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 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_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/...
```