Benchmark 0¶
All shell command blocks begin at the folder root: benchmark_0
Description¶
benchmark_0
is the first benchmark presented at:
BiATA 2022
ROADEF 2022
ISCO 2022
JOBIM 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
byimport html
\((\times 1)\)replacing all
cgi.escape
byhtml.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_0.py # [-h] see help
run QUAST evaluation
python3.9 scripts/evaluate_benchmark_0.py -d run/... # [-h] see help
extract stats in a tex table (e.g. for ISCO2022 conference)
python3.9 scripts/stats_to_tex_isco2022.py -d run/... # [-h] see help
generate figures with R
Rscript scripts/make_fig.R run/...