fraggler: A FreeBASIC repository from csoneson

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.

Install

pip install fraggler

Dependencies

Fraggler depends on:

pandas
numpy
scikit-learn
lmfit
scipy
biopython
panel
altair

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.

usage: fraggler [-h] -t {area,peak} -f FSA -o OUTPUT -l {LIZ,ROX,ORANGE,ROX500} -sc SAMPLE_CHANNEL
                 [-min_dist MIN_DISTANCE_BETWEEN_PEAKS] [-min_s_height MIN_SIZE_STANDARD_HEIGHT]
                 [-cp CUSTOM_PEAKS] [-height_sample PEAK_HEIGHT_SAMPLE_DATA]
                 [-min_ratio MIN_RATIO_TO_ALLOW_PEAK] [-distance DISTANCE_BETWEEN_ASSAYS]
                 [-peak_start SEARCH_PEAKS_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}
                        Which ladder to use
  -sc SAMPLE_CHANNEL, --sample_channel SAMPLE_CHANNEL
                        Which sample channel to use. E.g: 'DATA1', 'DATA2'...
  -min_dist MIN_DISTANCE_BETWEEN_PEAKS, --min_distance_between_peaks MIN_DISTANCE_BETWEEN_PEAKS
                        Minimum distance between size standard peaks
  -min_s_height MIN_SIZE_STANDARD_HEIGHT, --min_size_standard_height MIN_SIZE_STANDARD_HEIGHT
                        Minimun height of size standard peaks
  -cp CUSTOM_PEAKS, --custom_peaks CUSTOM_PEAKS
                        csv file with custom peaks to find
  -height_sample PEAK_HEIGHT_SAMPLE_DATA, --peak_height_sample_data PEAK_HEIGHT_SAMPLE_DATA
                        Minimum height of peaks in sample data
  -min_ratio MIN_RATIO_TO_ALLOW_PEAK, --min_ratio_to_allow_peak MIN_RATIO_TO_ALLOW_PEAK
                        Minimum ratio of the lowest peak compared to the heighest peak in the assay
  -distance DISTANCE_BETWEEN_ASSAYS, --distance_between_assays DISTANCE_BETWEEN_ASSAYS
                        Minimum distance between assays in a multiple assay experiment
  -peak_start SEARCH_PEAKS_START, --search_peaks_start SEARCH_PEAKS_START
                        Where to start searching for peaks in basepairs
  -m {gauss,voigt,lorentzian}, --peak_area_model {gauss,voigt,lorentzian}
                        Which peak finding model to use

Example of CLI command:

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	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.

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

csoneson/fraggler