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

make install INSTALL_PREFIX=~

should do the job.

interface tests

data prep

Download SRR3265401 - nice teteraploid Sacharomyces run I use often for testing.

smudgeplot plot

Defaults:

smudgeplot.py all data/Scer/kmerpairs_default_e2_text.smu -o data/Scer/240918_trial

Testing parameters:

smudgeplot.py all data/Scer/kmerpairs_default_e2_text.smu -o data/Scer/240918_trial_params -t "Species 1" -c 20 -ylim 80 -col_ramp magma --invert_cols

smudgeplot hetkmers

two different methods to extract homologous kmers

TODO

Dicots

This is a large dataset of the first 540 dicot genomes sequenced by the Tree of Life. Some of them are completed, some of them are with insufficient coverage or otherwise qc failed data. The idea here is to be able to tell those apart, get reasonable defaults so the generated plot is meaningful for a reasonable number (i.e. nearly all) of them.

time ./exec/smudgeplot.py plot data/dicots/smu_files/daAchMill1.k31_ploidy.smu.txt -o data/dicots/alt_plots/daAchMill1 --alt_plot -q 0.9

for smu in data/dicots/smu_files/*.smu.txt; do
    species=$(basename $smu)
    echo $species $smu
    time ./exec/smudgeplot.py plot $smu -o data/dicots/alt_plots/$species --alt_plot -q 0.9
done

for smu in data/dicots/smu_files/*.smu.txt; do
    species=$(basename $smu .smu.txt)
    echo $species $smu
    time ./exec/smudgeplot.py plot $smu -c 10 -o data/dicots/alt_plots_c10/$species --alt_plot -q 0.9
done

for smu in $(ls data/dicots/smu_files/*.smu.txt | head -20); do
    species=$(basename $smu .smu.txt)
    echo $species $smu
    smudgeplot.py all $smu -t $species -o data/dicots/automated_smudgeplots/$species
done