| info |
" > $html
-echo "| ----------------------------------- |
" >> $html
-
-#mkdir $PWD/igblastdatabase
-#unzip $dir/database.zip -d $PWD/igblastdatabase/
-#export IGDATA=$PWD/igblastdatabase/
-
-id=""
-forwardSlash="/"
-mergerInput=()
-echo "Before loop"
-count=1
-for current in "${inputFiles[@]}"
-do
- if [[ "$current" != *"$forwardSlash"* ]]; then
- id="$current"
- mergerInput+=($id)
- count=1
- continue
- fi
- echo "working on $current"
- fileName=$(basename $current)
- fileName="${fileName%.*}"
- parsedFileName="$PWD/$fileName.parsed"
- f=$(file $current)
- zipType="Zip archive"
- zxType="XZ compressed data"
- if [[ "$f" == *"$zipType"* ]] || [[ "$f" == *"$zxType"* ]]
- then
- echo "| Sample $count of patient $id is an archive file, using IMGT Loader |
" >> $html
- fileName=$(basename $current)
- bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName "${fileName}"
- else
- echo "| Sample $count of patient $id is not a zip file so assuming fasta/fastq, using igBLASTn |
" >> $html
- bash ${dir}/igblast/igblast.sh $current "$species" $locus $parsedFileName
- fi
- mergerInput+=($parsedFileName)
- count=$((count+1))
-done
-
-echo "| ----------------------------------- |
" >> $html
-echo "| merging |
" >> $html
-
-bash $dir/experimental_design/experimental_design.sh ${mergerInput[*]} $PWD/merged.txt
-
-echo "| done |
" >> $html
-echo "| ----------------------------------- |
" >> $html
-echo "| plotting |
" >> $html
-
-echo "after ED"
-
-bash $dir/report_clonality/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType "$species" "$locus" $filterproductive $clonality_method
-
diff -r 9185c3dfc679 -r 9c843eb06416 complete_immunerepertoire.xml.old
--- a/complete_immunerepertoire.xml.old Fri Jan 27 03:44:18 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,203 +0,0 @@
-
-
-
-complete.sh "
-#for $i, $f in enumerate($patients)
- "${f.id}"
- #for $j, $g in enumerate($f.samples)
- ${g.sample}
- #end for
-#end for
-" $out_file $out_file.files_path "$clonaltype"
-#if $gene_selection.source == "imgtdb"
- "${gene_selection.species}" "${gene_selection.locus}" $filterproductive ${clonality_method}
-#else
- "custom" "${gene_selection.vgenes};${gene_selection.dgenes};${gene_selection.jgenes}" $filterproductive $clonality_method
-#end if
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- igblastwrp
- weblogo
-
-
-
- The entire Immune Repertoire pipeline as a single tool, input several FASTA files or IMGT zip/txz files, give them an ID and it will BLAST/parse, merge and plot them.
-
- .. class:: warningmark
-
-Custom gene ordering based on position on genome:
-
-**Human**
-
-IGH::
-
- V:
- IGHV7-81,IGHV3-74,IGHV3-73,IGHV3-72,IGHV3-71,IGHV2-70,IGHV1-69,IGHV3-66,IGHV3-64,IGHV4-61,IGHV4-59,IGHV1-58,IGHV3-53,IGHV3-52,IGHV5-a,IGHV5-51,IGHV3-49,IGHV3-48,IGHV3-47,IGHV1-46,IGHV1-45,IGHV3-43,IGHV4-39,IGHV3-35,IGHV4-34,IGHV3-33,IGHV4-31,IGHV4-30-4,IGHV4-30-2,IGHV3-30-3,IGHV3-30,IGHV4-28,IGHV2-26,IGHV1-24,IGHV3-23,IGHV3-22,IGHV3-21,IGHV3-20,IGHV3-19,IGHV1-18,IGHV3-15,IGHV3-13,IGHV3-11,IGHV3-9,IGHV1-8,IGHV3-7,IGHV2-5,IGHV7-4-1,IGHV4-4,IGHV4-b,IGHV1-3,IGHV1-2,IGHV6-1
- D:
- IGHD1-1,IGHD2-2,IGHD3-3,IGHD6-6,IGHD1-7,IGHD2-8,IGHD3-9,IGHD3-10,IGHD4-11,IGHD5-12,IGHD6-13,IGHD1-14,IGHD2-15,IGHD3-16,IGHD4-17,IGHD5-18,IGHD6-19,IGHD1-20,IGHD2-21,IGHD3-22,IGHD4-23,IGHD5-24,IGHD6-25,IGHD1-26,IGHD7-27
- J:
- IGHJ1,IGHJ2,IGHJ3,IGHJ4,IGHJ5,IGHJ6
-
-
-IGK::
-
- V:
- IGKV3D-7,IGKV1D-8,IGKV1D-43,IGKV3D-11,IGKV1D-12,IGKV1D-13,IGKV3D-15,IGKV1D-16,IGKV1D-17,IGKV3D-20,IGKV2D-26,IGKV2D-28,IGKV2D-29,IGKV2D-30,IGKV1D-33,IGKV1D-39,IGKV2D-40,IGKV2-40,IGKV1-39,IGKV1-33,IGKV2-30,IGKV2-29,IGKV2-28,IGKV1-27,IGKV2-24,IGKV3-20,IGKV1-17,IGKV1-16,IGKV3-15,IGKV1-13,IGKV1-12,IGKV3-11,IGKV1-9,IGKV1-8,IGKV1-6,IGKV1-5,IGKV5-2,IGKV4-1
- J:
- IGKJ1,IGKJ2,IGKJ3,IGKJ4,IGKJ5
-
-
-IGL::
-
- V:
- IGLV4-69,IGLV8-61,IGLV4-60,IGLV6-57,IGLV5-52,IGLV1-51,IGLV9-49,IGLV1-47,IGLV7-46,IGLV5-45,IGLV1-44,IGLV7-43,IGLV1-41,IGLV1-40,IGLV5-39,IGLV5-37,IGLV1-36,IGLV3-27,IGLV3-25,IGLV2-23,IGLV3-22,IGLV3-21,IGLV3-19,IGLV2-18,IGLV3-16,IGLV2-14,IGLV3-12,IGLV2-11,IGLV3-10,IGLV3-9,IGLV2-8,IGLV4-3,IGLV3-1
- J:
- IGLJ1,IGLJ2,IGLJ3,IGLJ6,IGLJ7
-
-
-TRB::
-
- V:
- TRBV2,TRBV3-1,TRBV4-1,TRBV5-1,TRBV6-1,TRBV4-2,TRBV6-2,TRBV4-3,TRBV6-3,TRBV7-2,TRBV6-4,TRBV7-3,TRBV9,TRBV10-1,TRBV11-1,TRBV10-2,TRBV11-2,TRBV6-5,TRBV7-4,TRBV5-4,TRBV6-6,TRBV5-5,TRBV7-6,TRBV5-6,TRBV6-8,TRBV7-7,TRBV6-9,TRBV7-8,TRBV5-8,TRBV7-9,TRBV13,TRBV10-3,TRBV11-3,TRBV12-3,TRBV12-4,TRBV12-5,TRBV14,TRBV15,TRBV16,TRBV18,TRBV19,TRBV20-1,TRBV24-1,TRBV25-1,TRBV27,TRBV28,TRBV29-1,TRBV30
- D:
- TRBD1,TRBD2
- J:
- TRBJ1-1,TRBJ1-2,TRBJ1-3,TRBJ1-4,TRBJ1-5,TRBJ1-6,TRBJ2-1,TRBJ2-2,TRBJ2-3,TRBJ2-4,TRBJ2-5,TRBJ2-6,TRBJ2-7
-
-
-TRA::
-
- V:
- TRAV1-1,TRAV1-2,TRAV2,TRAV3,TRAV4,TRAV5,TRAV6,TRAV7,TRAV8-1,TRAV9-1,TRAV10,TRAV12-1,TRAV8-2,TRAV8-3,TRAV13-1,TRAV12-2,TRAV8-4,TRAV13-2,TRAV14/DV4,TRAV9-2,TRAV12-3,TRAV8-6,TRAV16,TRAV17,TRAV18,TRAV19,TRAV20,TRAV21,TRAV22,TRAV23/DV6,TRAV24,TRAV25,TRAV26-1,TRAV27,TRAV29/DV5,TRAV30,TRAV26-2,TRAV34,TRAV35,TRAV36/DV7,TRAV38-1,TRAV38-2/DV8,TRAV39,TRAV40,TRAV41
- J:
- TRAJ57,TRAJ56,TRAJ54,TRAJ53,TRAJ52,TRAJ50,TRAJ49,TRAJ48,TRAJ47,TRAJ46,TRAJ45,TRAJ44,TRAJ43,TRAJ42,TRAJ41,TRAJ40,TRAJ39,TRAJ38,TRAJ37,TRAJ36,TRAJ34,TRAJ33,TRAJ32,TRAJ31,TRAJ30,TRAJ29,TRAJ28,TRAJ27,TRAJ26,TRAJ24,TRAJ23,TRAJ22,TRAJ21,TRAJ20,TRAJ18,TRAJ17,TRAJ16,TRAJ15,TRAJ14,TRAJ13,TRAJ12,TRAJ11,TRAJ10,TRAJ9,TRAJ8,TRAJ7,TRAJ6,TRAJ5,TRAJ4,TRAJ3
-
-
-TRG::
-
- V:
- TRGV9,TRGV8,TRGV5,TRGV4,TRGV3,TRGV2
- J:
- TRGJ2,TRGJP2,TRGJ1,TRGJP1
-
-
-TRD::
-
- V:
- TRDV1,TRDV2,TRDV3
- D:
- TRDD1,TRDD2,TRDD3
- J:
- TRDJ1,TRDJ4,TRDJ2,TRDJ3
-
-
-**Mouse**
-
-TRB::
-
- V:
- TRBV1,TRBV2,TRBV3,TRBV4,TRBV5,TRBV12-1,TRBV13-1,TRBV12-2,TRBV13-2,TRBV13-3,TRBV14,TRBV15,TRBV16,TRBV17,TRBV19,TRBV20,TRBV23,TRBV24,TRBV26,TRBV29,TRBV30,TRBV31
- D:
- TRBD1,TRBD2
- J:
- TRBJ1-1,TRBJ1-2,TRBJ1-3,TRBJ1-4,TRBJ1-5,TRBJ2-1,TRBJ2-2,TRBJ2-3,TRBJ2-4,TRBJ2-5,TRBJ2-6,TRBJ2-7
-
-
-
-
diff -r 9185c3dfc679 -r 9c843eb06416 experimental_design.xml
--- a/experimental_design.xml Fri Jan 27 03:44:18 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-
-
-
- experimental_design/experimental_design.sh
- #for $i, $f in enumerate($patients)
- "$f.id"
- #for $j, $g in enumerate($f.samples)
- ${g.sample}
- #end for
- #end for
- $out_file
-
-
-
-
-
-
-
-
-
-
-
-
-
-Takes the ARGalaxy proprietary format and merges several samples and/or patients together.
-
-
-
- 10.1093/bioinformatics/btq281
-
-
- @ARTICLE{Kim07aninterior-point,
- author = {Seung-jean Kim and Kwangmoo Koh and Michael Lustig and Stephen Boyd and Dimitry Gorinevsky},
- title = {An interior-point method for large-scale l1-regularized logistic regression},
- journal = {Journal of Machine Learning Research},
- year = {2007},
- volume = {8},
- pages = {1519-1555}
- }
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff -r 9185c3dfc679 -r 9c843eb06416 igblastn.xml
--- a/igblastn.xml Fri Jan 27 03:44:18 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,107 +0,0 @@
-
-
-
- igblast/igblast.sh $input $species $locus $output
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- igblastwrp
-
-
-============
-iReport
-============
-
-This tool uses the online igBLAST website hosted by NCBI to blast a FASTA file, it retrieves the result and generates a convenient tabular format for further processing.
-
-**NOTE**
-
-.. class:: warningmark
-
-- Everything goes through the servers of NCBI, so if you have sensitive data that that isn't allowed to leave your local network, this isn't the tool the use.
-
-**USAGE**
-
-.. class:: infomark
-
-- This tool uses a free service provided by NCBI, and although there doesn't seem to be any restrictions on usage, avoid unnecessary usage to lighten the load on NCBI's servers.
-
-
-**INPUT**
-
-This tool accepts FASTA files as input:
-
-::
-
- >lcl|FLN1FA002RWEZA.1|
- ggctggagtgggtttcatacattagtagtaatagtggtgccatatactacgcagactctgtgaagggccgattcaccatc
- tccagaaacaatgccaaggactcactgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgc
- gagagcgatcccccggtattactatgatactagtggcccaaacgactactggggccagggaaccctggtcaccgtctcct
- cag
- >lcl|FLN1FA001BLION.1|
- aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccat
- taccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgtg
- cgagagtgggcagcagctggtctgatgcttttgattatctggggccaagggacaatggtcaccgtctcctcag
-
-**OUTPUT**
-
-The following data is used for ARGalaxy
-
-+-----------------+----------------------------------------------+
-| Column name | Column contents |
-+-----------------+----------------------------------------------+
-| ID | The Sequence ID provided by the sequencer. |
-+-----------------+----------------------------------------------+
-| VDJ Frame | In-frame/Out-frame |
-+-----------------+----------------------------------------------+
-| Top V Gene | The best matching V gene found. |
-+-----------------+----------------------------------------------+
-| Top D Gene | The best matching D gene found. |
-+-----------------+----------------------------------------------+
-| Top J Gene | The best matching J gene found. |
-+-----------------+----------------------------------------------+
-| CDR3 Seq | The CDR3 region. |
-+-----------------+----------------------------------------------+
-| CDR3 Length | The length of the CDR3 region. |
-+-----------------+----------------------------------------------+
-| CDR3 Seq DNA | The CDR3 sequence region. |
-+-----------------+----------------------------------------------+
-| CDR3 Length DNA | The length of the CDR3 sequence region. |
-+-----------------+----------------------------------------------+
-| Functionality | If sequence is productive/unproductive |
-+-----------------+----------------------------------------------+
-
-
-
-
diff -r 9185c3dfc679 -r 9c843eb06416 igparse.xml
--- a/igparse.xml Fri Jan 27 03:44:18 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-
-
-
- igblastparser/igparse.pl $input 0 2>/dev/null | grep -v "D:" | cut -f2- > $output
-
-
-
-
-
-
-
-
- Step 2 of the Immune Repertoire tools, extracts the relevant information needed from the reports generated by igblast (Step 1)
-
-
diff -r 9185c3dfc679 -r 9c843eb06416 imgt_loader.xml
--- a/imgt_loader.xml Fri Jan 27 03:44:18 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
-
-
-
- imgt_loader/imgt_loader.sh $in_file $out_file "tmp"
-
-
-
-
-
-
-
-
-**INPUT**
-
-This tool accepts an IMGT/HIGHV-QUEST ZIP file
-
-**OUTPUT**
-
-The following data is used for ARGalaxy
-
-+-----------------+----------------------------------------------+
-| Column name | Column contents |
-+-----------------+----------------------------------------------+
-| ID | The Sequence ID provided by the sequencer. |
-+-----------------+----------------------------------------------+
-| VDJ Frame | In-frame/Out-frame |
-+-----------------+----------------------------------------------+
-| Top V Gene | The best matching V gene found. |
-+-----------------+----------------------------------------------+
-| Top D Gene | The best matching D gene found. |
-+-----------------+----------------------------------------------+
-| Top J Gene | The best matching J gene found. |
-+-----------------+----------------------------------------------+
-| CDR3 Seq | The CDR3 region. |
-+-----------------+----------------------------------------------+
-| CDR3 Length | The length of the CDR3 region. |
-+-----------------+----------------------------------------------+
-| CDR3 Seq DNA | The CDR3 sequence region. |
-+-----------------+----------------------------------------------+
-| CDR3 Length DNA | The length of the CDR3 sequence region. |
-+-----------------+----------------------------------------------+
-| Functionality | If sequence is productive/unproductive |
-+-----------------+----------------------------------------------+
-
-
-
-
-
diff -r 9185c3dfc679 -r 9c843eb06416 report_clonality_igg.xml
--- a/report_clonality_igg.xml Fri Jan 27 03:44:18 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,197 +0,0 @@
-
-
-
-#if $gene_selection.source == "imgtdb"
- report_clonality/r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype" "${gene_selection.species}" "${gene_selection.locus}" $filterproductive $clonality_method
-#else
- report_clonality/r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype" "custom" "${gene_selection.vgenes};${gene_selection.dgenes};${gene_selection.jgenes}" $filterproductive $clonality_method
-#end if
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- weblogo
-
-
-
-**INPUT**
-
-One or more ARGalaxy proprietary format files combined with the ARGalaxy Experimental Design tool
-
-
-.. class:: warningmark
-
-Custom gene ordering based on position on genome:
-
-**Human**
-
-IGH::
-
- V:
- IGHV7-81,IGHV3-74,IGHV3-73,IGHV3-72,IGHV3-71,IGHV2-70,IGHV1-69,IGHV3-66,IGHV3-64,IGHV4-61,IGHV4-59,IGHV1-58,IGHV3-53,IGHV3-52,IGHV5-a,IGHV5-51,IGHV3-49,IGHV3-48,IGHV3-47,IGHV1-46,IGHV1-45,IGHV3-43,IGHV4-39,IGHV3-35,IGHV4-34,IGHV3-33,IGHV4-31,IGHV4-30-4,IGHV4-30-2,IGHV3-30-3,IGHV3-30,IGHV4-28,IGHV2-26,IGHV1-24,IGHV3-23,IGHV3-22,IGHV3-21,IGHV3-20,IGHV3-19,IGHV1-18,IGHV3-15,IGHV3-13,IGHV3-11,IGHV3-9,IGHV1-8,IGHV3-7,IGHV2-5,IGHV7-4-1,IGHV4-4,IGHV4-b,IGHV1-3,IGHV1-2,IGHV6-1
- D:
- IGHD1-1,IGHD2-2,IGHD3-3,IGHD6-6,IGHD1-7,IGHD2-8,IGHD3-9,IGHD3-10,IGHD4-11,IGHD5-12,IGHD6-13,IGHD1-14,IGHD2-15,IGHD3-16,IGHD4-17,IGHD5-18,IGHD6-19,IGHD1-20,IGHD2-21,IGHD3-22,IGHD4-23,IGHD5-24,IGHD6-25,IGHD1-26,IGHD7-27
- J:
- IGHJ1,IGHJ2,IGHJ3,IGHJ4,IGHJ5,IGHJ6
-
-
-IGK::
-
- V:
- IGKV3D-7,IGKV1D-8,IGKV1D-43,IGKV3D-11,IGKV1D-12,IGKV1D-13,IGKV3D-15,IGKV1D-16,IGKV1D-17,IGKV3D-20,IGKV2D-26,IGKV2D-28,IGKV2D-29,IGKV2D-30,IGKV1D-33,IGKV1D-39,IGKV2D-40,IGKV2-40,IGKV1-39,IGKV1-33,IGKV2-30,IGKV2-29,IGKV2-28,IGKV1-27,IGKV2-24,IGKV3-20,IGKV1-17,IGKV1-16,IGKV3-15,IGKV1-13,IGKV1-12,IGKV3-11,IGKV1-9,IGKV1-8,IGKV1-6,IGKV1-5,IGKV5-2,IGKV4-1
- J:
- IGKJ1,IGKJ2,IGKJ3,IGKJ4,IGKJ5
-
-
-IGL::
-
- V:
- IGLV4-69,IGLV8-61,IGLV4-60,IGLV6-57,IGLV5-52,IGLV1-51,IGLV9-49,IGLV1-47,IGLV7-46,IGLV5-45,IGLV1-44,IGLV7-43,IGLV1-41,IGLV1-40,IGLV5-39,IGLV5-37,IGLV1-36,IGLV3-27,IGLV3-25,IGLV2-23,IGLV3-22,IGLV3-21,IGLV3-19,IGLV2-18,IGLV3-16,IGLV2-14,IGLV3-12,IGLV2-11,IGLV3-10,IGLV3-9,IGLV2-8,IGLV4-3,IGLV3-1
- J:
- IGLJ1,IGLJ2,IGLJ3,IGLJ6,IGLJ7
-
-
-TRB::
-
- V:
- TRBV2,TRBV3-1,TRBV4-1,TRBV5-1,TRBV6-1,TRBV4-2,TRBV6-2,TRBV4-3,TRBV6-3,TRBV7-2,TRBV6-4,TRBV7-3,TRBV9,TRBV10-1,TRBV11-1,TRBV10-2,TRBV11-2,TRBV6-5,TRBV7-4,TRBV5-4,TRBV6-6,TRBV5-5,TRBV7-6,TRBV5-6,TRBV6-8,TRBV7-7,TRBV6-9,TRBV7-8,TRBV5-8,TRBV7-9,TRBV13,TRBV10-3,TRBV11-3,TRBV12-3,TRBV12-4,TRBV12-5,TRBV14,TRBV15,TRBV16,TRBV18,TRBV19,TRBV20-1,TRBV24-1,TRBV25-1,TRBV27,TRBV28,TRBV29-1,TRBV30
- D:
- TRBD1,TRBD2
- J:
- TRBJ1-1,TRBJ1-2,TRBJ1-3,TRBJ1-4,TRBJ1-5,TRBJ1-6,TRBJ2-1,TRBJ2-2,TRBJ2-3,TRBJ2-4,TRBJ2-5,TRBJ2-6,TRBJ2-7
-
-
-TRA::
-
- V:
- TRAV1-1,TRAV1-2,TRAV2,TRAV3,TRAV4,TRAV5,TRAV6,TRAV7,TRAV8-1,TRAV9-1,TRAV10,TRAV12-1,TRAV8-2,TRAV8-3,TRAV13-1,TRAV12-2,TRAV8-4,TRAV13-2,TRAV14/DV4,TRAV9-2,TRAV12-3,TRAV8-6,TRAV16,TRAV17,TRAV18,TRAV19,TRAV20,TRAV21,TRAV22,TRAV23/DV6,TRAV24,TRAV25,TRAV26-1,TRAV27,TRAV29/DV5,TRAV30,TRAV26-2,TRAV34,TRAV35,TRAV36/DV7,TRAV38-1,TRAV38-2/DV8,TRAV39,TRAV40,TRAV41
- J:
- TRAJ57,TRAJ56,TRAJ54,TRAJ53,TRAJ52,TRAJ50,TRAJ49,TRAJ48,TRAJ47,TRAJ46,TRAJ45,TRAJ44,TRAJ43,TRAJ42,TRAJ41,TRAJ40,TRAJ39,TRAJ38,TRAJ37,TRAJ36,TRAJ34,TRAJ33,TRAJ32,TRAJ31,TRAJ30,TRAJ29,TRAJ28,TRAJ27,TRAJ26,TRAJ24,TRAJ23,TRAJ22,TRAJ21,TRAJ20,TRAJ18,TRAJ17,TRAJ16,TRAJ15,TRAJ14,TRAJ13,TRAJ12,TRAJ11,TRAJ10,TRAJ9,TRAJ8,TRAJ7,TRAJ6,TRAJ5,TRAJ4,TRAJ3
-
-
-TRG::
-
- V:
- TRGV9,TRGV8,TRGV5,TRGV4,TRGV3,TRGV2
- J:
- TRGJ2,TRGJP2,TRGJ1,TRGJP1
-
-
-TRD::
-
- V:
- TRDV1,TRDV2,TRDV3
- D:
- TRDD1,TRDD2,TRDD3
- J:
- TRDJ1,TRDJ4,TRDJ2,TRDJ3
-
-
-**Mouse**
-
-TRB::
-
- V:
- TRBV1,TRBV2,TRBV3,TRBV4,TRBV5,TRBV12-1,TRBV13-1,TRBV12-2,TRBV13-2,TRBV13-3,TRBV14,TRBV15,TRBV16,TRBV17,TRBV19,TRBV20,TRBV23,TRBV24,TRBV26,TRBV29,TRBV30,TRBV31
- D:
- TRBD1,TRBD2
- J:
- TRBJ1-1,TRBJ1-2,TRBJ1-3,TRBJ1-4,TRBJ1-5,TRBJ2-1,TRBJ2-2,TRBJ2-3,TRBJ2-4,TRBJ2-5,TRBJ2-6,TRBJ2-7
-
-
-**OUTPUT**
-
-It generates the following result:
-
-