Usage:
python scripts/generate_random_alignment.py 1 2000 500 aa
python scripts/trim.py -i random_ali_seed1_l2000_n500_AA.fasta -n 100 --chi2 -o examples/outplots_aa --plot
python scripts/generate_random_alignment.py 1 2000 500 nt
python scripts/trim.py -i random_ali_seed1_l2000_n500_NT.fasta -n 100 --chi2 -o examples/outplots_aa --plot
benshmark:
- 10k columns times 30k sequences, trimming and plots
# ~4.5 min
python scripts/generate_random_alignment.py 1 10000 30000 nt
# ~4.5 min
python scripts/trim.py -i random_ali_seed1_l10000_n30000_NT.fasta -n 10000 --chi2 -o outplots_big_nt_chi2.fasta --plot
Note for testing: size of output FASTA file is 233891093.
- 10k columns times 50k sequences, trimming, no plots (plotting requires too much memory)
# ~7 min
python scripts/generate_random_alignment.py 1 10000 50000 nt
# ~2 min 1 CPU
python scripts/trim.py -i random_ali_seed1_l10000_n50000_NT.fasta -n 25000 -C 1 -o outplots_huge_nt.fasta
# ~4 min 1 CPU
python scripts/trim.py -i random_ali_seed1_l10000_n50000_NT.fasta -n 25000 --chi2 -C 1 -o outplots_huge_nt_chi2.fasta
# ~40 sec 8 CPUs
python scripts/trim.py -i random_ali_seed1_l10000_n50000_NT.fasta -n 25000 --chi2 -C 8 -o outplots_huge_nt_chi2.fasta
# ~20 sec 8 CPUs
python scripts/trim.py -i random_ali_seed1_l10000_n50000_NT.fasta -n 25000 -C 8 -o outplots_huge_nt.fasta
Note for testing: size of output FASTA files are 474429401 without --chi2 paramenter and 375931371 with it.