Benchmark 2

All shell command blocks begin at the folder root: benchmark_2

Description

benchmark_2 is the benchmark presented at:

• WABI 2022

Data format

NODE line

NODE   node_name   contig_name   multiplicity   X_coord   Y_coord

• node_name in the graph, a contig is represented by 2 nodes : contig_name_L and contig_name_R

• contig_name name of the contig

• multiplicity number of occurrence of the contigs

  • x = don’t know

  • * = zero or more

  • 1 = one or more

  • s = one or more (start contig)

  • 1, 2, 3, ... exact number of occurrences

• X_coord X coordinate used for the graphic representation

• Y_coord Y coordinate used for the graphic representation

LINK line

LINK  node_name_1  node_name_2  type   ident   color   sequence

• node_name_* the 2 nodes that are linked

• type

  • intra: the 2 nodes belongs to the same contig

  • inter: the 2 nodes come from different contigs

• ident identifier used to display graph

  • intra = contig_name

  • inter = link length

• color color of the link

  • intra = reflect the coverage

  • inter = grey

• sequence ATGC string of the link (* means link of size 0)

CONTIG line

CONTIG  name  coverage   sequence

• name name of the contig

• coverage average coverage of the contig

• sequence ATGC string of the contig

Install & configurations

1. Python environment

• You need to install virtualenv

  pip install virtualenv
  

• Create python virtual environment

  ./config/install_venv39.sh
  

• Activate the environment

  source .venv_39/bin/activate
  

Always make sure the environment is activated!

(.venv_39) # command lines may be prefix by the environment name

2. QUAST

QUAST is used to evaluate the scaffolding (and the pre-assembly).

One fix is automatically done in .venv_39/lib/python3.9/site-packages/quast_libs/site_packages/jsontemplate/jsontemplate.py:

• replacing import cgi by import html \((\times 1)\)

• replacing all cgi.escape by html.escape \((\times 6)\)

see issue 157

sed -i 's/cgi/html/' .venv_39/lib/python3.9/site-packages/> quast_libs/site_packages/jsontemplate/jsontemplate.py

Usage

• source the environment

  source .venv_39/bin/activate
  

• run the benchmark

  python3.9 scripts/run_benchmark_2.py  # [-h] see help
  

• run QUAST evaluation

  python3.9 scripts/evaluate_benchmark_2.py -d run/...  # [-h] see help
  

• extract stats in a tex table (e.g. for WABI2022 conference)

  python3.9 scripts/stats_to_tex_wabi2022.py -d run/...  # [-h] see help
  

• generate figures with R

  Rscript scripts/make_fig.R run/...  # [-h] see help
  

Miscellaneous

• remove quast directories in run/...

  find . -maxdepth 2 -type d -name 'quast' | xargs rm -rf