Description

Fraggler is for fragment analysis in Python! Fraggler is a Python package that provides functionality for analyzing and generating reports for fsa files. It offers a Python API, command-line tool, and GUI interface.

Install

bash pip install fraggler

Dependencies

Fraggler depends on:

• pandas
• scikit-learn
• lmfit
• scipy
• biopython
• panel
• altair
• PySide6

Python API

To get an overview how the library can be used in a python environment, please look at the tutorial.ipynb.

CLI

Usage

To generate peak area reports and a peak table for all input files, use the fraggler -t area or fraggler -t peak command followed by the required arguments and any optional flags.

```bash usage: fraggler [-h] -t {area,peak} -f FSA -o OUTPUT -l {LIZ,ROX,ORANGE,ROX500} -sc SAMPLE_CHANNEL [-mindist MINDISTANCEBETWEENPEAKS] [-minsheight MINSIZESTANDARD_HEIGHT] [-cp CUSTOM_PEAKS] [-heightsample PEAKHEIGHTSAMPLEDATA] [-minratio MINRATIOTOALLOW_PEAK] [-distance DISTANCEBETWEENASSAYS] [-peakstart SEARCHPEAKS_START] [-m {gauss,voigt,lorentzian}]

Analyze your Fragment analysis files!

options: -h, --help show this help message and exit -t {area,peak}, --type {area,peak} Fraggler area or fraggler peak -f FSA, --fsa FSA fsa file to analyze -o OUTPUT, --output OUTPUT Output folder -l {LIZ,ROX,ORANGE,ROX500}, --ladder {LIZ,ROX,ORANGE,ROX500,LIZ500} Which ladder to use -sc SAMPLECHANNEL, --samplechannel SAMPLECHANNEL Which sample channel to use. E.g: 'DATA1', 'DATA2'... -mindist MINDISTANCEBETWEENPEAKS, --mindistancebetweenpeaks MINDISTANCEBETWEENPEAKS Minimum distance between size standard peaks -minsheight MINSIZESTANDARDHEIGHT, --minsizestandardheight MINSIZESTANDARDHEIGHT Minimun height of size standard peaks -cp CUSTOMPEAKS, --custompeaks CUSTOMPEAKS csv file with custom peaks to find -heightsample PEAKHEIGHTSAMPLEDATA, --peakheightsampledata PEAKHEIGHTSAMPLEDATA Minimum height of peaks in sample data -minratio MINRATIOTOALLOWPEAK, --minratiotoallowpeak MINRATIOTOALLOWPEAK Minimum ratio of the lowest peak compared to the heighest peak in the assay -distance DISTANCEBETWEENASSAYS, --distancebetweenassays DISTANCEBETWEENASSAYS Minimum distance between assays in a multiple assay experiment -peakstart SEARCHPEAKSSTART, --searchpeaksstart SEARCHPEAKSSTART Where to start searching for peaks in basepairs -m {gauss,voigt,lorentzian}, --peakareamodel {gauss,voigt,lorentzian} Which peak finding model to use ```

Example of CLI command:

bash fraggler -t area -f demo/ -o testing_fraggler -l LIZ -sc DATA1

Peak finding

• If not specified, fraggler finds peaks agnostic in the fsa file. To specifiy custom assays with certain peaks and intervals, the user can add a .csv file to the --custom_peaks argument. The csv file MUST have the following shape:

| name | start | stop | amount | minratio | which | peakdistance | | ---- | ----- | ---- | ------ | --------- | ----- | ------------- | | prt1 | 140 | 150 | 2 | 0.2 | FIRST | 5 |

Example how how a file could look:

txt name,start,stop,amount,min_ratio,which,peak_distance prt1,135,155,2,0.2,FIRST, prt3,190,205,,0.2,FIRST, prt2,222,236,2,0.2,FIRST,5 prt4,262,290,5,,,

• name: Name of the assay
• start: Start of the assay in basepairs
• stop: Stop of the assay in basepairs
• amount: Optional. Amount of peaks in assay. If left empty every peak in the interval is included.
• min_ratio: Optional. Only peaks with the a ratio of the min_ratio of the highest peak is included, e.g. if min_ratio == .02, only peaks with a height of 20 is included, if the highest peak is 100 units
• which: LARGEST | FIRST. Can be left empty. Which peak should be included if there are more peaks than the amount. if FIRST is set, then the two first peaks are chosen. If LARGEST are set, then the two largests peaks in the area are chosen. Defaults to LARGEST
• peak_distance: Optional. Distance between peaks must be under this value.

GUI Integration

The GUI for Fraggler offers an accessible way to analyze FSA files without needing to interact with the command line directly. It allows users to upload files, set parameters, and generate analysis reports visually. The GUI is built using PyQt and offers a sidebar navigation for file browsing, options for report generation, and an output view for results.

Running the GUI

To run the Fraggler GUI after installing the package, use the following command:

bash fraggler-gui

GUI Features

• File Explorer: Navigate and select FSA files for analysis.
• Parameter Setup: Choose analysis type, set peak detection parameters, and specify custom peaks.
• Report Generation: Display and export detailed reports in HTML format, including peak area and peak tables.

Documentation

Click here to get full documentation of API.

Output

One example of the report generated from fraggler area can be seen here: Example report

Citation

If you use fraggler, please cite the paper!

Contributions

Please check out How to contribute