1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
|
#!/bin/bash
echo "Setting stuff up"
cur_fol=$PWD
cd ~/AwesomeAssembler && source utils/setup.sh
cd $cur_fol
echo "Running filter"
Reads_filter --las $1.las --db $1 --config ~/AwesomeAssembler/utils/nominal.ini -x $1
echo "Running hinging"
hinging --las $1.las --db $1 --config ~/AwesomeAssembler/utils/nominal.ini -o $1.$USER -x $1
echo "Running Visualise"
python3 /usr/lib/hinge/Visualise_graph.py $1.edges.hinges hinge_list.txt
echo "Running Condense"
python3 /usr/lib/hinge/condense_graph.py $1.edges.hinges
echo "Putting ground truth and condensing"
if [ -e "$1.mapping.1.json" ]
then
python3 /usr/lib/hinge/condense_graph_with_aln_json.py $1.edges.hinges $1.mapping.1.json
fi
|
