-
Notifications
You must be signed in to change notification settings - Fork 0
/
create_simulated_datasets.sh
38 lines (31 loc) · 1.36 KB
/
create_simulated_datasets.sh
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
29
30
31
32
33
34
35
36
37
38
#!/bin/bash
# S.agalactiae
declare -a cluster100=("ERR3468293" "SRR7283372" "SRR2062125" "SRR7281691" "ERR1910678" )
declare -a cluster30=("SRR5063572" "ERR1741401" "SRR5061557" "SRR3320830" "ERR1659686" )
declare -a cluster20=("ERR1741950" "SRR7282364" "SRR6050836" "ERR1672714" "ERR3467983" )
for val in ${cluster100[@]};do
seqtk sample -s100 ${val}_1.fastq 100000 > ${val}_1.100.fastq
seqtk sample -s100 ${val}_2.fastq 100000 > ${val}_2.100.fastq
done
for val in ${cluster30[@]};do
seqtk sample -s100 ${val}_1.fastq 30000 > ${val}_1.30.fastq
seqtk sample -s100 ${val}_2.fastq 30000 > ${val}_2.30.fastq
done
for val in ${cluster20[@]};do
seqtk sample -s100 ${val}_1.fastq 20000 > ${val}_1.20.fastq
seqtk sample -s100 ${val}_2.fastq 20000 > ${val}_2.20.fastq
done
# A.baumannii
declare -a cluster=( "SRR2559327" "SRR3131147" "DRR039843" "SRR5477434" "SRR1030409" "SRR1015318" )
for val in ${cluster[@]};do
seqtk sample -s100 ${val}_1.fastq 100000 > ${val}_1.100.fastq
seqtk sample -s100 ${val}_2.fastq 100000 > ${val}_2.100.fastq
done
for val in ${cluster[@]};do
seqtk sample -s100 ${val}_1.fastq 30000 > ${val}_1.30.fastq
seqtk sample -s100 ${val}_2.fastq 30000 > ${val}_2.30.fastq
done
for val in ${cluster[@]};do
seqtk sample -s100 ${val}_1.fastq 20000 > ${val}_1.20.fastq
seqtk sample -s100 ${val}_2.fastq 20000 > ${val}_2.20.fastq
done