-
Notifications
You must be signed in to change notification settings - Fork 2
/
Codeshell.pl
249 lines (134 loc) · 9.81 KB
/
Codeshell.pl
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
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
qs|grep step02.uniform.s |cut -d "." -f1|tr '\n' ' ' kill all the procees READ THE RELATE FILE IN READ
nohup perl ~dna/Environment/qsub-sge.pl --Resource mem=500G --CPU 32
ls *.sh|perl -ne 'chomp;print "$_ "if(!-f"$_.check")' ###read all the check.sh file
ex..cat step03.20180807.ustack.sh step03.20180807.ustack.sh.reqsub.sh step03.ustacks.sh_00024.sh
step03.ustacks.sh_00025.sh step03.ustacks.sh_00028.sh step03.ustacks.sh_00033.sh step03.ustacks.sh_00049.sh
> step03.20180808.ustack.sh
le total.gt|cut -f 1|uniq -c read uniq chromosome
le total.gt|cut -f 1|uniq |wc -l
tar -zxvf filename.tar.gz
tar -zcvf filename.tar.gz newfolder here
BAIDU Cloud
majorDNA1120
#tree
lfs quota /mnt/ilustre/ -h
Rscript /mnt/ilustre/users/long.huang/Pipeline/GIT/bioinformatics/Pipeline/07.POP/bin/bin/tree.R --infile pop.nj.tree --group g.list --outfile ./
##before BSA
## make the fq.list
ls *1.fastq.gz|perl -e 'print "Sample Initial Name\tSample Analysis Name\tBatch\tLibrary\tFile Name\n";while(<>){chomp;@name=split(/\./,$_);$ne=$name[0];$ny=$_;$ny=~s/1.fastq.gz/2.fastq.gz/g; print "$ne\t$ne\tbatch1\tWGS\t$_,$ny\n"}' >fr.list
RF *1.fastq.gz|perl -ne 'chomp;@name=split(/\//,$_);@ne=split(/\./,$name[-1]);$nea=$ne[0];$ny=$_;$ny=~s/1.fastq.gz/2.fastq.gz/g; print "$nea\t$_\t$ny\tWGS\n"' >fqa.list
###sangerupload
SangerUpload -i /mnt/ilustre/users/meng.luo/project/maoguangzhi_BSA/maoguangzhi_bsa/ -c 'VXDKZZ|0bd8a0aa4e81018a015f7cd1aa515211' -m sanger -l maoguangzhi
##download data
python /mnt/ilustre/users/dna/Environment/cloud/dataexchange-V2/download.py -c '' -t ./ -m sanger
##print gene in mutmap on linux use the perl
le region.threshold.gene.total|perl -ne 'chomp;($n1,$n2)=split(/\s+/,$_,2);if ($n1 =~ /@/){print "$_\n"}'
####write the ID sample name > the group.list
head -n1000 step01.vcf-filter/pop.recode.vcf|grep "#C"|cut -f 10-100|sed 's/\t/\n/g'|perl -ne 'chomp;print "$_\t1\n"' >group.list
##liangzhiqiang
##remove the de.list
grep -v -f de.list total.list >11.list
##take out the de.list
grep -f de.list total.list >22.list
cat total.list 22.list >all.list
cut -f1 all.list|sort -u|wc -l
le all.list |sort|wc -l
cut -f1 all.list|sort -u
###liangzhiqiang no reference genome
cut -f1 all.list|sort|uniq|perl -ne 'chomp;$m=rand()*1;print "$_\t$m\n"'|sort -k2,2|head -n50|cut -f1 >sample.list
cut -f1 all.list|sort|uniq|perl -ne 'chomp;$m++;print "$_\t$m\n"' >group.list
less step02.uniform.sh|perl -ne 'chomp;$na=(split(/\s+/))[-1];$nb=(split(/\./,$na))[2]; print "$nb.check\n"'
less step02.uniform.sh|perl -ne 'chomp;$na=(split(/\s+/))[-1];$nb=(split(/\./,$na))[2]; print "touch /mnt/ilustre/users/meng.luo/project/liangzhiqiang_NOREF_20180831/data/02.$nb.check\n"'
less step02.uniform.sh|perl -ne 'chomp;$na=(split(/\s+/))[-1];$nb=(split(/\./,$na))[2]; print "touch /mnt/ilustre/users/meng.luo/project/liangzhiqiang_NOREF_20180831/data/02.$nb.check\n"' >02.sh
###collinearrity
map
##map not right with empty
Fragaria_vesca_v4.0.a1.fasta|perl -ne 'chomp;@a=split; next if(/^$/ ||$a[0] eq ""); print "$_\n"' >Fragaria_vesca.fa
samtools faidx Fragaria_vesca.fa
head -n7 Fragaria_vesca.fa.fai|cut -f1,2 >chrlength.map
le mappp.mp|cut -f1,4,5|grep Fvb|perl -ne '@a=split;@b=split(/\:/,$a[0]);print "$b[0]\t$a[1]\t$a[2]\n"' >mappp.map
perl /mnt/ilustre/users/long.huang/bin/Bin/old/genetic_map/v1.2.1/graph/drawAligmentRalationMap.pl -m ../mapp1.map -a mapp1.map -k map1 -o ./
cairosvg -f png map1.svg >map1.png
###comsumetimes
RAxML_info.pop
le RAxML_info.pop|grep ": Time"|cut -d " " -f3|awk '{s+=$1}END{print s}'|le
###delete duplicatble
le mapp2.map|cut -f1|uniq -d >de2.list
grep -v -f dep.list mm2.map >de_mm2.map
perl /mnt/ilustre/users/long.huang/bin/Bin/old/genetic_map/v1.2.1/graph/drawAligmentRalationMap.pl -m ../mapp1.map -a mapp1.map -k map1 -o ./
cairosvg -f png mm1.svg >mm1.png
##check all users/space
lfs quota -u meng.luo /mnt/ilustre/
perl snp.indel.number.pl -infile index-calc.result.index -outfile 3-10.csv
grep '@chr' region.threshold.vcf.total|sed 's/\t/,/g' >3-11.csv
grep '@chr' region.threshold.gene.total|sed 's/\t/,/g'|sed 's/#@chr/Chromosome ID/g'|sed 's/@//g'|sed 's/pos1/Start/g'|sed 's/pos2/end/g' >3-12.csv
grep '@chr' region.threshold.gene.total|sed 's/\t/,/g' >
###all work use the tools for make more work effectively
perl -e '@a=glob("*/05.annovar/*/work_flow/");print join("\ncd ",@a),"\n"' > work.sh
less -S work.sh |sed 's/snp\.indel\.number\.pl/"/mnt/ilustre/users/meng.luo/project/liujianxiang_20180903/01MJ20171213041_bsa_mutmap/05.annovar/C10XC/work_flow/snp.indel.number.pl"/g'|less -S
readlink -f ../*/*/*/work_flow|perl -ne '@a=split(/\//,$_);print $a[-2],"\n"'
*/05.annovar/*/work_flow/
##variation step01 to make the GCTA figure
for i in `ls` ;do mv -f $i `echo $i|sed 's/:/-/'`;done
sed -i 's/:/-/g' *.stat
le 01.fastq-qc.sh|perl -ne 'chomp;@st=split/\&&/;print "$st[-1]\n"' >01fig.sh
lfs quota -u meng.luo /mnt/ilustre/
Disk quotas for user meng.luo (uid 804):
Filesystem kbytes quota limit grace files quota limit grace
/mnt/ilustre/ 14989243096 0 0 - 134076 0 0 -
亲本平均测序深度为16.11X(总的数据量（多少G/基因组的大小）)，子代平均测序深度为10.33X。样品与参考基因组平均比对效率为93.37 %，
平均覆盖深度为16.10X(最后一列)，基因组覆盖度为%（至少一个碱基覆盖（第三列））（3-5.table）。
运行过的命令要记得保存一份！
##change the Total.lg file name #Gmap
le pop.filtered.marker|cut -f1|grep -v "#" |perl -ne 'chomp;my @a=split(/\_/,$_);if(!exists $hash{$a[0]}){print "\n>$a[0]\n$_";$hash{$a[0]}=1}else{print " $_ ";}'|less -S >LG12
##check error
ls *.sh|perl -ne 'chomp;print "$_ "if(!-f"$_.check")'
新的上传数据
python /mnt/ilustre/users/meng.luo/Pipeline/V3/get_file_list.py -i /mnt/ilustre/users/meng.luo/project/meiyongxian_MJ20180807035/data -l outfile
python /mnt/ilustre/users/meng.luo/Pipeline/V3/upload.py -i /mnt/ilustre/users/meng.luo/project/meiyongxian_MJ20180807035/data -l outfile -c "NTMPAW|618d3db615ca3d000cbbdc3bbb6f0ede" -m "nsanger"
##new
python /mnt/ilustre/users/meng.luo/Pipeline/V3/get_file_list.py -i ./ -l outfile
python /mnt/ilustre/users/meng.luo/Pipeline/V3/upload.py -i ./ -l outfile -c "DGQTDR|7532229f97ee86116f47331df107c43a" -m "nsanger"
##download data
python ~chunxiang.xue/scripts/i-sanger/V3/download.py -c 'OGHFOJ|bc4638361a7614f0fc5c01fcb2c1f1d2' -t ./ -m nsanger
python /mnt/ilustre/users/dna/Environment/cloud/dataexchange-V2/download.py -c '' -t ./ -m sanger
python /mnt/ilustre/users/qingmei.cui/dataexchange/V3/download.py -c '' -t ./ -m nsanger
python ~chunxiang.xue/scripts/i-sanger/V3/download.py -c '' -t ./ -m nsanger
qstat|grep rna. |cut -d "." -f1|tr '\n' ' '
qdel kill the processs
# list the mechine
lfs df
qsource
qcheck
qstatf
qhost
##PCA change the name for the GCTA
le pop.recode.vcf |perl -ne 'chomp;if(/^#/ || /^##/){print "$_\n";}else{my ($chr,$all)=split/\s+/,$_,2;print "Un\t$all\n"}'>pop.un.vcf
##提取表中的结果!两个表中是一样的结果!
less -S ~long.huang/newmdt/WTH/2018-11-27/result/gatk/fst-thetapi-tajima/pop2_pop3.fst.thetapi.tajima.pop1.select.snp ~long.huang/newmdt/WTH/2018-11-27/vcf/gatk.snp.table|perl -ne '@a=split;$b=$a[0]."-".$a[1];$stat{$b}++;print $_ if($stat{$b} > 1);' >pop2_pop3.fst.thetapi.tajima.pop1.select.snp.table && less -S ~long.huang/newmdt/WTH/2018-11-27/result/gatk/fst-thetapi-tajima/pop2_pop3.fst.thetapi.tajima.pop2.select.snp ~long.huang/newmdt/WTH/2018-11-27/vcf/gatk.snp.table|perl -ne '@a=split;$b=$a[0]."-".$a[1];$stat{$b}++;print $_ if($stat{$b} > 1);' >pop2_pop3.fst.thetapi.tajima.pop2.select.snp.table
##修改提取的区域
le sgRNA.region |grep "chr7"|cut -f 1,2,3|perl -ne 'chomp;my ($a,$b,$c)=split/\s+/,$_;my $start=$b-5000;my $end=$c+5000;print "$a\t$start\t$end\n";'>5K.S2.chr7.pos
#get fa.list for qc
RF */*1_001.fastq.gz|perl -ne 'chomp;@name=split(/\//,$_);@ne=split(/\./,$name[-1]);$nea=$ne[0];$ny=$_;$ny=~s/1_001.fastq.gz/2_001.fastq.gz/g; print "$nea\t$_\t$ny\n"' >fqa.list
# bwa
bwa index -a bwtsw M.clean.1.fa
bwa mem -t 4 /mnt/ilustre/users/minghao.zhang/newmdt/Project/MJ20180612007_wanhuihua_Gmap/var_20180619/02.ref-config/ref query.fq > query.sam
bwa mem -M -a -t 8 -R "@RG\tID:2\tLG:M\tLB:1\tPL:illumina\tSM:M\tPU:run_barcode\tCN:MajorBioDS:reseq" \
/mnt/ilustre/centos7users/meng.luo/project/yuanjie_MJ20190619038/bwa/1/M.clean.1.fa \
/mnt/ilustre/centos7users/meng.luo/project/yuanjie_MJ20190619038/04.bam-sort/Z.sort.mapped.bam.R1.fastq.gz\
/mnt/ilustre/centos7users/meng.luo/project/yuanjie_MJ20190619038/04.bam-sort/Z.sort.mapped.bam.R2.fastq.gz \
| samtools view -bS - > /mnt/ilustre/centos7users/meng.luo/project/yuanjie_MJ20190619038/bwa/1/Z.b1.bam
#blast
blat /mnt/ilustre/users/minghao.zhang/newmdt/Genome/newGenome/Rosa_chinensis/01.newref/ref.fa all.fa -t=dna -q=dna -out=blast ssr3
makeblastdb -in /mnt/ilustre/users/minghao.zhang/newmdt/Genome/newGenome/Rosa_chinensis/01.newref/ref.fa \
-dbtype nucl -title ssr1 -parse_seqids -out ssr1 -logfile ssr1.log && blastn -query /mnt/ilustre/users/meng.luo/project/wanhuihhua/SSR/query1.fa \
-db /mnt/ilustre/users/meng.luo/project/wanhuihhua/SSR/ssr1 -evalue 1e-5 -num_threads 8 -outfmt 7 -out ssr1
#bowtie
bowtie-build M.clean.1.fa M.clean.1.fa
bowtie -f -n 1 -e 80 -l 18 -a -m 5 --best --strata --al M.clean.1.mapped --un M.clean.1.unmapped M.clean.1.fa \
/mnt/ilustre/centos7users/meng.luo/project/yuanjie_MJ20190619038/04.bam-sort/Z.sort.mapped.bam.fa M.clean.1.bwt 2> M.clean.1.log
#install
python setup.py install --prefix=/mnt/ilustre/centos7users/meng.luo/.env/bin
#
jupyter nbconvert --to html *