Small script to quickly plot the spatial distribution of raw data from fastq files.
pip install -r requirements.txt
python setup.py build
python setup.py install
plotRawDataDistribution.py \
--barcode-file LP_Lot_number_x.txt \
--reads-file R1.fastq.gz \
--img-file raw_data_dist.pdf
$ plotRawDataDistribution.py --help
usage: plotRawDataDistribution.py [-h] -r <file> -b <file> -i <file>
[-s <int>] [-p <int>] [-c <str>] [-v]
optional arguments:
-h, --help show this help message and exit
-r <file>, --reads-file <file>
barcode reads file/fwd read/first read/read one (must
be gzipped fastq format)
-b <file>, --barcode-file <file>
ID file with barcodes and positions
-i <file>, --img-file <file>
file name for the output image (pdf)
-s <int>, --stop-after <int>
stop after this many reads
-p <int>, --plot-every <int>
print plot to pdf after this many reads
-c <str>, --color-map <str>
choose colormap for the plot ("red" or "heat", red is
default)
-v, --verbose print more stuff to stderr