Hilbert Mapper is a C++ implementation of Hilbert's space filling curve to represent read coverage on genomic sequences. Although it can be used to represent any unidimensional vector of positive numerical data.
git clone https://github.com/AntoineHo/HilMa.git
cd HilMa
chmod +x install.sh
./install.sh
reading a samtools depth output file:
python hilma.py sam [coverage file from samtools depth] [contig ID]
awk, grep, custom script, ... outputting integer unidimensional data to stdout:
[stdin] | python hilma.py vector - [output prefix]
reading a custom coverage file:
python hilma.py custom [column of IDs] [column of values] [coverage file] [ID of sequence to plot]
This usage may change in future commits!
samtools depth mybam.bam > mybam.cov
python hilma.py mybam.cov contig3
grep contig3 mybam.cov | awk '{print $3}' | python hilma.py vector - custom_prefix
python hilma.py custom custom.cov 0 3 contig_002