From 909f38c081703e27135cab112724aff2eef0d419 Mon Sep 17 00:00:00 2001
From: Mathieu Giraud <mathieu@vidjil.org>
Date: Sun, 28 Feb 2016 19:09:08 +0100
Subject: [PATCH] tests: CDR3/JUNCTION, difficult or non-working sequences

---
 algo/tests/should-vdj-tests/0000-nck-TRB.should-vdj.fa     | 3 +++
 algo/tests/should-vdj-tests/0000-nck-TRD.should-vdj.fa     | 3 ++-
 algo/tests/should-vdj-tests/0147-lil-IGH-TRG.should-vdj.fa | 1 +
 algo/tests/should-vdj-tests/segment_simul.should-vdj.fa    | 3 ++-
 4 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/algo/tests/should-vdj-tests/0000-nck-TRB.should-vdj.fa b/algo/tests/should-vdj-tests/0000-nck-TRB.should-vdj.fa
index 22be73a15..5bc6ef4f6 100644
--- a/algo/tests/should-vdj-tests/0000-nck-TRB.should-vdj.fa
+++ b/algo/tests/should-vdj-tests/0000-nck-TRB.should-vdj.fa
@@ -1,7 +1,10 @@
 >TRBV6-1*01 3/5/2 TRBJ2-7*01  [TRB]
+# {CASKVSP!YEQYF} # TODO: insert at the end of V
 GAGGGTACCACTGACAAAGGAGAAGTCCCCAATGGCTACAATGTCTCCAGATTAAACAAACGGGAGTTCTCGCTCAGGCTGGAGTCGGCTGCTCCCTCCCAGACATCTGTGTACTTCTGTGCCAGCAAGGTGAGTCCCCCTACGAGCAGTACTTCGGGCCGG
 # AGC commun aux deux segments
+
 >TRBV7-2*02 0/0/3 TRBJ2-3*01  [TRB]
+# {CASSFSTDTQYF} # TODO: insert at the end of V
 TTACCCTTTACTGGTACCGGCAGAGGCTGGGGCAGGGCCTGGAGTTTTTAATTTACTTCCAAGGCAACAGTGCACCAGACAAATCAGGGCTGCCCAGTGATCGCTTCTCTGCAGAGAGGACTGGGGAATCCGTCTCCACTCTGACGATCCAGCGCACACAGCAGGAGGACTCGGCCGTGTATCTCTGTGCCAGCAGCTTTAGCACAGATACGCAGTATTTTGGCCCAGGCACCCGGCTGACAGTGCTCGGTAAGCGGG
 
 >TRBV11-2*01 1/4/0 TRBJ2-7*01  [TRB]  {CASSLGPSYEQYF}
diff --git a/algo/tests/should-vdj-tests/0000-nck-TRD.should-vdj.fa b/algo/tests/should-vdj-tests/0000-nck-TRD.should-vdj.fa
index 7248f8669..be96444b5 100644
--- a/algo/tests/should-vdj-tests/0000-nck-TRD.should-vdj.fa
+++ b/algo/tests/should-vdj-tests/0000-nck-TRD.should-vdj.fa
@@ -4,7 +4,8 @@ CAAAAAGTGGTCGCTATTCTGTCAACTTCAAGAAAGCAGCGAAATCCGTCGCCTTAACCATTTCAGCCTTACAGCTAGAA
 >TRAV29/DV5*01 0/9/0 TRDD3 3/9/2 TRDJ1*01  [TRD]
 GAtAAAAATGAAGatGGAAGaTTcaCTGTCTTCTTAAAcAAAAGTGCcaAGCACCTCTCTCTGCACATTGTGCCCTCCCAGCCTGGAGACTCTGCAGTGTACTTCTGTGCAGCAAGCGCGAATCCTGACTGGGGGATCGAGGGGGAACCGATAAACTCATCTTTGGAAAAGGAACCCGTGTGACTGTGGAACA
 
->TRDV1 5/14/0 TRDJ1*01  [TRD]
+>TRDV1 5/14/0 TRDJ1*01  [TRD]  {CALGTLSRV!TDKLIF}
+# IMGT/JunctionAnalysis: {CALGTLS!VYTDKLIF}
 GCCttAcAGCtAGAAgattcAGCAAaGtACtnttGtGCtCttGGGACCCtttCCcGtGtACACCGATAAACtCAtCtttGGAAAAgGAACCCGtGtGACtGTGGAACA
 
 
diff --git a/algo/tests/should-vdj-tests/0147-lil-IGH-TRG.should-vdj.fa b/algo/tests/should-vdj-tests/0147-lil-IGH-TRG.should-vdj.fa
index d56014715..b9ac65b38 100644
--- a/algo/tests/should-vdj-tests/0147-lil-IGH-TRG.should-vdj.fa
+++ b/algo/tests/should-vdj-tests/0147-lil-IGH-TRG.should-vdj.fa
@@ -5,6 +5,7 @@ CGTCTTCTGTACTATGACGTCTCCAACTCAAAGGATGTGTTGGAATCAGGACTCAGTCCAGGAAAGTATTATACTCATAC
 GGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACGACATGCACTGGGTCCGCCAAGCTACAGGAAAAGGTCTGGAGTGGGTCTCAGCTATTGGTACTGCTGGTGACACATACTATCCAGGCTCCGTGAAGGGCCGATTCACCATCTCCAGAGAAAATGCCAAGAACTCCTTGTATCTTCAAATGAACAGCCTGAGAGCCGGGGACACGGCTGTGTATTACTGTGCAAGAGTGAGGCGGAGAGATCGGGGGATTGTAGTGGTGGTAGCTGCTACTCAACGGTAAGTTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGT
 
 # or IGHV3-74*01 (-9)
+# There could be {CQQYNRLWTF}, but the Cys104 is one nucleotide outside of V3-74*02 7/
 >IGHV3-74*02 7/CCGCGGT/6 IGHD3-9*01 4/CTTCGAACA/7 IGHJ4*02  [IGH]
 GGAGTCGGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGCCGCGGTCGATATTTTGACTGGTTATTACTTCGAACATGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGT
 
diff --git a/algo/tests/should-vdj-tests/segment_simul.should-vdj.fa b/algo/tests/should-vdj-tests/segment_simul.should-vdj.fa
index 873e9a16d..54c2fdae0 100644
--- a/algo/tests/should-vdj-tests/segment_simul.should-vdj.fa
+++ b/algo/tests/should-vdj-tests/segment_simul.should-vdj.fa
@@ -5,7 +5,8 @@
 # With only one D, this is:
 # IGHV5-10-1*01 2/CTTC/3 IGHD1-14*01 1/GTTA/5 IGHJ5*01  [IGH]
 
->IGHV5-10-1*01 2/CTTC/3 IGHD1-14*01 1//23 IGHD3-16*01 8//7 IGHJ5*01  [IGH]
+>IGHV5-10-1*01 2/CTTC/3 IGHD1-14*01 1//23 IGHD3-16*01 8//7 IGHJ5*01  [IGH]  {CATS*PEPVM!FDSW}
+# IMGT/JunctionAnalysis: {CATS*PEPV!WFDSW}
 aagtccatcagcactgcctacctgcagtggagcagcctgaaggcctcggacaccgccatgtattactgtgcga
 CTTC
 ataaccggaacca
-- 
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