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