benchmark

README

Benchmark

Dataset and results is described at http://shenwei356.github.io/fakit/benchmark

The benchmark needs be performed in Linux-like operating systems.

Install softwares

Softwares

1. fakit. (Go). Version v0.1.4.
2. fasta_utilities. (Perl). Version 3dcc0bc. Lots of dependencies to install_.
3. fastx_toolkit. (Perl). Version 0.0.13. Can't handle multi-line FASTA files_.
4. pyfaidx. (Python). Version 0.4.7.1.
5. seqmagick. (Python). Version 0.6.1
6. seqtk. (C). Version 1.0-r82-dirty.

Attention: the fasta_utilities uses Perl module Term-ProgressBar which make it failed to run when using benchmark script run_benchmark_00_all.pl. Please change the source code of ProgressBar.pm (for me, the path is /usr/share/perl5/vendor_perl/Term/ProgressBar.pm). Add the code below after line 535:

$config{bar_width} = 1 if $config{bar_width} < 1;

The edited code is

} else {
  $config{bar_width}  = $target;
  $config{bar_width} = 1 if $config{bar_width} < 1;   # new line
  die "configured bar_width $config{bar_width} < 1"
  if $config{bar_width} < 1;
}

Data preparation

http://blog.shenwei.me/fakit/benchmark/#datasets

Run tests

Usage:

1. Run all tests:

perl run_benchmark_00_all.pl run_*.sh

2. Run one test:

perl run_benchmark_00_all.pl run_benchmark_04_remove_duplicated_seqs_by_name.sh

3. Custom repeate times:

perl run_benchmark_00_all.pl -n 5 run_benchmark_04_remove_duplicated_seqs_by_name.sh

Plot result

Before this, you need to run

perl run_benchmark_00_all.pl run_*.sh

Libraries ggplot2 and scales are needed.

Run:

./plot.R