tests/README.md

In tbenavi1/smudgeplot:

Manual tests

This is a place for manual tests that have not been automated (yet?). Don't forget to re-install the package/script before execution. Somehting like

Rscript install.R
install -C exec/smudgeplot /usr/local/bin
install -C exec/smudgeplot_plot.R /usr/local/bin

should do the job.

interface tests

smudgeplot plot

./exec/smudgeplot plot tests/data/toy_middle_coverages.tsv -o tests/data/toy_middle_R -n 100 -nbins 20

generates a smudgeplot from the toy data.

smudgeplot hetkmers

two different methods to extract homologous kmers

All

./exec/smudgeplot hetkmers -o tests/data/toy_all tests/data/toy_kmer_k21.dump

Middle

./exec/smudgeplot hetkmers -o tests/data/toy_middle tests/data/toy_kmer_k21.dump --middle

generates two files tests/data/toy_middle_coverages.tsv and tests/data/toy_middle_sequences.tsv with coverages and sequences of kmer pairs.

smudgeplot kmer extraction

exec/smudgeplot.py extract -cov tests/data/toy_all_coverages.tsv -seq tests/data/toy_all_sequences.tsv   -minc 400 -maxc 410 -minr 0.49 -maxr 0.5 | head

would extract 80 lines made of 20 kmers pairs, but showing only the first ten.

tbenavi1/smudgeplot documentation built on Feb. 2, 2024, 6:23 p.m.