fraggler 2.0.1

Fragment Analysis package in python!

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 both a Python API and a command-line tool.

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Features

Peak Area Report Generation: Fraggler allows you to generate peak area reports for all input files. The package calculates peak areas based on specified parameters and generates a report summarizing the results.

Combined Peak Table Generation: Fraggler provides a command-line tool to generate a combined dataframe of peaks for all input files. This allows you to easily analyze and compare peaks across multiple files.

Customization Options: Fraggler offers various customization options to tailor the analysis to your specific needs. You can specify parameters such as ladder type, peak model, minimum ratio, minimum height, cutoff value, trace channel, peak height, and even provide a custom peaks file for specific assays and intervals.

Install

pip install fraggler

Dependencies

Fraggler depends on:

• pandas
• numpy
• scikit-learn
• networkx
• lmfit
• scipy
• biopython
• panel
• fire
• colorama
• altair

Python API

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

CLI

fraggler area and fraggler peak

Usage

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

• 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	min_ratio	which	peak_distance
prt1	140	150	2	0.2	FIRST	5

Example how how a file could look:

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.

Positional Arguments

The following positional arguments are required:

• IN_PATH: Type str. Specifies the input path.
• OUT_FOLDER: Type str. Specifies the output folder.
• LADDER: Type str. Specifies the ladder used in the experiment.

Flags

The following flags can be used with the fraggler peak or fraggler area command:

• -l, --ladder=LADDER: Type str. Specifies the ladder. Default value: 'LIZ'.
• --peak_model=PEAK_MODEL: Type str. Specifies the peak model. Default value: 'gauss'.
• --min_ratio=MIN_RATIO: Type float. Specifies the minimum ratio. Default value: 0.3.
• --min_height=MIN_HEIGHT: Type int. Specifies the minimum height. Default value: 100.
• --cutoff=CUTOFF: Type int. Specifies the cutoff value. Default value: 175.
• -t, --trace_channel=TRACE_CHANNEL: Type str. Specifies the trace channel. Default value: 'DATA9'.
• --peak_height=PEAK_HEIGHT: Type int. Specifies the peak height. Default value: 200.
• --custom_peaks=CUSTOM_PEAKS: Type Optional[str]. Specifies custom peaks. Default value: None.
• -e, --excel=EXCEL: Type: bool, Default: True

Typical usage

fraggler area IN_FOLDER OUT_FOLDER LIZ --min_ratio=0.2 

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

Contributions

Please check out How to contribute