annotate wrapper.sh @ 55:6cd12c71c3d3 draft

Uploaded
author davidvanzessen
date Wed, 14 Jun 2017 11:14:00 -0400
parents f5fe63533c58
children ee807645b224
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
1 #!/bin/bash
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
2 #set -e
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
3 dir="$(cd "$(dirname "$0")" && pwd)"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
4 input=$1
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
5 method=$2
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
6 log=$3 #becomes the main html page at the end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
7 outdir=$4
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
8 output="$outdir/index.html" #copied to $log location at the end
34
96c1276ceefe Uploaded
davidvanzessen
parents: 33
diff changeset
9 title="$5"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
10 include_fr1=$6
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
11 functionality=$7
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
12 unique=$8
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
13 naive_output=$9
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
14 naive_output_ca=${10}
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
15 naive_output_cg=${11}
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
16 naive_output_cm=${12}
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
17 naive_output_ce=${13}
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
18 naive_output_all=${14}
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
19 filter_unique=${15}
49
f5fe63533c58 Uploaded
davidvanzessen
parents: 47
diff changeset
20 filter_unique_count=${16}
f5fe63533c58 Uploaded
davidvanzessen
parents: 47
diff changeset
21 class_filter=${17}
f5fe63533c58 Uploaded
davidvanzessen
parents: 47
diff changeset
22 empty_region_filter=${18}
f5fe63533c58 Uploaded
davidvanzessen
parents: 47
diff changeset
23 fast=${19}
f5fe63533c58 Uploaded
davidvanzessen
parents: 47
diff changeset
24
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
25 mkdir $outdir
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
26
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
27 tar -xzf $dir/style.tar.gz -C $outdir
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
28
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
29 echo "---------------- read parameters ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
30 echo "---------------- read parameters ----------------<br />" > $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
31
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
32 echo "unpacking IMGT file"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
33
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
34 type="`file $input`"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
35 if [[ "$type" == *"Zip archive"* ]] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
36 echo "Zip archive"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
37 echo "unzip $input -d $PWD/files/"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
38 unzip $input -d $PWD/files/
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
39 elif [[ "$type" == *"XZ compressed data"* ]] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
40 echo "ZX archive"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
41 echo "tar -xJf $input -C $PWD/files/"
34
96c1276ceefe Uploaded
davidvanzessen
parents: 33
diff changeset
42 mkdir -p "$PWD/files/$title"
96c1276ceefe Uploaded
davidvanzessen
parents: 33
diff changeset
43 tar -xJf $input -C "$PWD/files/$title"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
44 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
45
35
744e5e2e3556 Uploaded
davidvanzessen
parents: 34
diff changeset
46 cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt
744e5e2e3556 Uploaded
davidvanzessen
parents: 34
diff changeset
47 cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt
40
ca2512e1e3ab Uploaded
davidvanzessen
parents: 39
diff changeset
48 cat "`find $PWD/files/ -name "4_*"`" > $PWD/gapped_aa.txt
35
744e5e2e3556 Uploaded
davidvanzessen
parents: 34
diff changeset
49 cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
744e5e2e3556 Uploaded
davidvanzessen
parents: 34
diff changeset
50 cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
744e5e2e3556 Uploaded
davidvanzessen
parents: 34
diff changeset
51 cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
744e5e2e3556 Uploaded
davidvanzessen
parents: 34
diff changeset
52 cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
744e5e2e3556 Uploaded
davidvanzessen
parents: 34
diff changeset
53 cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
54
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
55 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
56 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
57 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
58 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
59 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
60 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
61
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
62 echo "---------------- class identification ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
63 echo "---------------- class identification ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
64
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
65 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
66
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
67 echo "---------------- merge_and_filter.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
68 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
69
49
f5fe63533c58 Uploaded
davidvanzessen
parents: 47
diff changeset
70 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt "$PWD/gapped_aa.txt" $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${filter_unique_count} ${class_filter} ${empty_region_filter} 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
71
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
72 if [[ "$fast" == "no" ]] ; then
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
73
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
74 echo "---------------- creating new IMGT zips ----------------"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
75 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
76
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
77 mkdir $outdir/new_IMGT
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
78
36
43d182135230 Uploaded
davidvanzessen
parents: 35
diff changeset
79 cat "`find $PWD/files/ -name "1_*"`" > "$outdir/new_IMGT/1_Summary.txt"
43d182135230 Uploaded
davidvanzessen
parents: 35
diff changeset
80 cat "`find $PWD/files/ -name "2_*"`" > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
43d182135230 Uploaded
davidvanzessen
parents: 35
diff changeset
81 cat "`find $PWD/files/ -name "3_*"`" > "$outdir/new_IMGT/3_Nt-sequences.txt"
43d182135230 Uploaded
davidvanzessen
parents: 35
diff changeset
82 cat "`find $PWD/files/ -name "4_*"`" > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
43d182135230 Uploaded
davidvanzessen
parents: 35
diff changeset
83 cat "`find $PWD/files/ -name "5_*"`" > "$outdir/new_IMGT/5_AA-sequences.txt"
43d182135230 Uploaded
davidvanzessen
parents: 35
diff changeset
84 cat "`find $PWD/files/ -name "6_*"`" > "$outdir/new_IMGT/6_Junction.txt"
43d182135230 Uploaded
davidvanzessen
parents: 35
diff changeset
85 cat "`find $PWD/files/ -name "7_*"`" > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
43d182135230 Uploaded
davidvanzessen
parents: 35
diff changeset
86 cat "`find $PWD/files/ -name "8_*"`" > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
43d182135230 Uploaded
davidvanzessen
parents: 35
diff changeset
87 cat "`find $PWD/files/ -name "9_*"`" > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
43d182135230 Uploaded
davidvanzessen
parents: 35
diff changeset
88 cat "`find $PWD/files/ -name "10_*"`" > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
89
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
90 mkdir $outdir/new_IMGT_IGA
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
91 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
92
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
93 mkdir $outdir/new_IMGT_IGA1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
94 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
95
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
96 mkdir $outdir/new_IMGT_IGA2
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
97 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
98
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
99 mkdir $outdir/new_IMGT_IGG
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
100 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
101
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
102 mkdir $outdir/new_IMGT_IGG1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
103 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
104
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
105 mkdir $outdir/new_IMGT_IGG2
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
106 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
107
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
108 mkdir $outdir/new_IMGT_IGG3
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
109 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
110
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
111 mkdir $outdir/new_IMGT_IGG4
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
112 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
113
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
114 mkdir $outdir/new_IMGT_IGM
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
115 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
116
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
117 mkdir $outdir/new_IMGT_IGE
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
118 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
119
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
120 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
121
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
122 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
123 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
124 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
125
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
126 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
127 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
128 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
129 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
130 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
131
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
132 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
133
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
134 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
135
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
136
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
137 tmp="$PWD"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
138 cd $outdir/new_IMGT/ #tar weirdness...
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
139 tar -cJf ../new_IMGT.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
140
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
141 cd $outdir/new_IMGT_IGA/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
142 tar -cJf ../new_IMGT_IGA.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
143
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
144 cd $outdir/new_IMGT_IGA1/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
145 tar -cJf ../new_IMGT_IGA1.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
146
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
147 cd $outdir/new_IMGT_IGA2/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
148 tar -cJf ../new_IMGT_IGA2.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
149
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
150 cd $outdir/new_IMGT_IGG/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
151 tar -cJf ../new_IMGT_IGG.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
152
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
153 cd $outdir/new_IMGT_IGG1/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
154 tar -cJf ../new_IMGT_IGG1.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
155
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
156 cd $outdir/new_IMGT_IGG2/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
157 tar -cJf ../new_IMGT_IGG2.txz *
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
158
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
159 cd $outdir/new_IMGT_IGG3/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
160 tar -cJf ../new_IMGT_IGG3.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
161
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
162 cd $outdir/new_IMGT_IGG4/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
163 tar -cJf ../new_IMGT_IGG4.txz *
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
164
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
165 cd $outdir/new_IMGT_IGM/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
166 tar -cJf ../new_IMGT_IGM.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
167
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
168 cd $outdir/new_IMGT_IGE/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
169 tar -cJf ../new_IMGT_IGE.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
170
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
171 cd $tmp
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
172 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
173
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
174 echo "---------------- shm_csr.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
175 echo "---------------- shm_csr.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
176
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
177 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
178 echo "R mutation analysis"
1
faae21ba5c63 Uploaded
davidvanzessen
parents: 0
diff changeset
179 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
180
43
77a7ac76c7b9 Uploaded
davidvanzessen
parents: 42
diff changeset
181 echo "---------------- plot_pdfs.r ----------------"
77a7ac76c7b9 Uploaded
davidvanzessen
parents: 42
diff changeset
182 echo "---------------- plot_pdfs.r ----------------<br />" >> $log
77a7ac76c7b9 Uploaded
davidvanzessen
parents: 42
diff changeset
183
77a7ac76c7b9 Uploaded
davidvanzessen
parents: 42
diff changeset
184 echo "Rscript $dir/shm_csr.r $outdir/pdfplots.RData $outdir 2>&1"
77a7ac76c7b9 Uploaded
davidvanzessen
parents: 42
diff changeset
185
77a7ac76c7b9 Uploaded
davidvanzessen
parents: 42
diff changeset
186 Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir" 2>&1
77a7ac76c7b9 Uploaded
davidvanzessen
parents: 42
diff changeset
187
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
188 echo "---------------- shm_csr.py ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
189 echo "---------------- shm_csr.py ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
190
1
faae21ba5c63 Uploaded
davidvanzessen
parents: 0
diff changeset
191 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
192
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
193 echo "---------------- aa_histogram.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
194 echo "---------------- aa_histogram.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
195
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
196 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
197 if [ -e "$outdir/aa_histogram_.png" ]; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
198 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
199 mv $outdir/aa_histogram_.pdf $outdir/aa_histogram.pdf
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
200 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
29
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
201 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
202 mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
203 mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
204 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
205
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
206 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
207
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
208 funcs=(sum mean median)
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
209 funcs=(sum)
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
210
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
211 echo "---------------- sequence_overview.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
212 echo "---------------- sequence_overview.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
213
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
214 mkdir $outdir/sequence_overview
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
215
7
ad9be244b104 Uploaded
davidvanzessen
parents: 6
diff changeset
216 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt ${empty_region_filter} 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
217
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
218 echo "<table border='1'>" > $outdir/base_overview.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
219
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
220 while IFS=$'\t' read ID class seq A C G T
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
221 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
222 echo "<tr><td>$ID</td><td>$seq</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
223 done < $outdir/sequence_overview/ntoverview.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
224
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
225 echo "<html><center><h1>$title</h1></center>" > $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
226 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
227 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
228 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
229 echo "<script type='text/javascript' src='script.js'></script>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
230 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
231 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
232
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
233 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
234 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
235 total_count=$((matched_count + unmatched_count))
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
236 perc_count=$((unmatched_count / total_count * 100))
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
237 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
238 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
239
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
240 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
241 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
242 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
243
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
244 echo "---------------- main tables ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
245 echo "---------------- main tables ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
246
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
247 echo "<div class='tabber'>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
248 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
249
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
250 for func in ${funcs[@]}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
251 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
252
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
253 echo "---------------- $func table ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
254 echo "---------------- $func table ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
255
47
64711f461c8e Uploaded
davidvanzessen
parents: 45
diff changeset
256 cat $outdir/mutations_${func}.txt $outdir/shm_overview_tandem_row.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
257
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
258 echo "---------------- pattern_plots.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
259 echo "---------------- pattern_plots.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
260
43
77a7ac76c7b9 Uploaded
davidvanzessen
parents: 42
diff changeset
261 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/aid_motives $outdir/relative_mutations $outdir/absolute_mutations $outdir/shm_overview.txt 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
262
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
263 echo "<table class='pure-table pure-table-striped'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
264 echo "<thead><tr><th>info</th>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
265
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
266 if [ "${class_filter}" != "101_101" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
267
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
268 for gene in ${genes[@]}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
269 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
270 tmp=`cat $outdir/${gene}_${func}_n.txt`
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
271 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
272 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
273
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
274 tmp=`cat $outdir/all_${func}_n.txt`
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
275 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
276 tmp=`cat $outdir/unmatched_${func}_n.txt`
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
277 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
278
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
279 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
280 do
47
64711f461c8e Uploaded
davidvanzessen
parents: 45
diff changeset
281 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] || [ "$name" == "Tandems/Expected (ratio)" ] ; then #meh
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
282 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz})</td><td>${ca1x}/${ca1y} (${ca1z})</td><td>${ca2x}/${ca2y} (${ca2z})</td><td>${cgx}/${cgy} (${cgz})</td><td>${cg1x}/${cg1y} (${cg1z})</td><td>${cg2x}/${cg2y} (${cg2z})</td><td>${cg3x}/${cg3y} (${cg3z})</td><td>${cg4x}/${cg4y} (${cg4z})</td><td>${cmx}/${cmy} (${cmz})</td><td>${cex}/${cey} (${cez})</td><td>${allx}/${ally} (${allz})</td><td>${unx}/${uny} (${unz})</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
283 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
284 echo "<tr><td>$name</td><td>${caz}%</td><td>${ca1z}%</td><td>${ca2z}%</td><td>${cgz}%</td><td>${cg1z}%</td><td>${cg2z}%</td><td>${cg3z}%</td><td>${cg4z}%</td><td>${cmz}%</td><td>${cez}%</td><td>${allz}%</td><td>${unz}%</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
285 else
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
286 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz}%)</td><td>${ca1x}/${ca1y} (${ca1z}%)</td><td>${ca2x}/${ca2y} (${ca2z}%)</td><td>${cgx}/${cgy} (${cgz}%)</td><td>${cg1x}/${cg1y} (${cg1z}%)</td><td>${cg2x}/${cg2y} (${cg2z}%)</td><td>${cg3x}/${cg3y} (${cg3z}%)</td><td>${cg4x}/${cg4y} (${cg4z}%)</td><td>${cmx}/${cmy} (${cmz}%)</td><td>${cex}/${cey} (${cez}%)</td><td>${allx}/${ally} (${allz}%)</td><td>${unx}/${uny} (${unz}%)</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
287 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
288 done < $outdir/data_${func}.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
289
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
290 else
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
291 tmp=`cat $outdir/all_${func}_n.txt`
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
292 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
293
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
294 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
295 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
296 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
297 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
298 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
299 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
300 else
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
301 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
302 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
303 done < $outdir/data_${func}.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
304
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
305 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
306 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
307 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
308 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
309
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
310 echo "<a href='aid_motives.pdf'><img src='aid_motives.png' /></a><br />" >> $output
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
311 echo "<a href='relative_mutations.pdf'><img src='relative_mutations.png' /></a><br />" >> $output
43
77a7ac76c7b9 Uploaded
davidvanzessen
parents: 42
diff changeset
312 echo "<a href='absolute_mutations.pdf'><img src='absolute_mutations.png' /></a><br />" >> $output
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
313 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
314 cat $dir/shm_overview.htm >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
315 echo "</div>" >> $output #SHM overview tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
316
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
317 echo "---------------- images ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
318 echo "---------------- images ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
319
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
320 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'></a>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
321
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
322 if [ -a $outdir/scatter.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
323 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
324 echo "<a href='scatter.pdf'><img src='scatter.png'/><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
325 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
326 if [ -a $outdir/frequency_ranges.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
327 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
328 echo "<a href='frequency_ranges.pdf'><img src='frequency_ranges.png'/></a><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
329 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
330
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
331 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
332 cat $dir/shm_frequency.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
333
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
334 echo "</div>" >> $output #SHM frequency tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
335
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
336 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
337
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
338 echo "<table border='0'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
339
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
340 for gene in ${genes[@]}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
341 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
342 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
343 echo "<td><h1>${gene}</h1></td>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
344
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
345 if [ -e $outdir/transitions_heatmap_${gene}.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
346 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
347 echo "<td><a href='transitions_heatmap_${gene}.pdf'><img src='transitions_heatmap_${gene}.png' /></a></td>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
348 else
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
349 echo "<td></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
350 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
351
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
352 if [ -e $outdir/transitions_stacked_${gene}.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
353 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
354 echo "<td><a href='transitions_stacked_${gene}.pdf'><img src='transitions_stacked_${gene}.png' /></a></td>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
355 else
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
356 echo "<td></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
357 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
358
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
359 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
360 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
361 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
362 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
363 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
364 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
365 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
366 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
367 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
368 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
369 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
370 done < $outdir/transitions_${gene}_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
371 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
372
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
373 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
374 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
375
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
376 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
377 echo "<td><h1>All</h1></td>" >> $output
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
378 echo "<td><a href='transitions_heatmap_all.pdf'><img src='transitions_heatmap_all.png' /></a></td>" >> $output
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
379 echo "<td><a href='transitions_stacked_all.pdf'><img src='transitions_stacked_all.png' /></a></td>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
380 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
381 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
382 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
383 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
384 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
385 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
386 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
387 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
388 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
389 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
390 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
391 done < $outdir/transitions_all_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
392 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
393
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
394 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
395
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
396 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
397
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
398 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
399 cat $dir/shm_transition.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
400
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
401 echo "</div>" >> $output #transition tables tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
402
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
403 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
404
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
405 if [ -e $outdir/aa_histogram.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
406 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
407 echo "<a href='aa_histogram.pdf'><img src='aa_histogram.png'/></a><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
408 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
409
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
410 if [ -e $outdir/aa_histogram_IGA.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
411 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
412 echo "<a href='aa_histogram_IGA.pdf'><img src='aa_histogram_IGA.png'/></a><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
413 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
414
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
415 if [ -e $outdir/aa_histogram_IGG.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
416 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
417 echo "<a href='aa_histogram_IGG.pdf'><img src='aa_histogram_IGG.png'/></a><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
418 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
419
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
420 if [ -e $outdir/aa_histogram_IGM.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
421 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
422 echo "<a href='aa_histogram_IGM.pdf'><img src='aa_histogram_IGM.png'/></a><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
423 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
424
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
425 if [ -e $outdir/aa_histogram_IGE.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
426 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
427 echo "<a href='aa_histogram_IGE.pdf'><img src='aa_histogram_IGE.png'/></a><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
428 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
429
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
430
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
431
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
432 if [[ "$fast" == "no" ]] ; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
433
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
434
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
435
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
436 echo "---------------- baseline ----------------"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
437 echo "---------------- baseline ----------------<br />" >> $log
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
438 tmp="$PWD"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
439
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
440 mkdir $outdir/baseline
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
441
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
442 echo "<center><h1>BASELINe</h1>" >> $output
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
443 header_substring="Based on CDR1, FR2, CDR2, FR3 (27:27:38:55:65:104:-)"
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
444
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
445 baseline_boundaries="27:27:38:55:65:104:-"
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
446
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
447 if [[ "${empty_region_filter}" == "leader" ]] ; then
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
448 baseline_boundaries="1:26:38:55:65:104:-"
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
449 header_substring="Based on FR1, CDR1, FR2, CDR2, FR3 (1:26:38:55:65:104,-)"
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
450 fi
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
451
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
452 echo "<p>${header_substring}</p></center>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
453
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
454 mkdir $outdir/baseline/IGA_IGG_IGM
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
455 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
456 cd $outdir/baseline/IGA_IGG_IGM
41
b8ac74723ab0 Uploaded
davidvanzessen
parents: 40
diff changeset
457 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT.txz "IGA_IGG_IGM_IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
458 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
459 echo "No sequences" > "$outdir/baseline.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
460 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
461
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
462 mkdir $outdir/baseline/IGA
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
463 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
464 cd $outdir/baseline/IGA
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
465 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
466 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
467 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
468 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
469
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
470 mkdir $outdir/baseline/IGG
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
471 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
472 cd $outdir/baseline/IGG
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
473 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
474 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
475 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
476 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
477
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
478 mkdir $outdir/baseline/IGM
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
479 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
480 cd $outdir/baseline/IGM
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
481 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
482 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
483 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
484 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
485
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
486 mkdir $outdir/baseline/IGE
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
487 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
488 cd $outdir/baseline/IGE
37
767dd9327009 Uploaded
davidvanzessen
parents: 36
diff changeset
489 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
490 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
491 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
492 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
493
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
494 cd $tmp
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
495
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
496 echo "Cleaning up *.RData files"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
497 find $outdir/baseline -name "*.RData" -type f -delete
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
498
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
499 if [ -e $outdir/baseline.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
500 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
501 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
502 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
503
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
504 if [ -e $outdir/baseline_IGA.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
505 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
506 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
507 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
508
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
509 if [ -e $outdir/baseline_IGG.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
510 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
511 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
512 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
513
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
514 if [ -e $outdir/baseline_IGM.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
515 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
516 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
517 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
518
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
519 if [ -e $outdir/baseline_IGE.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
520 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
521 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
522 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
523 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
524
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
525 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
526 cat $dir/shm_selection.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
527
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
528 echo "</div>" >> $output #antigen selection tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
529
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
530 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
531
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
532 if [ -e $outdir/IGA.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
533 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
534 echo "<a href='IGA.pdf'><img src='IGA.png'/></a><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
535 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
536 if [ -e $outdir/IGG.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
537 then
42
1cf60ae234b4 Uploaded
davidvanzessen
parents: 41
diff changeset
538 echo "<a href='IGG.pdf'><img src='IGG.png'/></a><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
539 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
540
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
541 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
542 cat $dir/shm_csr.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
543
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
544 echo "</div>" >> $output #CSR tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
545
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
546 if [[ "$fast" == "no" ]] ; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
547
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
548 echo "---------------- change-o MakeDB ----------------"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
549
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
550 mkdir $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
551
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
552 tmp="$PWD"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
553
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
554 cd $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
555
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
556 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
557 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-defined_clones-summary.txt
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
558 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-db-defined_first_clones.txt 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
559
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
560 mkdir $outdir/new_IMGT_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
561 cp $outdir/new_IMGT/* $outdir/new_IMGT_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
562
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
563 Rscript $dir/new_imgt.r $outdir/new_IMGT_changeo $outdir/change_o/change-o-db-defined_first_clones.txt "-" 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
564
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
565 cd $outdir/new_IMGT_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
566 tar -cJf ../new_IMGT_first_seq_of_clone.txz *
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
567 cd $outdir/change_o
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
568
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
569 rm -rf $outdir/new_IMGT_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
570
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
571 Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/merged.txt "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" $outdir/change_o/change-o-db-defined_clones.txt 2>&1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
572 echo "Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/$outdir/merged.txt 'all' 'Sequence.ID,best_match' 'Sequence.ID' 'Sequence.ID' '\t' $outdir/change_o/change-o-db-defined_clones.txt 2>&1"
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
573
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
574 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
575 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
576 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGA.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGA.txt $outdir/change_o/change-o-defined_clones-summary-IGA.txt
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
577 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGA.txt $outdir/change_o/change-o-db-defined_first_clones-IGA.txt 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
578
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
579 mkdir $outdir/new_IMGT_IGA_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
580 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
581
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
582 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA_changeo $outdir/change_o/change-o-db-defined_first_clones-IGA.txt "-" 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
583
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
584 cd $outdir/new_IMGT_IGA_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
585 tar -cJf ../new_IMGT_IGA_first_seq_of_clone.txz *
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
586
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
587 rm -rf $outdir/new_IMGT_IGA_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
588
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
589 cd $outdir/change_o
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
590 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
591 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
592 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
593 fi
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
594
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
595 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
596 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
597 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGG.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGG.txt $outdir/change_o/change-o-defined_clones-summary-IGG.txt
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
598 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGG.txt $outdir/change_o/change-o-db-defined_first_clones-IGG.txt 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
599
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
600 mkdir $outdir/new_IMGT_IGG_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
601 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
602
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
603 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG_changeo $outdir/change_o/change-o-db-defined_first_clones-IGG.txt "-" 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
604
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
605 cd $outdir/new_IMGT_IGG_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
606 tar -cJf ../new_IMGT_IGG_first_seq_of_clone.txz *
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
607 rm -rf $outdir/new_IMGT_IGG_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
608
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
609 cd $outdir/change_o
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
610 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
611 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
612 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
613 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
614
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
615 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
616 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
617 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGM.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-defined_clones-summary-IGM.txt
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
618 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-db-defined_first_clones-IGM.txt 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
619
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
620 mkdir $outdir/new_IMGT_IGM_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
621 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
622
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
623 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM_changeo $outdir/change_o/change-o-db-defined_first_clones-IGM.txt "-" 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
624
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
625 cd $outdir/new_IMGT_IGM_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
626 tar -cJf ../new_IMGT_IGM_first_seq_of_clone.txz *
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
627
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
628 rm -rf $outdir/new_IMGT_IGM_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
629
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
630 cd $outdir/change_o
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
631 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
632 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
633 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
634 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
635
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
636 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
637 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
638 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGE.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-defined_clones-summary-IGE.txt
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
639 Rscript $dir/change_o/select_first_in_clone.r $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-db-defined_first_clones-IGE.txt 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
640
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
641 mkdir $outdir/new_IMGT_IGE_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
642 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
643
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
644 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE_changeo $outdir/change_o/change-o-db-defined_first_clones-IGE.txt "-" 2>&1
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
645
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
646 cd $outdir/new_IMGT_IGE_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
647 tar -cJf ../new_IMGT_IGE_first_seq_of_clone.txz *
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
648
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
649 rm -rf $outdir/new_IMGT_IGE_changeo
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
650
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
651 cd $outdir/change_o
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
652 else
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
653 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
654 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
655 fi
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
656
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
657 cd "$tmp"
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
658
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
659 rm -rf $outdir/new_IMGT
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
660 rm -rf $outdir/new_IMGT_IGA/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
661 rm -rf $outdir/new_IMGT_IGA1/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
662 rm -rf $outdir/new_IMGT_IGA2/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
663 rm -rf $outdir/new_IMGT_IGG/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
664 rm -rf $outdir/new_IMGT_IGG1/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
665 rm -rf $outdir/new_IMGT_IGG2/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
666 rm -rf $outdir/new_IMGT_IGG3/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
667 rm -rf $outdir/new_IMGT_IGG4/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
668 rm -rf $outdir/new_IMGT_IGM/
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
669 rm -rf $outdir/new_IMGT_IGE/
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
670
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
671 echo "<div class='tabbertab' title='Clonal Relation' style='width: 7000px;'>" >> $output #clonality tab
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
672
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
673 function clonality_table {
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
674 local infile=$1
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
675 local outfile=$2
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
676
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
677 echo "<table class='pure-table pure-table-striped'>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
678 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
679
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
680 first='true'
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
681
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
682 while read size clones seqs
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
683 do
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
684 if [[ "$first" == "true" ]]; then
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
685 first="false"
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
686 continue
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
687 fi
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
688 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
689 done < $infile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
690
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
691 echo "</table>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
692 }
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
693 echo "<div class='tabber'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
694
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
695 echo "<div class='tabbertab' title='All'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
696 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
697 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
698
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
699 echo "<div class='tabbertab' title='IGA'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
700 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
701 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
702
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
703 echo "<div class='tabbertab' title='IGG'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
704 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
705 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
706
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
707 echo "<div class='tabbertab' title='IGM'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
708 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
709 echo "</div>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
710
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
711 echo "<div class='tabbertab' title='IGE'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
712 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
713 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
714
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
715 echo "<div class='tabbertab' title='Overlap' style='width: 7000px;'>" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
716 cat "$outdir/sequence_overview/index.html" | sed -e 's:</td>:</td>\n:g' | sed "s:href='\(.*\).html:href='sequence_overview/\1.html:g" >> $output # rewrite href to 'sequence_overview/..."
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
717 echo "</div>" >> $output
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
718
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
719 echo "</div>" >> $output #clonality tabber end
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
720
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
721 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
722 cat $dir/shm_clonality.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
723
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
724 echo "</div>" >> $output #clonality tab end
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
725
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
726 fi
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
727
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
728 echo "<div class='tabbertab' title='Downloads'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
729
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
730 echo "<table class='pure-table pure-table-striped'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
731 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
732 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
733 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
734 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
735
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
736 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
737 echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='shm_overview.txt' download='shm_overview.txt' >Download</a></td></tr>" >> $output
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
738 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt' download='motif_per_seq.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
739 echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt' download='mutation_by_id.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
740 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
741 echo "<tr><td>The data used to generate the percentage of mutations in AID and pol eta motives plot</td><td><a href='aid_motives.txt' download='aid_motives.txt' >Download</a></td></tr>" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
742 echo "<tr><td>The data used to generate the relative mutation patterns plot</td><td><a href='relative_mutations.txt' download='relative_mutations.txt' >Download</a></td></tr>" >> $output
43
77a7ac76c7b9 Uploaded
davidvanzessen
parents: 42
diff changeset
743 echo "<tr><td>The data used to generate the absolute mutation patterns plot</td><td><a href='absolute_mutations.txt' download='absolute_mutations.txt' >Download</a></td></tr>" >> $output
47
64711f461c8e Uploaded
davidvanzessen
parents: 45
diff changeset
744 echo "<tr><td>Data about tandem mutations by ID</td><td><a href='tandems_by_id.txt' download='tandems_by_id.txt' >Download</a></td></tr>" >> $output
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
745
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
746 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
747 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
748 echo "<tr><td>The data used to generate the frequency by class plot</td><td><a href='frequency_ranges_classes.txt' download='frequency_ranges_classes.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
749 echo "<tr><td>The data for frequency by subclass</td><td><a href='frequency_ranges_subclasses.txt' download='frequency_ranges_subclasses.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
750
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
751 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
752 echo "<tr><td>The data for the 'all' transition plot</td><td><a href='transitions_all_sum.txt' download='transitions_all_sum.txt' >Download</a></td></tr>" >> $output
45
b66e8946ba75 Uploaded
davidvanzessen
parents: 43
diff changeset
753 echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transitions_IGA_sum.txt' download='transitions_IGA_sum.txt' >Download</a></td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
754 echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transitions_IGA1_sum.txt' download='transitions_IGA1_sum.txt' >Download</a></td></tr>" >> $output
30
33a7c49d48a7 Uploaded
davidvanzessen
parents: 29
diff changeset
755 echo "<tr><td>The data for the 'IGA2' transition plot</td><td><a href='transitions_IGA2_sum.txt' download='transitions_IGA2_sum.txt' >Download</a></td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
756 echo "<tr><td>The data for the 'IGG' transition plot</td><td><a href='transitions_IGG_sum.txt' download='transitions_IGG_sum.txt' >Download</a></td></tr>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
757 echo "<tr><td>The data for the 'IGG1' transition plot</td><td><a href='transitions_IGG1_sum.txt' download='transitions_IGG1_sum.txt' >Download</a></td></tr>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
758 echo "<tr><td>The data for the 'IGG2' transition plot</td><td><a href='transitions_IGG2_sum.txt' download='transitions_IGG2_sum.txt' >Download</a></td></tr>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
759 echo "<tr><td>The data for the 'IGG3' transition plot</td><td><a href='transitions_IGG3_sum.txt' download='transitions_IGG3_sum.txt' >Download</a></td></tr>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
760 echo "<tr><td>The data for the 'IGG4' transition plot</td><td><a href='transitions_IGG4_sum.txt' download='transitions_IGG4_sum.txt' >Download</a></td></tr>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
761 echo "<tr><td>The data for the 'IGM' transition plot</td><td><a href='transitions_IGM_sum.txt' download='transitions_IGM_sum.txt' >Download</a></td></tr>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
762 echo "<tr><td>The data for the 'IGE' transition plot</td><td><a href='transitions_IGE_sum.txt' download='transitions_IGE_sum.txt' >Download</a></td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
763
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
764 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
765 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt' download='aa_id_mutations.txt' >Download</a></td></tr>" >> $output
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
766 echo "<tr><td>Presence of AA per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
767
29
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
768 echo "<tr><td>The data used to generate the aa mutation frequency plot</td><td><a href='aa_histogram_sum.txt' download='aa_histogram_sum.txt' >Download</a></td></tr>" >> $output
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
769 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGA</td><td><a href='aa_histogram_sum_IGA.txt' download='aa_histogram_sum_IGA.txt' >Download</a></td></tr>" >> $output
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
770 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGG</td><td><a href='aa_histogram_sum_IGG.txt' download='aa_histogram_sum_IGG.txt' >Download</a></td></tr>" >> $output
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
771 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGM</td><td><a href='aa_histogram_sum_IGM.txt' download='aa_histogram_sum_IGM.txt' >Download</a></td></tr>" >> $output
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
772 echo "<tr><td>The data used to generate the aa mutation frequency plot for IGE</td><td><a href='aa_histogram_sum_IGE.txt' download='aa_histogram_sum_IGE.txt' >Download</a></td></tr>" >> $output
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
773
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
774 echo "<tr><td>Baseline PDF (<a href='http://selection.med.yale.edu/baseline/'>http://selection.med.yale.edu/baseline/</a>)</td><td><a href='baseline.pdf' download='baseline.pdf' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
775 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
776 echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
777 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
778 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
779 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
780 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
781 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
31
fe44a905aee9 Uploaded
davidvanzessen
parents: 30
diff changeset
782 echo "<tr><td>Baseline IGE PDF</td><td><a href='baseline_IGE.pdf' download='baseline_IGE.pdf' >Download</a></td></tr>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
783 echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
784
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
785 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
786 echo "<tr><td>The data for the IGA subclass distribution plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
787 echo "<tr><td>The data for the IGG subclass distribution plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
788
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
789
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
790 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
791 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
792 echo "<tr><td>The Change-O DB file with defined clones and subclass annotation</td><td><a href='change_o/change-o-db-defined_clones.txt' download='change_o/change-o-db-defined_clones.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
793 echo "<tr><td>The Change-O DB defined clones summary file</td><td><a href='change_o/change-o-defined_clones-summary.txt' download='change_o/change-o-defined_clones-summary.txt' >Download</a></td></tr>" >> $output
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
794 echo "<tr><td>An IMGT archive with just just the first sequence of a clone</td><td><a href='new_IMGT_first_seq_of_clone.txz' download='new_IMGT_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
795
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
796 echo "<tr><td>The Change-O DB file with defined clones of IGA</td><td><a href='change_o/change-o-db-defined_clones-IGA.txt' download='change_o/change-o-db-defined_clones-IGA.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
797 echo "<tr><td>The Change-O DB defined clones summary file of IGA</td><td><a href='change_o/change-o-defined_clones-summary-IGA.txt' download='change_o/change-o-defined_clones-summary-IGA.txt' >Download</a></td></tr>" >> $output
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
798 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGA)</td><td><a href='new_IMGT_IGA_first_seq_of_clone.txz' download='new_IMGT_IGA_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
799
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
800 echo "<tr><td>The Change-O DB file with defined clones of IGG</td><td><a href='change_o/change-o-db-defined_clones-IGG.txt' download='change_o/change-o-db-defined_clones-IGG.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
801 echo "<tr><td>The Change-O DB defined clones summary file of IGG</td><td><a href='change_o/change-o-defined_clones-summary-IGG.txt' download='change_o/change-o-defined_clones-summary-IGG.txt' >Download</a></td></tr>" >> $output
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
802 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGG)</td><td><a href='new_IMGT_IGG_first_seq_of_clone.txz' download='new_IMGT_IGG_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
803
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
804 echo "<tr><td>The Change-O DB file with defined clones of IGM</td><td><a href='change_o/change-o-db-defined_clones-IGM.txt' download='change_o/change-o-db-defined_clones-IGM.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
805 echo "<tr><td>The Change-O DB defined clones summary file of IGM</td><td><a href='change_o/change-o-defined_clones-summary-IGM.txt' download='change_o/change-o-defined_clones-summary-IGM.txt' >Download</a></td></tr>" >> $output
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
806 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGM)</td><td><a href='new_IMGT_IGM_first_seq_of_clone.txz' download='new_IMGT_IGM_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
807
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
808 echo "<tr><td>The Change-O DB file with defined clones of IGE</td><td><a href='change_o/change-o-db-defined_clones-IGE.txt' download='change_o/change-o-db-defined_clones-IGE.txt' >Download</a></td></tr>" >> $output
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
809 echo "<tr><td>The Change-O DB defined clones summary file of IGE</td><td><a href='change_o/change-o-defined_clones-summary-IGE.txt' download='change_o/change-o-defined_clones-summary-IGE.txt' >Download</a></td></tr>" >> $output
55
6cd12c71c3d3 Uploaded
davidvanzessen
parents: 49
diff changeset
810 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGE)</td><td><a href='new_IMGT_IGE_first_seq_of_clone.txz' download='new_IMGT_IGE_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
811
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
812 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
813 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz' download='new_IMGT.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
814 echo "<tr><td>An IMGT archive with just the matched and filtered IGA sequences</td><td><a href='new_IMGT_IGA.txz' download='new_IMGT_IGA.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
815 echo "<tr><td>An IMGT archive with just the matched and filtered IGA1 sequences</td><td><a href='new_IMGT_IGA1.txz' download='new_IMGT_IGA1.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
816 echo "<tr><td>An IMGT archive with just the matched and filtered IGA2 sequences</td><td><a href='new_IMGT_IGA2.txz' download='new_IMGT_IGA2.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
817 echo "<tr><td>An IMGT archive with just the matched and filtered IGG sequences</td><td><a href='new_IMGT_IGG.txz' download='new_IMGT_IGG.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
818 echo "<tr><td>An IMGT archive with just the matched and filtered IGG1 sequences</td><td><a href='new_IMGT_IGG1.txz' download='new_IMGT_IGG1.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
819 echo "<tr><td>An IMGT archive with just the matched and filtered IGG2 sequences</td><td><a href='new_IMGT_IGG2.txz' download='new_IMGT_IGG2.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
820 echo "<tr><td>An IMGT archive with just the matched and filtered IGG3 sequences</td><td><a href='new_IMGT_IGG3.txz' download='new_IMGT_IGG3.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
821 echo "<tr><td>An IMGT archive with just the matched and filtered IGG4 sequences</td><td><a href='new_IMGT_IGG4.txz' download='new_IMGT_IGG4.txz' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
822 echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='new_IMGT_IGM.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output
31
fe44a905aee9 Uploaded
davidvanzessen
parents: 30
diff changeset
823 echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='new_IMGT_IGE.txz' download='new_IMGT_IGE.txz' >Download</a></td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
824
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
825 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
826
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
827 echo "<br />" >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
828 cat $dir/shm_downloads.htm >> $output
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
829
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
830 echo "</div>" >> $output #downloads tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
831
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
832 echo "</div>" >> $output #tabs end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
833
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
834 echo "</html>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
835
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
836
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
837 echo "---------------- naive_output.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
838 echo "---------------- naive_output.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
839
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
840 if [[ "$naive_output" == "yes" ]]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
841 then
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
842 echo "output naive output"
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
843 if [[ "${class_filter}" == "101_101" ]]
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
844 then
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
845 echo "copy new_IMGT.txz to ${naive_output_all}"
21
c281993e515b Uploaded
davidvanzessen
parents: 20
diff changeset
846 cp $outdir/new_IMGT.txz ${naive_output_all}
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
847 else
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
848 echo "copy for classes"
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
849 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
850 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
851 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
852 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
853 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
854 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
855
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
856 echo "</table>" >> $outdir/base_overview.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
857
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
858 mv $log $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
859
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
860 echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)<br />" > $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
861 echo "<table border = 1>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
862 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
863 tIFS="$TMP"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
864 IFS=$'\t'
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
865 while read step seq perc
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
866 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
867 echo "<tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
868 echo "<td>$step</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
869 echo "<td>$seq</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
870 echo "<td>${perc}%</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
871 echo "</tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
872 done < $outdir/filtering_steps.txt
39
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
873 echo "</table>" >> $log
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
874 echo "<br />" >> $log
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
875 cat $dir/shm_first.htm >> $log
a24f8c93583a Uploaded
davidvanzessen
parents: 37
diff changeset
876 echo "</center></html>" >> $log
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
877
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
878 IFS="$tIFS"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
879
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
880
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
881 echo "---------------- Done! ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
882 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
883
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
884
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
885
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
886
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
887
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
888
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
889
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
890
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
891
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
892
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
893
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
894
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
895
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
896
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
897
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
898
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
899
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
900
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
901
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
902
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
903