Skip to content

Latest commit

 

History

History
44 lines (33 loc) · 1.49 KB

README.md

File metadata and controls

44 lines (33 loc) · 1.49 KB
Raw

logicali

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.