PublicScripts/batchCopyfastq.sh at main · damioresegun/PublicScripts · GitHub

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
39
40
41
42
43
44
45
46
47
48
49
#!/bin/bash

#for batch copying demultiplexed output from qcat from individual fastq outputs from guppy
guppyOut="$HOME/ReBaseCall/QcatDemultiplex/5xBarc/qcat_0/"
batchSave="$HOME/ReBaseCall/QcatDemultiplex/5xBarc/Consensus/"
cp ${guppyOut}/* $batchSave
gupsta=$(dirname $guppyOut)
cd $gupsta
pwd
for f in ${gupsta}/qcat_1/*
do
file=$(basename $f)
fname="${file%.*}"
echo $fname
cat $f >> ${batchSave}/${fname}.fastq
done
cd ${gupsta}
echo
echo "qcat1 done"
echo
for f in ${gupsta}/qcat_2/*
do
file=$(basename $f)
fname="${file%.*}"
echo $fname
cat $f >> ${batchSave}/${fname}.fastq
done
echo
echo "qcat2 done"
echo
for f in ${gupsta}/qcat_3/*
do
file=$(basename $f)
fname="${file%.*}"
echo $fname
cat $f >> ${batchSave}/${fname}.fastq
done
echo
echo "qcat3 done"
echo
for f in ${gupsta}/qcat_4/*
do
file=$(basename $f)
fname="${file%.*}"
echo $fname
cat $f >> ${batchSave}/${fname}.fastq
done
echo
echo "qcat4 done"