annotate wrapper.sh @ 33:22fabe161cf3 draft

Uploaded
author davidvanzessen
date Thu, 15 Dec 2016 09:44:17 -0500
parents 4c5ba6b5d10d
children 96c1276ceefe
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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
9 title=$5
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=${15}
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
20 class_filter=${16}
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
21 empty_region_filter=${17}
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
22 fast=${18}
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
23 mkdir $outdir
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
24
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
25 tar -xzf $dir/style.tar.gz -C $outdir
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
26
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
27 echo "---------------- read parameters ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
28 echo "---------------- read parameters ----------------<br />" > $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
29
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
30 echo "unpacking IMGT file"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
31
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
32 type="`file $input`"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
33 if [[ "$type" == *"Zip archive"* ]] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
34 echo "Zip archive"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
35 echo "unzip $input -d $PWD/files/"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
36 unzip $input -d $PWD/files/
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
37 elif [[ "$type" == *"XZ compressed data"* ]] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
38 echo "ZX archive"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
39 echo "tar -xJf $input -C $PWD/files/"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
40 mkdir -p $PWD/files/$title
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
41 tar -xJf $input -C $PWD/files/$title
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
42 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
43
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
44 cat `find $PWD/files/ -name "1_*"` > $PWD/summary.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
45 cat `find $PWD/files/ -name "3_*"` > $PWD/sequences.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
46 cat `find $PWD/files/ -name "5_*"` > $PWD/aa.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
47 cat `find $PWD/files/ -name "6_*"` > $PWD/junction.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
48 cat `find $PWD/files/ -name "7_*"` > $PWD/mutationanalysis.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
49 cat `find $PWD/files/ -name "8_*"` > $PWD/mutationstats.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
50 cat `find $PWD/files/ -name "10_*"` > $PWD/hotspots.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
51
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
52 if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
53 echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
54 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
55 BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
56 echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
57 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
58
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
59 echo "---------------- class identification ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
60 echo "---------------- class identification ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
61
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
62 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
63
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
64 echo "---------------- merge_and_filter.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
65 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
66
14
59765d2c8890 Uploaded
davidvanzessen
parents: 7
diff changeset
67 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $PWD/aa.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
68
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
69 if [[ "$fast" == "no" ]] ; then
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
70
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
71 echo "---------------- creating new IMGT zips ----------------"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
72 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
73
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
74 mkdir $outdir/new_IMGT
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
75
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
76 cat `find $PWD/files/ -name "1_*"` > "$outdir/new_IMGT/1_Summary.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
77 cat `find $PWD/files/ -name "2_*"` > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
78 cat `find $PWD/files/ -name "3_*"` > "$outdir/new_IMGT/3_Nt-sequences.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
79 cat `find $PWD/files/ -name "4_*"` > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
80 cat `find $PWD/files/ -name "5_*"` > "$outdir/new_IMGT/5_AA-sequences.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
81 cat `find $PWD/files/ -name "6_*"` > "$outdir/new_IMGT/6_Junction.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
82 cat `find $PWD/files/ -name "7_*"` > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
83 cat `find $PWD/files/ -name "8_*"` > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
84 cat `find $PWD/files/ -name "9_*"` > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
85 cat `find $PWD/files/ -name "10_*"` > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
86
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
87 mkdir $outdir/new_IMGT_IGA
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
88 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
89
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
90 mkdir $outdir/new_IMGT_IGA1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
91 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
92
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
93 mkdir $outdir/new_IMGT_IGA2
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
94 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
95
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
96 mkdir $outdir/new_IMGT_IGG
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
97 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
98
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
99 mkdir $outdir/new_IMGT_IGG1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
100 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
101
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
102 mkdir $outdir/new_IMGT_IGG2
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
103 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
104
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
105 mkdir $outdir/new_IMGT_IGG3
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
106 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
107
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
108 mkdir $outdir/new_IMGT_IGG4
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
109 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
110
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
111 mkdir $outdir/new_IMGT_IGM
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
112 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
113
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
114 mkdir $outdir/new_IMGT_IGE
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
115 cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
116
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
117 Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
118
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
119 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
120 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
121 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
122
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
123 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
124 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
125 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
126 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
127 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
128
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
129 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
130
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
131 Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
132
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
133
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
134 tmp="$PWD"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
135 cd $outdir/new_IMGT/ #tar weirdness...
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
136 tar -cJf ../new_IMGT.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
137
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
138 cd $outdir/new_IMGT_IGA/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
139 tar -cJf ../new_IMGT_IGA.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
140
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
141 cd $outdir/new_IMGT_IGA1/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
142 tar -cJf ../new_IMGT_IGA1.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
143
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
144 cd $outdir/new_IMGT_IGA2/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
145 tar -cJf ../new_IMGT_IGA2.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
146
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
147 cd $outdir/new_IMGT_IGG/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
148 tar -cJf ../new_IMGT_IGG.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
149
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
150 cd $outdir/new_IMGT_IGG1/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
151 tar -cJf ../new_IMGT_IGG1.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
152
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
153 cd $outdir/new_IMGT_IGG2/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
154 tar -cJf ../new_IMGT_IGG2.txz *
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
155
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
156 cd $outdir/new_IMGT_IGG3/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
157 tar -cJf ../new_IMGT_IGG3.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
158
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
159 cd $outdir/new_IMGT_IGG4/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
160 tar -cJf ../new_IMGT_IGG4.txz *
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
161
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
162 cd $outdir/new_IMGT_IGM/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
163 tar -cJf ../new_IMGT_IGM.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
164
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
165 cd $outdir/new_IMGT_IGE/
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
166 tar -cJf ../new_IMGT_IGE.txz *
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
167
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
168 cd $tmp
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
169 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
170
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
171 echo "---------------- shm_csr.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
172 echo "---------------- shm_csr.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
173
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
174 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
175 echo "R mutation analysis"
1
faae21ba5c63 Uploaded
davidvanzessen
parents: 0
diff changeset
176 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
177
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
178 echo "---------------- shm_csr.py ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
179 echo "---------------- shm_csr.py ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
180
1
faae21ba5c63 Uploaded
davidvanzessen
parents: 0
diff changeset
181 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
182
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
183 echo "---------------- aa_histogram.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
184 echo "---------------- aa_histogram.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
185
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
186 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
187 if [ -e "$outdir/aa_histogram_.png" ]; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
188 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
189 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
29
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
190 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
191 mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
192 mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
193 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
194
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
195 genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
196
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
197 funcs=(sum mean median)
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
198 funcs=(sum)
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
199
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
200 echo "---------------- sequence_overview.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
201 echo "---------------- sequence_overview.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
202
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
203 mkdir $outdir/sequence_overview
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
204
7
ad9be244b104 Uploaded
davidvanzessen
parents: 6
diff changeset
205 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
206
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
207 echo "<table border='1'>" > $outdir/base_overview.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
208
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
209 while IFS=$'\t' read ID class seq A C G T
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
210 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
211 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
212 done < $outdir/sequence_overview/ntoverview.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
213
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
214 echo "<html><center><h1>$title</h1></center>" > $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
215 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
216 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
217 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
218 echo "<script type='text/javascript' src='script.js'></script>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
219 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
220 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
221
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
222 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
223 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
224 total_count=$((matched_count + unmatched_count))
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
225 perc_count=$((unmatched_count / total_count * 100))
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
226 perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
227 perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
228
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
229 echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
230 echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
231 echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
232
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
233 echo "---------------- main tables ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
234 echo "---------------- main tables ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
235
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
236 echo "<div class='tabber'>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
237 echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
238
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
239 for func in ${funcs[@]}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
240 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
241
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
242 echo "---------------- $func table ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
243 echo "---------------- $func table ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
244
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
245 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
246
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
247 echo "---------------- pattern_plots.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
248 echo "---------------- pattern_plots.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
249
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
250 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/plot1 $outdir/plot2 $outdir/plot3 $outdir/shm_overview.txt 2>&1
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
251
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
252 echo "<table class='pure-table pure-table-striped'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
253 echo "<thead><tr><th>info</th>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
254
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
255 if [ "${class_filter}" != "101_101" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
256
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
257 for gene in ${genes[@]}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
258 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
259 tmp=`cat $outdir/${gene}_${func}_n.txt`
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
260 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
261 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
262
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
263 tmp=`cat $outdir/all_${func}_n.txt`
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
264 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
265 tmp=`cat $outdir/unmatched_${func}_n.txt`
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
266 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
267
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
268 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
269 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
270 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
271 echo "<tr><td>$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>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
272 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
273 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>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
274 else
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
275 echo "<tr><td>$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
276 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
277 done < $outdir/data_${func}.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
278
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
279 else
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
280 tmp=`cat $outdir/all_${func}_n.txt`
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
281 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
282
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
283 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz cex cey cez unx uny unz allx ally allz
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
284 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
285 if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
286 echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
287 elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
288 echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
289 else
3
275ab5175fd6 Uploaded
davidvanzessen
parents: 2
diff changeset
290 echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
291 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
292 done < $outdir/data_${func}.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
293
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
294 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
295 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
296 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
297 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
298
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
299 echo "<img src='plot1.png' /><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
300 echo "<img src='plot2.png' /><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
301 echo "<img src='plot3.png' /><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
302
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
303 echo "</div>" >> $output #SHM overview tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
304
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
305 echo "---------------- images ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
306 echo "---------------- images ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
307
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
308 echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
309
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
310 if [ -a $outdir/scatter.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
311 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
312 echo "<img src='scatter.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
313 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
314 if [ -a $outdir/frequency_ranges.png ]
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
315 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
316 echo "<img src='frequency_ranges.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
317 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
318
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
319 echo "</div>" >> $output #SHM frequency tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
320
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
321 echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
322
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
323 echo "<table border='0'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
324
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
325 for gene in ${genes[@]}
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
326 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
327 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
328 echo "<td><h1>${gene}</h1></td>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
329
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
330 if [ -e $outdir/transitions_heatmap_${gene}.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
331 then
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
332 echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
333 else
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
334 echo "<td></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
335 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
336
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
337 if [ -e $outdir/transitions_stacked_${gene}.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
338 then
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
339 echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
340 else
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
341 echo "<td></td>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
342 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
343
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
344 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
345 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
346 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
347 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
348 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
349 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
350 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
351 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
352 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
353 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
354 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
355 done < $outdir/transitions_${gene}_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
356 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
357
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
358 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
359 done
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
360
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
361 echo "<tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
362 echo "<td><h1>All</h1></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
363 echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
364 echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
365 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
366 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
367 first="true"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
368 while IFS=, read from a c g t
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
369 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
370 if [ "$first" == "true" ] ; then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
371 echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
372 first="false"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
373 else
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
374 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
375 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
376 done < $outdir/transitions_all_sum.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
377 echo "</table></td>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
378
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
379 echo "</tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
380
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
381 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
382
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
383 echo "</div>" >> $output #transition tables tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
384
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
385 echo "<div class='tabbertab' title='Antigen Selection'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
386
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
387 if [ -e $outdir/aa_histogram.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
388 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
389 echo "<img src='aa_histogram.png'/><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
390 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
391
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
392 if [ -e $outdir/aa_histogram_IGA.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
393 then
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
394 echo "<img src='aa_histogram_IGA.png'/><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
395 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
396
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
397 if [ -e $outdir/aa_histogram_IGG.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
398 then
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
399 echo "<img src='aa_histogram_IGG.png'/><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
400 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
401
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
402 if [ -e $outdir/aa_histogram_IGM.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
403 then
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
404 echo "<img src='aa_histogram_IGM.png'/><br />" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
405 fi
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
406
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
407 if [ -e $outdir/aa_histogram_IGE.png ]
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
408 then
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
409 echo "<img src='aa_histogram_IGE.png'/><br />" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
410 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
411
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
412
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
413
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
414 if [[ "$fast" == "no" ]] ; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
415
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
416 echo "---------------- baseline ----------------"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
417 echo "---------------- baseline ----------------<br />" >> $log
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
418 tmp="$PWD"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
419
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
420 mkdir $outdir/baseline
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
421
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
422
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
423 mkdir $outdir/baseline/IGA_IGG_IGM
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
424 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
425 cd $outdir/baseline/IGA_IGG_IGM
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
426 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "IGA_IGG_IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
427 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
428 echo "No sequences" > "$outdir/baseline.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
429 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
430
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
431 mkdir $outdir/baseline/IGA
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
432 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
433 cd $outdir/baseline/IGA
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
434 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
435 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
436 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
437 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
438
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
439 mkdir $outdir/baseline/IGG
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
440 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
441 cd $outdir/baseline/IGG
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
442 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
443 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
444 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
445 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
446
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
447 mkdir $outdir/baseline/IGM
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
448 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
449 cd $outdir/baseline/IGM
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
450 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
451 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
452 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
453 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
454
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
455 mkdir $outdir/baseline/IGE
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
456 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
457 cd $outdir/baseline/IGE
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
458 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
459 else
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
460 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
461 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
462
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
463 cd $tmp
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
464
33
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
465 echo "Cleaning up *.RData files"
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
466 find $outdir/baseline -name "*.RData" -type f -delete
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
467
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
468 if [ -e $outdir/baseline.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
469 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
470 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
471 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
472
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
473 if [ -e $outdir/baseline_IGA.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
474 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
475 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
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 if [ -e $outdir/baseline_IGG.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
479 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
480 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
481 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
482
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
483 if [ -e $outdir/baseline_IGM.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
484 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
485 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
486 fi
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
487
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
488 if [ -e $outdir/baseline_IGE.pdf ]
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
489 then
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
490 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
22fabe161cf3 Uploaded
davidvanzessen
parents: 32
diff changeset
491 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
492 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
493
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
494 echo "</div>" >> $output #antigen selection tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
495
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
496 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
497
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
498 if [ -e $outdir/IGA.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
499 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
500 echo "<img src='IGA.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
501 fi
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
502 if [ -e $outdir/IGG.png ]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
503 then
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
504 echo "<img src='IGG.png'/><br />" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
505 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
506
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
507 echo "</div>" >> $output #CSR tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
508
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
509 if [[ "$fast" == "no" ]] ; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
510
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
511 echo "---------------- change-o MakeDB ----------------"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
512
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
513 mkdir $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
514
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
515 tmp="$PWD"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
516
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
517 cd $outdir/change_o
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
518
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
519 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
520 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
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
521
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
522 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
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
523
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
524 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"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
525
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
526 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
527 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
528 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 $outdir/change_o/change-o-defined_clones-summary-IGA.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
529 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
530 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
531 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
532 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
533
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
534 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
535 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
536 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 $outdir/change_o/change-o-defined_clones-summary-IGG.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
537 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
538 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
539 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
540 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
541
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
542 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
543 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
544 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 $outdir/change_o/change-o-defined_clones-summary-IGM.txt
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
545 else
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
546 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
547 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
548 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
549
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
550 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
551 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
552 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 $outdir/change_o/change-o-defined_clones-summary-IGE.txt
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
553 else
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
554 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
555 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
556 fi
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
557
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
558 PWD="$tmp"
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
559
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
560 echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
561
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
562 function clonality_table {
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
563 local infile=$1
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
564 local outfile=$2
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
565
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
566 echo "<table class='pure-table pure-table-striped'>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
567 echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
568
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
569 first='true'
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
570
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
571 while read size clones seqs
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
572 do
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
573 if [[ "$first" == "true" ]]; then
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
574 first="false"
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
575 continue
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
576 fi
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
577 echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
578 done < $infile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
579
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
580 echo "</table>" >> $outfile
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
581 }
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
582 echo "<div class='tabber'>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
583
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
584 echo "<div class='tabbertab' title='All'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
585 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
586 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
587
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
588 echo "<div class='tabbertab' title='IGA'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
589 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
590 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
591
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
592 echo "<div class='tabbertab' title='IGG'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
593 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
594 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
595
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
596 echo "<div class='tabbertab' title='IGM'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
597 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
598 echo "</div>" >> $output
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
599
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
600 echo "<div class='tabbertab' title='IGE'>" >> $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
601 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
602 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
603
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
604 echo "<div class='tabbertab' title='Overlap'>" >> $output
31
fe44a905aee9 Uploaded
davidvanzessen
parents: 30
diff changeset
605 cat "$outdir/sequence_overview/index.html" | sed "s%href='\(.*\).html%href='sequence_overview/\1.html%g" >> $output # rewrite href to 'sequence_overview/..."
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
606 echo "</div>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
607
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
608
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
609 echo "</div>" >> $output #clonality tabber end
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
610
16
4e596473c25c Uploaded
davidvanzessen
parents: 14
diff changeset
611 echo "</div>" >> $output #clonality tab end
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
612
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
613 fi
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
614
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
615 echo "<div class='tabbertab' title='Downloads'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
616
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
617 echo "<table class='pure-table pure-table-striped'>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
618 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
619 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
620 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
621 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
622
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
623 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
624 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
625 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
626 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
627 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
628 echo "<tr><td>The data used to generate the RGYW/WRCY and TW/WA plot</td><td><a href='plot1.txt' download='plot1.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
629 echo "<tr><td>The data used to generate the relative transition and transversion plot</td><td><a href='plot2.txt' download='plot2.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
630 echo "<tr><td>The data used to generate the absolute transition and transversion plot</td><td><a href='plot3.txt' download='plot3.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
631
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
632 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
633 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
634 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
635 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
636
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
637 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
23
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
638 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
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
639 echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transitions_IGA_sum.txt' download='transitions_all_sum.txt' >Download</a></td></tr>" >> $output
81453585dfc3 Uploaded
davidvanzessen
parents: 21
diff changeset
640 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
641 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
642 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
643 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
644 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
645 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
646 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
647 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
648 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
649
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
650 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
651 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
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
652 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
653
29
80c4eebf7bc9 Uploaded
davidvanzessen
parents: 28
diff changeset
654 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
655 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
656 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
657 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
658 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
659
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
660 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
661 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
662 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
663 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
664 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
665 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
666 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
667 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
668 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
669 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
670
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
671 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
672 echo "<tr><td>The data for the CSR IGA pie plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
673 echo "<tr><td>The data for the CSR IGG pie plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
674
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
675 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>" >> $output
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
676 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
677 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
678 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
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
679 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
680 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
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
681 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
682 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
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
683 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
684 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
6
2ddb9a21f635 Uploaded
davidvanzessen
parents: 5
diff changeset
685 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
686 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
2
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
687
e85fec274cde Uploaded
davidvanzessen
parents: 1
diff changeset
688 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
689 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
690 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
691 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
692 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
693 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
694 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
695 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
696 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
697 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
698 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
699 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
700
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
701 echo "</table>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
702
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
703 echo "</div>" >> $output #downloads tab end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
704
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
705 echo "</div>" >> $output #tabs end
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
706
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
707 echo "</html>" >> $output
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
708
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
709
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
710 echo "---------------- naive_output.r ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
711 echo "---------------- naive_output.r ----------------<br />" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
712
5
012a738edf5a Uploaded
davidvanzessen
parents: 4
diff changeset
713 if [[ "$naive_output" == "yes" ]]
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
714 then
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
715 echo "output naive output"
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
716 if [[ "${class_filter}" == "101_101" ]]
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
717 then
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
718 echo "copy new_IMGT.txz to ${naive_output_all}"
21
c281993e515b Uploaded
davidvanzessen
parents: 20
diff changeset
719 cp $outdir/new_IMGT.txz ${naive_output_all}
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
720 else
28
c0ecc31829bd Uploaded
davidvanzessen
parents: 26
diff changeset
721 echo "copy for classes"
18
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
722 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
723 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
724 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
725 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
949a30f04d9b Uploaded
davidvanzessen
parents: 16
diff changeset
726 fi
0
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
727 fi
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
728
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
729 echo "</table>" >> $outdir/base_overview.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
730
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
731 mv $log $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
732
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
733 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
734 echo "<table border = 1>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
735 echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
736 tIFS="$TMP"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
737 IFS=$'\t'
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
738 while read step seq perc
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
739 do
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
740 echo "<tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
741 echo "<td>$step</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
742 echo "<td>$seq</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
743 echo "<td>${perc}%</td>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
744 echo "</tr>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
745 done < $outdir/filtering_steps.txt
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
746 echo "</table border></center></html>" >> $log
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
747
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
748 IFS="$tIFS"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
749
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
750
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
751 echo "---------------- Done! ----------------"
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
752 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
753
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
754
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
755
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
756
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
757
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
758
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
759
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
760
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
761
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
762
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
763
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
764
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
765
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
766
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
767
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
768
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
769
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
770
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
771
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
772
c33d93683a09 Uploaded
davidvanzessen
parents:
diff changeset
773