

PDF Report Generation for GunShotMatch.

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Installation

python3 -m pip install gunshotmatch-reports --user

python3 -m pip install git+https://github.com/GunShotMatch/gunshotmatch-reports@master --user

Contents

`gunshotmatch_reports.alignment`

CSV reports of alignment between reference projects and unknown samples.

New in version 0.5.0.

Classes:

CSVRow([peak_no, name, rt, area, …])

Represents data for a peak in a CSV report.

Functions:

`csv_two_projects`(p1, padded_p1_cp, p2, …)	Returns CSV report for the alignment between the given projects.
`csv_two_projects_and_unknown`(p1, …[, …])	Returns CSV report for the alignment between the given projects and unknown.
`get_csv_data`(project, cp, max_area)	Return data for the CSV report for given peak in the given project.

namedtuple CSVRow(peak_no='', name='', rt='', area='', area_percentage='', match_factor='')[source]

Bases: NamedTuple

Represents data for a peak in a CSV report.

Fields

peak_no (str) – Alias for field number 0
name (str) – Alias for field number 1
rt (str) – Alias for field number 2
area (str) – Alias for field number 3
area_percentage (str) – Alias for field number 4
match_factor (str) – Alias for field number 5

__repr__(): Return a nicely formatted representation string

classmethod header()[source]

Returns the CSV column headers.

Return type: Tuple[str, str, str, str, str, str]

csv_two_projects(p1, padded_p1_cp, p2, padded_p2_cp)[source]

Returns CSV report for the alignment between the given projects.

Parameters

p1 (Project) – The first project.
padded_p1_cp (MutableSequence[Optional[ConsolidatedPeak]]) – Padded consolidated peak list for the first project.
p2 (Project) – The second project.
padded_p2_cp (MutableSequence[Optional[ConsolidatedPeak]]) – Padded consolidated peak list for the second project.

Return type

str

csv_two_projects_and_unknown(p1, padded_p1_cp, p2, padded_p2_cp, u, padded_u_cp, *, pair_only=False)[source]

Returns CSV report for the alignment between the given projects and unknown.

Parameters

p1 (Project) – The first project.
padded_p1_cp (MutableSequence[Optional[ConsolidatedPeak]]) – Padded consolidated peak list for the first project.
p2 (Project) – The second project.
padded_p2_cp (MutableSequence[Optional[ConsolidatedPeak]]) – Padded consolidated peak list for the second project.
u (Project) – The unknown sample.
padded_u_cp (MutableSequence[Optional[ConsolidatedPeak]]) – Padded consolidated peak list for the unknown sample.
pair_only (bool) – Only show peaks in common between two or more of the projects/unknown. Default False.

Return type

str

get_csv_data(project, cp, max_area)[source]

Return data for the CSV report for given peak in the given project.

Parameters

project (Project)
cp (Optional[ConsolidatedPeak])
max_area (float) – The maximum peak area in the project.

Return type

CSVRow

`gunshotmatch_reports.chromatogram`

PDF Chromatogram Generator.

Functions:

build_chromatogram_report(project[, …])

Construct a chromatogram report for the given project and write to the chosen file.

build_chromatogram_report(project, pdf_filename=None)[source]

Construct a chromatogram report for the given project and write to the chosen file.

Parameters

project (Project)
pdf_filename (Union[str, Path, PathLike, None]) – Optional output filename. Defaults to project_name_chromatogram.pdf.

Return type

str

`gunshotmatch_reports.peaks`

Peak Report Generator.

Classes:

`CSVReports`(project)	Class for producing CSV peak reports.
`PeakMetadataTable`(project)	Helper class for peak metadata for insertion into a PDF or CSV report.
`PeakSummary`(peak_no, name, rt, area, …)	Summary data for a `ConsolidatedPeak`.

Functions:

build_peak_report(project[, pdf_filename, …])

Construct a peak report for the given project and write to the chosen file.

class CSVReports(project)[source]

Bases: object

Class for producing CSV peak reports.

Parameters: project (Project) – A GunShotMatch project.

New in version 0.4.0.

Methods:

`overview_csv`()	Produce an overview report of the peaks, giving the name, retention time and peak area of the peaks.
`summary_csv`()	Produce a summary report of the peaks, giving the individual retention times and hits.

overview_csv()[source]

Produce an overview report of the peaks, giving the name, retention time and peak area of the peaks.

The output columns are as follows:

Peak No.
Name – The name of the top hit
Rt – Mean retention time
Area – Mean peak area
Area % – Mean peak area as a percentage of the largest peak
MF – Mean match factor for the top hit
Rejected – Whether the peak has been rejected (e.g. with PeakViewer)

The peaks are sorted from largest to smallest.

Return type: str

summary_csv()[source]

Produce a summary report of the peaks, giving the individual retention times and hits.

The table for each peak mirrors the table in the PDF peak report (build_peak_report()). The peaks are sorted from largest to smallest.

Return type: str

class PeakMetadataTable(project)[source]

Bases: object

Helper class for peak metadata for insertion into a PDF or CSV report.

Parameters: project (Project) – A GunShotMatch project.

New in version 0.3.0.

Attributes:

`area_percentages`	Peak areas as percentage of largest peak
`max_peak_number`	The total number of peaks in the project.
`num_rows`	Maximum number of rows for the metadata table.
`project`	A GunShotMatch project.

Methods:

`get_summary_for_peak`(peak, peak_number)	Return a formatted summary of the peak.
`get_table_for_peak`(peak, peak_number)	Return tabulated data on the peak, with individual peak areas, retention times, and the top 5 hits.

area_percentages: Peak areas as percentage of largest peak

get_summary_for_peak(peak, peak_number)[source]

Return a formatted summary of the peak.

Parameters

peak (ConsolidatedPeak)
peak_number (int) – The peak number, 1-indexed.

Return type

PeakSummary

get_table_for_peak(peak, peak_number)[source]

Return tabulated data on the peak, with individual peak areas, retention times, and the top 5 hits.

Parameters

peak (ConsolidatedPeak)
peak_number (int) – The peak number, 1-indexed.

Return type

List[Tuple[str, str, str, str, str, str, str, str, str]]

max_peak_number: The total number of peaks in the project.

num_rows: Maximum number of rows for the metadata table.

project: A GunShotMatch project.

namedtuple PeakSummary(peak_no, name, rt, area, area_percentage, mf, rejected)[source]

Bases: NamedTuple

Summary data for a ConsolidatedPeak.

Formatted for insertion into a PDF or CSV peak report.

New in version 0.3.0.

Fields

peak_no (str) – Peak number, 1-indexed
name (str) – The name of the top hit
rt (str) – Mean retention time
area (str) – Mean peak area
area_percentage (str) – Mean peak area as a percentage of the largest peak
mf (str) – Mean match factor for the top hit
rejected (str) – Whether the peak has been rejected (e.g. with PeakViewer)

__repr__(): Return a nicely formatted representation string

build_peak_report(project, pdf_filename=None, *, title_every_page=False)[source]

Construct a peak report for the given project and write to the chosen file.

Parameters

project (Project)
pdf_filename (Union[str, Path, PathLike, None]) – Optional output filename. Defaults to project_name_peak_report.pdf.

Return type

str

Returns

The output filename.

`gunshotmatch_reports.utils`

Utility functions.

Functions:

`extend_list`(l, fillvalue, length)	Extend list to the given length with fillvalue.
`figure_to_drawing`(figure)	Convert a matplotlib figure to a reportlab drawing.
`save_pdf`(fig, filename)	Save a PDF without a creation date.
`save_svg`(fig, filename)	Save an SVG with fixed hashsalt and without a creation date.
`scale`(drawing, scale)	Scale reportlab.graphics.shapes.Drawing() object while maintaining aspect ratio.

extend_list(l, fillvalue, length)[source]

Extend list to the given length with fillvalue.

Parameters

l (List[~_T])
fillvalue (~_T)
length (int)

Return type

List[~_T]

figure_to_drawing(figure)[source]

Convert a matplotlib figure to a reportlab drawing.

Parameters: figure (Figure)
Return type: Drawing

save_pdf(fig, filename)[source]

Save a PDF without a creation date.

Parameters

fig (Figure)
filename (Union[str, Path, PathLike])

New in version 0.6.0.

save_svg(fig, filename)[source]

Save an SVG with fixed hashsalt and without a creation date.

Parameters

fig (Figure)
filename (Union[str, Path, PathLike])

New in version 0.6.0.

scale(drawing, scale)[source]

Scale reportlab.graphics.shapes.Drawing() object while maintaining aspect ratio.

Parameters

drawing (Drawing)
scale (float)

Return type

Drawing

Contributing

gunshotmatch-reports uses tox to automate testing and packaging, and pre-commit to maintain code quality.

Install pre-commit with pip and install the git hook:

python -m pip install pre-commit
pre-commit install

Coding style

formate is used for code formatting.

It can be run manually via pre-commit:

pre-commit run formate -a

Or, to run the complete autoformatting suite:

pre-commit run -a

Automated tests

Tests are run with tox and pytest. To run tests for a specific Python version, such as Python 3.6:

tox -e py36

To run tests for all Python versions, simply run:

tox

Type Annotations

Type annotations are checked using mypy. Run mypy using tox:

tox -e mypy

Build documentation locally

The documentation is powered by Sphinx. A local copy of the documentation can be built with tox:

tox -e docs

Downloading source code

The gunshotmatch-reports source code is available on GitHub, and can be accessed from the following URL: https://github.com/GunShotMatch/gunshotmatch-reports

If you have git installed, you can clone the repository with the following command:

git clone https://github.com/GunShotMatch/gunshotmatch-reports

Cloning into 'gunshotmatch-reports'...
remote: Enumerating objects: 47, done.
remote: Counting objects: 100% (47/47), done.
remote: Compressing objects: 100% (41/41), done.
remote: Total 173 (delta 16), reused 17 (delta 6), pack-reused 126
Receiving objects: 100% (173/173), 126.56 KiB | 678.00 KiB/s, done.
Resolving deltas: 100% (66/66), done.

Alternatively, the code can be downloaded in a ‘zip’ file by clicking:

Clone or download –> Download Zip

Downloading a ‘zip’ file of the source code

Building from source

The recommended way to build gunshotmatch-reports is to use tox:

tox -e build

The source and wheel distributions will be in the directory dist.

If you wish, you may also use pep517.build or another PEP 517-compatible build tool.

License

gunshotmatch-reports is licensed under the MIT License

A short and simple permissive license with conditions only requiring preservation of copyright and license notices. Licensed works, modifications, and larger works may be distributed under different terms and without source code.

Permissions	Conditions	Limitations
Commercial use Modification Distribution Private use	License and copyright notice	Liability Warranty

See more information on choosealicense.com ➩

Copyright (c) 2024 Dominic Davis-Foster

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE
OR OTHER DEALINGS IN THE SOFTWARE.

View the Function Index or browse the Source Code.

Browse the GitHub Repository

gunshotmatch-reports

Installation

Contents

gunshotmatch_reports.alignment

gunshotmatch_reports.chromatogram

gunshotmatch_reports.peaks

gunshotmatch_reports.utils

Contributing

Coding style

Automated tests

Type Annotations

Build documentation locally

Downloading source code

Building from source

License

`gunshotmatch_reports.alignment`

`gunshotmatch_reports.chromatogram`

`gunshotmatch_reports.peaks`

`gunshotmatch_reports.utils`