Python script to plot fragment sizes from two csv files (minIon and fragmentanalyzer).
git clone https://github.com/elhb/fragplot.git
cd fragplot
python setup.py install
usage: fragplot [-h] [-csv <file>] [-fq <file>] [-fcsv <file>] -o <file>
[-s <int>] [-e <int>] [-b <int>]
NOTE:
You must supply either one "--minion_csv" or one "--minion_fq" as well as a "--out_file" for the program to work!
ALSO:
Only the sequences in the fastq that has the term "Basecall_2D_2d" in the header will be used.
optional arguments:
-h, --help show this help message and exit
-csv <file>, --minion_csv <file>
minion csv filename
-fq <file>, --minion_fq <file>
minion fastq filename
-fcsv <file>, --fragge_csv <file>
fragmentanalyzer csv
-o <file>, --out_file <file>
output .pdf or .png filename
-s <int>, --range_start <int>
start of the range to plot in the pdf
-e <int>, --range_end <int>
end of the range to plot in the pdf
-b <int>, --bin_size <int>
size in base pairs for the bins in the minion
histograms, each point in the line represents the
middle point of the bin, ie if bin size is 10 (the
default value) the frequenzy off all reads with length
0-10 vill be plotted as y-value for x=5, likewise if
bin_size is 100, freq of reads with lengths 0-100bp
will get x=50.
fragplot --minion_csv example_data/minion.csv --fragge_csv=example_data/electropherogram.csv -o example_data/example_output_2.png -s 100 -e 10000