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
50
51
52
53
54
55
56
57
58
59
60
61
62
|
echo
echo "================================================================================"
printf " FeatureCounts Common Scenario Tests\n http://subread.sourceforge.net/\n"
echo "================================================================================"
echo
infiles="/usr/local/work/liao/Rsubread/testsuit/SEQC2011_for_3tests_wild-coorsorted-Picard-SamtAgain.bam /usr/local/work/liao/Rsubread/testsuit/SEQC2011-A-FCpaper-SAM1.4.junc"
for inf in $infiles
do
intag="complex"
if [[ $inf =~ FCpaper ]]
then
intag="simple"
fi
for level in GENE EXON
do
op_level=
if [[ $level == "EXON" ]]
then
op_level=" -f "
fi
for moverlap in YES NO
do
op_moverlap=
if [[ $moverlap == "YES" ]]
then
op_moverlap=" -O "
fi
for mmapping in YES NO
do
op_mmapping=
if [[ $mmapping == "YES" ]]
then
op_mmapping=" -M "
fi
for fraction in YES NO
do
op_fraction=
if [[ $fraction == "YES" ]]
then
if [[ $mmapping == "NO" ]]
then
continue
fi
op_fraction=" --fraction "
fi
ora=data/commonusage-$intag-$level-$moverlap-$mmapping-$fraction.FC
echo $ora
../../bin/featureCounts -a /usr/local/work/liao/Rsubread/testsuit/ensembl-for_3tests-shuf.GTF -o data/del4.FC $op_level $op_moverlap $op_mmapping $op_fraction -T7 -p $inf &>/dev/null
cat $ora|grep -v ^#|grep -vi Geneid |md5sum
cat data/del4.FC |grep -v ^#|grep -vi Geneid |md5sum
cat $ora.summary|grep -v ^#|grep -vi Status |md5sum
cat data/del4.FC.summary |grep -v ^#|grep -v Status |md5sum
rm -f data/del4*
done
done
done
done
done
|
