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comparison wrapper.sh @ 93:8fcf31272f6e draft

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planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
author rhpvorderman
date Mon, 06 Mar 2023 11:36:32 +0000
parents cf8ad181628f
children 84e9e5c8c101
comparison
equal deleted inserted replaced
92:cf8ad181628f 93:8fcf31272f6e
20 filter_unique_count=${16} 20 filter_unique_count=${16}
21 class_filter=${17} 21 class_filter=${17}
22 empty_region_filter=${18} 22 empty_region_filter=${18}
23 fast=${19} 23 fast=${19}
24 24
25 BASENAME=$(basename $input)
26 # Cut off .txz or .tgz suffix
27 NEW_IMGT_PREFIX="new_IMGT_${BASENAME%.*}"
28
25 #exec 5> debug_output.txt 29 #exec 5> debug_output.txt
26 #BASH_XTRACEFD="5" 30 #BASH_XTRACEFD="5"
27 ## Busybox date does not support '+%s.%N'. So use the slower python instead. 31 ## Busybox date does not support '+%s.%N'. So use a custom program. Can be
28 ## Using -S python does not do 'import site' which shortens the command 32 ## Compiled with cc -Os show_time_as_float.c -o show_time_as_float
29 ## to 10 milliseconds. 33 #PS4='$(${dir}/show_time_as_float) $LINENO: '
30 #PS4='$(python -Sc "import time; print(time.time())") $LINENO: '
31 #set -x 34 #set -x
32 35
33 mkdir -p $outdir 36 mkdir -p $outdir
34 37
35 tar -xzf $dir/style.tar.gz -C $outdir 38 tar -xzf $dir/style.tar.gz -C $outdir
37 echo "---------------- read parameters ----------------" 40 echo "---------------- read parameters ----------------"
38 echo "---------------- read parameters ----------------<br />" > $log 41 echo "---------------- read parameters ----------------<br />" > $log
39 42
40 echo "unpacking IMGT file" 43 echo "unpacking IMGT file"
41 44
42 type="`file $input`" 45 type="`file -L $input`"
43 if [[ "$type" == *"Zip archive"* ]] ; then 46 if [[ "$type" == *"Zip archive"* ]] ; then
44 echo "Zip archive" 47 echo "Zip archive"
45 echo "unzip $input -d $PWD/files/" 48 echo "unzip $input -d $PWD/files/"
46 unzip $input -d $PWD/files/ 49 unzip $input -d $PWD/files/
47 elif [[ "$type" == *"XZ compressed data"* ]] ; then 50 elif [[ "$type" == *"XZ compressed data"* ]] ; then
83 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt 86 python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
84 87
85 echo "---------------- merge_and_filter.r ----------------" 88 echo "---------------- merge_and_filter.r ----------------"
86 echo "---------------- merge_and_filter.r ----------------<br />" >> $log 89 echo "---------------- merge_and_filter.r ----------------<br />" >> $log
87 90
88 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 91 Rscript $dir/merge_and_filter.r \
92 $PWD/summary.txt \
93 $PWD/sequences.txt \
94 $PWD/mutationanalysis.txt \
95 $PWD/mutationstats.txt \
96 $PWD/hotspots.txt \
97 "$PWD/gapped_aa.txt" \
98 $outdir/identified_genes.txt \
99 $outdir/merged.txt \
100 $outdir/before_unique_filter.txt \
101 $outdir/unmatched.txt \
102 $method \
103 $functionality \
104 $unique \
105 ${filter_unique} \
106 ${filter_unique_count} \
107 ${class_filter} \
108 ${empty_region_filter}
89 109
90 echo "---------------- creating new IMGT zips ----------------" 110 echo "---------------- creating new IMGT zips ----------------"
91 echo "---------------- creating new IMGT zips ----------------<br />" >> $log 111 echo "---------------- creating new IMGT zips ----------------<br />" >> $log
92 112
93 python $dir/split_imgt_file.py --outdir $outdir $input $outdir/merged.txt \ 113 python $dir/split_imgt_file.py --outdir $outdir $input $outdir/merged.txt \
94 --prefix new_IMGT \ 114 --prefix "${NEW_IMGT_PREFIX}" \
95 - IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE 115 - IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE
96 116
97 117
98 echo "---------------- shm_csr.r ----------------" 118 echo "---------------- shm_csr.r ----------------"
99 echo "---------------- shm_csr.r ----------------<br />" >> $log 119 echo "---------------- shm_csr.r ----------------<br />" >> $log
100 120
101 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched" 121 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
102 echo "R mutation analysis" 122 echo "R mutation analysis"
103 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1 123 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter}
104 124
105 echo "---------- Split naive memory IGM ---------" 125 echo "---------- Split naive memory IGM ---------"
106 echo "---------- Split naive memory IGM ---------<br />" >> $log 126 echo "---------- Split naive memory IGM ---------<br />" >> $log
107 127
108 python $dir/igm_naive_mutations.py $outdir/scatter.txt $outdir/igm_naive_mutations.txt \ 128 python $dir/igm_naive_mutations.py $outdir/scatter.txt $outdir/igm_naive_mutations.txt \
109 $outdir/igm_naive_memory_mutations.txt 129 $outdir/igm_naive_memory_mutations.txt
110 130
111 python $dir/split_imgt_file.py --outdir $outdir $outdir/new_IMGT_IGM.txz \ 131 python $dir/split_imgt_file.py --outdir $outdir $outdir/${NEW_IMGT_PREFIX}_IGM.txz \
112 $outdir/igm_naive_mutations.txt \ 132 $outdir/igm_naive_mutations.txt \
113 --prefix new_IMGT_IGM_NAIVE - 133 --prefix "${NEW_IMGT_PREFIX}_IGM_NAIVE" -
114 134
115 python $dir/split_imgt_file.py --outdir $outdir $outdir/new_IMGT_IGM.txz \ 135 python $dir/split_imgt_file.py --outdir $outdir $outdir/${NEW_IMGT_PREFIX}_IGM.txz \
116 $outdir/igm_naive_memory_mutations.txt \ 136 $outdir/igm_naive_memory_mutations.txt \
117 --prefix new_IMGT_IGM_NAIVE_MEMORY - 137 --prefix "${NEW_IMGT_PREFIX}_IGM_NAIVE_MEMORY" -
118 138
119 echo "---------------- plot_pdfs.r ----------------" 139 echo "---------------- plot_pdfs.r ----------------"
120 echo "---------------- plot_pdfs.r ----------------<br />" >> $log 140 echo "---------------- plot_pdfs.r ----------------<br />" >> $log
121 141
122 echo "Rscript $dir/shm_csr.r $outdir/pdfplots.RData $outdir 2>&1" 142 echo "Rscript $dir/shm_csr.r $outdir/pdfplots.RData $outdir"
123 143
124 Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir" 2>&1 144 Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir"
125 145
126 echo "---------------- shm_csr.py ----------------" 146 echo "---------------- shm_csr.py ----------------"
127 echo "---------------- shm_csr.py ----------------<br />" >> $log 147 echo "---------------- shm_csr.py ----------------<br />" >> $log
128 148
129 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt 149 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt
130 150
131 echo "---------------- aa_histogram.r ----------------" 151 echo "---------------- aa_histogram.r ----------------"
132 echo "---------------- aa_histogram.r ----------------<br />" >> $log 152 echo "---------------- aa_histogram.r ----------------<br />" >> $log
133 153
134 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1 154 Rscript $dir/aa_histogram.r \
155 $outdir/aa_id_mutations.txt \
156 $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" \
157 $outdir/
158
135 if [ -e "$outdir/aa_histogram_.png" ]; then 159 if [ -e "$outdir/aa_histogram_.png" ]; then
136 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png 160 mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
137 mv $outdir/aa_histogram_.pdf $outdir/aa_histogram.pdf 161 mv $outdir/aa_histogram_.pdf $outdir/aa_histogram.pdf
138 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt 162 mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
139 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt 163 mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
151 175
152 mkdir $outdir/sequence_overview 176 mkdir $outdir/sequence_overview
153 177
154 python $dir/sequence_overview.py --before-unique $outdir/before_unique_filter.txt \ 178 python $dir/sequence_overview.py --before-unique $outdir/before_unique_filter.txt \
155 --outdir $outdir/sequence_overview --empty-region-filter ${empty_region_filter} 179 --outdir $outdir/sequence_overview --empty-region-filter ${empty_region_filter}
156 Rscript $dir/nt_overview.r $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt ${empty_region_filter} 2>&1 180 Rscript $dir/nt_overview.r \
181 $outdir/merged.txt \
182 $outdir/sequence_overview \
183 $classes \
184 $outdir/hotspot_analysis_sum.txt \
185 ${empty_region_filter}
157 186
158 echo "<table border='1'>" > $outdir/base_overview.html 187 echo "<table border='1'>" > $outdir/base_overview.html
159 188
160 while IFS=$'\t' read ID class seq A C G T 189 while IFS=$'\t' read ID class seq A C G T
161 do 190 do
196 cat $outdir/mutations_${func}.txt $outdir/shm_overview_tandem_row.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt 225 cat $outdir/mutations_${func}.txt $outdir/shm_overview_tandem_row.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
197 226
198 echo "---------------- pattern_plots.r ----------------" 227 echo "---------------- pattern_plots.r ----------------"
199 echo "---------------- pattern_plots.r ----------------<br />" >> $log 228 echo "---------------- pattern_plots.r ----------------<br />" >> $log
200 229
201 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/aid_motives $outdir/relative_mutations $outdir/absolute_mutations $outdir/shm_overview.txt 2>&1 230 Rscript $dir/pattern_plots.r \
231 $outdir/data_${func}.txt \
232 $outdir/aid_motives \
233 $outdir/relative_mutations \
234 $outdir/absolute_mutations \
235 $outdir/shm_overview.txt
202 236
203 echo "<table class='pure-table pure-table-striped'>" >> $output 237 echo "<table class='pure-table pure-table-striped'>" >> $output
204 echo "<thead><tr><th>info</th>" >> $output 238 echo "<thead><tr><th>info</th>" >> $output
205 239
206 if [ "${class_filter}" != "101_101" ] ; then 240 if [ "${class_filter}" != "101_101_all" ] ; then
207 241
208 for gene in ${genes[@]} 242 for gene in ${genes[@]}
209 do 243 do
210 tmp=`cat $outdir/${gene}_${func}_n.txt` 244 tmp=`cat $outdir/${gene}_${func}_n.txt`
211 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output 245 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
395 fi 429 fi
396 430
397 echo "<p>${header_substring}</p></center>" >> $output 431 echo "<p>${header_substring}</p></center>" >> $output
398 432
399 mkdir $outdir/baseline/IGA_IGG_IGM 433 mkdir $outdir/baseline/IGA_IGG_IGM
400 if [[ "$(count_imgt_lines $outdir/new_IMGT.txz)" -gt "1" ]]; then 434 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}.txz)" -gt "1" ]]; then
401 cd $outdir/baseline/IGA_IGG_IGM 435 cd $outdir/baseline/IGA_IGG_IGM
402 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" 436 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}.txz "IGA_IGG_IGM_IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
403 else 437 else
404 echo "No sequences" > "$outdir/baseline.txt" 438 echo "No sequences" > "$outdir/baseline.txt"
405 fi 439 fi
406 440
407 mkdir $outdir/baseline/IGA 441 mkdir $outdir/baseline/IGA
408 if [[ "$(count_imgt_lines $outdir/new_IMGT_IGA.txz)" -gt "1" ]]; then 442 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGA.txz)" -gt "1" ]]; then
409 cd $outdir/baseline/IGA 443 cd $outdir/baseline/IGA
410 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" 444 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
411 else 445 else
412 echo "No IGA sequences" > "$outdir/baseline_IGA.txt" 446 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
413 fi 447 fi
414 448
415 mkdir $outdir/baseline/IGG 449 mkdir $outdir/baseline/IGG
416 if [[ "$(count_imgt_lines $outdir/new_IMGT_IGG.txz)" -gt "1" ]]; then 450 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGG.txz)" -gt "1" ]]; then
417 cd $outdir/baseline/IGG 451 cd $outdir/baseline/IGG
418 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" 452 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
419 else 453 else
420 echo "No IGG sequences" > "$outdir/baseline_IGG.txt" 454 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
421 fi 455 fi
422 456
423 mkdir $outdir/baseline/IGM 457 mkdir $outdir/baseline/IGM
424 if [[ "$(count_imgt_lines $outdir/new_IMGT_IGM.txz)" -gt "1" ]]; then 458 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGM.txz)" -gt "1" ]]; then
425 cd $outdir/baseline/IGM 459 cd $outdir/baseline/IGM
426 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" 460 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}_IGM.txz "IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
427 else 461 else
428 echo "No IGM sequences" > "$outdir/baseline_IGM.txt" 462 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
429 fi 463 fi
430 464
431 mkdir $outdir/baseline/IGE 465 mkdir $outdir/baseline/IGE
432 if [[ "$(count_imgt_lines $outdir/new_IMGT_IGE.txz)" -gt "1" ]]; then 466 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGE.txz)" -gt "1" ]]; then
433 cd $outdir/baseline/IGE 467 cd $outdir/baseline/IGE
434 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" 468 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "${baseline_boundaries}" $outdir/${NEW_IMGT_PREFIX}_IGE.txz "IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
435 else 469 else
436 echo "No IGE sequences" > "$outdir/baseline_IGE.txt" 470 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
437 fi 471 fi
438 472
439 cd $tmp 473 cd $tmp
496 530
497 tmp="$PWD" 531 tmp="$PWD"
498 532
499 cd $outdir/change_o 533 cd $outdir/change_o
500 534
501 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt 535 bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}.txz false false false $outdir/change_o/change-o-db.txt
502 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 536 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
503 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>&1 537 Rscript $dir/change_o/select_first_in_clone.r \
504 538 $outdir/change_o/change-o-db-defined_clones.txt \
505 python $dir/split_imgt_file.py --outdir $outdir --prefix new_IMGT_first_seq_of_clone \ 539 $outdir/change_o/change-o-db-defined_first_clones.txt
506 $outdir/new_IMGT.txz $outdir/change_o/change-o-db-defined_first_clones.txt \ 540
541 python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_first_seq_of_clone \
542 $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones.txt \
507 "-" 543 "-"
508 544
509 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>&1 545 Rscript $dir/merge.r \
510 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" 546 $outdir/change_o/change-o-db-defined_clones.txt \
511 547 $outdir/merged.txt \
512 if [[ "$(count_imgt_lines $outdir/new_IMGT_IGA.txz)" -gt "1" ]]; then 548 "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" \
513 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt 549 $outdir/change_o/change-o-db-defined_clones.txt
550 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' $outdir/change_o/change-o-db-defined_clones.txt"
551
552 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGA.txz)" -gt "1" ]]; then
553 bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
514 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 554 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
515 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>&1 555 Rscript $dir/change_o/select_first_in_clone.r \
516 556 $outdir/change_o/change-o-db-defined_clones-IGA.txt \
517 python $dir/split_imgt_file.py --outdir $outdir --prefix new_IMGT_IGA_first_seq_of_clone \ 557 $outdir/change_o/change-o-db-defined_first_clones-IGA.txt
518 $outdir/new_IMGT.txz $outdir/change_o/change-o-db-defined_first_clones-IGA.txt \ 558
559 python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_IGA_first_seq_of_clone \
560 $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones-IGA.txt \
519 "-" 561 "-"
520 562
521 else 563 else
522 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt" 564 echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
523 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt" 565 echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
524 fi 566 fi
525 567
526 if [[ "$(count_imgt_lines $outdir/new_IMGT_IGG.txz)" -gt "1" ]]; then 568 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGG.txz)" -gt "1" ]]; then
527 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt 569 bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
528 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 570 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
529 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>&1 571 Rscript $dir/change_o/select_first_in_clone.r \
530 572 $outdir/change_o/change-o-db-defined_clones-IGG.txt \
531 python $dir/split_imgt_file.py --outdir $outdir --prefix new_IMGT_IGG_first_seq_of_clone \ 573 $outdir/change_o/change-o-db-defined_first_clones-IGG.txt
532 $outdir/new_IMGT.txz $outdir/change_o/change-o-db-defined_first_clones-IGG.txt \ 574
575 python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_IGG_first_seq_of_clone \
576 $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones-IGG.txt \
533 "-" 577 "-"
534 578
535 else 579 else
536 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt" 580 echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
537 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt" 581 echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
538 fi 582 fi
539 583
540 if [[ "$(count_imgt_lines $outdir/new_IMGT_IGM.txz)" -gt "1" ]]; then 584 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGM.txz)" -gt "1" ]]; then
541 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt 585 bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
542 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 586 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
543 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>&1 587 Rscript $dir/change_o/select_first_in_clone.r \
544 588 $outdir/change_o/change-o-db-defined_clones-IGM.txt \
545 python $dir/split_imgt_file.py --outdir $outdir --prefix new_IMGT_IGM_first_seq_of_clone \ 589 $outdir/change_o/change-o-db-defined_first_clones-IGM.txt
546 $outdir/new_IMGT.txz $outdir/change_o/change-o-db-defined_first_clones-IGM.txt \ 590
591 python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_IGM_first_seq_of_clone \
592 $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones-IGM.txt \
547 "-" 593 "-"
548 594
549 else 595 else
550 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt" 596 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
551 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt" 597 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
552 fi 598 fi
553 599
554 if [[ "$(count_imgt_lines $outdir/new_IMGT_IGE.txz)" -gt "1" ]]; then 600 if [[ "$(count_imgt_lines $outdir/${NEW_IMGT_PREFIX}_IGE.txz)" -gt "1" ]]; then
555 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt 601 bash $dir/change_o/makedb.sh $outdir/${NEW_IMGT_PREFIX}_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
556 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 602 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
557 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>&1 603 Rscript $dir/change_o/select_first_in_clone.r \
558 604 $outdir/change_o/change-o-db-defined_clones-IGE.txt \
559 python $dir/split_imgt_file.py --outdir $outdir --prefix new_IMGT_IGE_first_seq_of_clone \ 605 $outdir/change_o/change-o-db-defined_first_clones-IGE.txt
560 $outdir/new_IMGT.txz $outdir/change_o/change-o-db-defined_first_clones-IGE.txt \ 606
607 python $dir/split_imgt_file.py --outdir $outdir --prefix ${NEW_IMGT_PREFIX}_IGE_first_seq_of_clone \
608 $outdir/${NEW_IMGT_PREFIX}.txz $outdir/change_o/change-o-db-defined_first_clones-IGE.txt \
561 "-" 609 "-"
562 610
563 else 611 else
564 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt" 612 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
565 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt" 613 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
712 760
713 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output 761 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonal Relation</td></tr>" >> $output
714 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output 762 echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
715 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 763 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
716 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 764 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
717 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>" >> $output 765 echo "<tr><td>An IMGT archive with just just the first sequence of a clone</td><td><a href='${NEW_IMGT_PREFIX}_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
718 766
719 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 767 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
720 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 768 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
721 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>" >> $output 769 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGA)</td><td><a href='${NEW_IMGT_PREFIX}_IGA_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_IGA_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
722 770
723 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 771 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
724 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 772 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
725 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>" >> $output 773 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGG)</td><td><a href='${NEW_IMGT_PREFIX}_IGG_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_IGG_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
726 774
727 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 775 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
728 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 776 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
729 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>" >> $output 777 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGM)</td><td><a href='${NEW_IMGT_PREFIX}_IGM_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_IGM_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
730 778
731 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 779 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
732 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 780 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
733 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>" >> $output 781 echo "<tr><td>An IMGT archive with just just the first sequence of a clone (IGE)</td><td><a href='${NEW_IMGT_PREFIX}_IGE_first_seq_of_clone.txz' download='${NEW_IMGT_PREFIX}_IGE_first_seq_of_clone.txz' >Download</a></td></tr>" >> $output
734 782
735 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output 783 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
736 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>" >> $output 784 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='${NEW_IMGT_PREFIX}.txz' download='${NEW_IMGT_PREFIX}.txz' >Download</a></td></tr>" >> $output
737 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>" >> $output 785 echo "<tr><td>An IMGT archive with just the matched and filtered IGA sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGA.txz' download='${NEW_IMGT_PREFIX}_IGA.txz' >Download</a></td></tr>" >> $output
738 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>" >> $output 786 echo "<tr><td>An IMGT archive with just the matched and filtered IGA1 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGA1.txz' download='${NEW_IMGT_PREFIX}_IGA1.txz' >Download</a></td></tr>" >> $output
739 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>" >> $output 787 echo "<tr><td>An IMGT archive with just the matched and filtered IGA2 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGA2.txz' download='${NEW_IMGT_PREFIX}_IGA2.txz' >Download</a></td></tr>" >> $output
740 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>" >> $output 788 echo "<tr><td>An IMGT archive with just the matched and filtered IGG sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG.txz' download='${NEW_IMGT_PREFIX}_IGG.txz' >Download</a></td></tr>" >> $output
741 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>" >> $output 789 echo "<tr><td>An IMGT archive with just the matched and filtered IGG1 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG1.txz' download='${NEW_IMGT_PREFIX}_IGG1.txz' >Download</a></td></tr>" >> $output
742 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>" >> $output 790 echo "<tr><td>An IMGT archive with just the matched and filtered IGG2 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG2.txz' download='${NEW_IMGT_PREFIX}_IGG2.txz' >Download</a></td></tr>" >> $output
743 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>" >> $output 791 echo "<tr><td>An IMGT archive with just the matched and filtered IGG3 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG3.txz' download='${NEW_IMGT_PREFIX}_IGG3.txz' >Download</a></td></tr>" >> $output
744 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>" >> $output 792 echo "<tr><td>An IMGT archive with just the matched and filtered IGG4 sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGG4.txz' download='${NEW_IMGT_PREFIX}_IGG4.txz' >Download</a></td></tr>" >> $output
745 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>" >> $output 793 echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGM.txz' download='${NEW_IMGT_PREFIX}_IGM.txz' >Download</a></td></tr>" >> $output
746 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>" >> $output 794 echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='${NEW_IMGT_PREFIX}_IGE.txz' download='${NEW_IMGT_PREFIX}_IGE.txz' >Download</a></td></tr>" >> $output
747 echo "<tr><td>An IMGT archive with just the matched and filtered naive IGM sequences (mutations below 2%)</td><td><a href='new_IMGT_IGM_NAIVE.txz' download='new_IMGT_IGM_NAIVE.txz' >Download</a></td></tr>" >> $output 795 echo "<tr><td>An IMGT archive with just the matched and filtered naive IGM sequences (mutations below 2%)</td><td><a href='${NEW_IMGT_PREFIX}_IGM_NAIVE.txz' download='${NEW_IMGT_PREFIX}_IGM_NAIVE.txz' >Download</a></td></tr>" >> $output
748 echo "<tr><td>An IMGT archive with just the matched and filtered naive memory IGM sequences (mutations 2% or higher)</td><td><a href='new_IMGT_IGM_NAIVE_MEMORY.txz' download='new_IMGT_IGM_NAIVE_MEMORY.txz' >Download</a></td></tr>" >> $output 796 echo "<tr><td>An IMGT archive with just the matched and filtered naive memory IGM sequences (mutations 2% or higher)</td><td><a href='${NEW_IMGT_PREFIX}_IGM_NAIVE_MEMORY.txz' download='${NEW_IMGT_PREFIX}_IGM_NAIVE_MEMORY.txz' >Download</a></td></tr>" >> $output
749 echo "</table>" >> $output 797 echo "</table>" >> $output
750 798
751 echo "<br />" >> $output 799 echo "<br />" >> $output
752 cat $dir/shm_downloads.htm >> $output 800 cat $dir/shm_downloads.htm >> $output
753 801
762 echo "---------------- naive_output.r ----------------<br />" >> $log 810 echo "---------------- naive_output.r ----------------<br />" >> $log
763 811
764 if [[ "$naive_output" == "yes" ]] 812 if [[ "$naive_output" == "yes" ]]
765 then 813 then
766 echo "output naive output" 814 echo "output naive output"
767 if [[ "${class_filter}" == "101_101" ]] 815 if [[ "${class_filter}" == "101_101_all" ]]
768 then 816 then
769 echo "copy new_IMGT.txz to ${naive_output_all}" 817 echo "copy ${NEW_IMGT_PREFIX}.txz to ${naive_output_all}"
770 cp $outdir/new_IMGT.txz ${naive_output_all} 818 cp $outdir/${NEW_IMGT_PREFIX}.txz ${naive_output_all}
771 else 819 else
772 echo "copy for classes" 820 echo "copy for classes"
773 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca} 821 cp $outdir/${NEW_IMGT_PREFIX}_IGA.txz ${naive_output_ca}
774 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg} 822 cp $outdir/${NEW_IMGT_PREFIX}_IGG.txz ${naive_output_cg}
775 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm} 823 cp $outdir/${NEW_IMGT_PREFIX}_IGM.txz ${naive_output_cm}
776 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce} 824 cp $outdir/${NEW_IMGT_PREFIX}_IGE.txz ${naive_output_ce}
777 fi 825 fi
778 fi 826 fi
779 827
780 echo "</table>" >> $outdir/base_overview.html 828 echo "</table>" >> $outdir/base_overview.html
781 829