tests: CDR3/JUNCTION, some working sequences

algo/tests/clones_lec.should_get

-!LAUNCH: ../../vidjil -G ../../germline/TRG -c clones ../../data/segment_lec.fa
+!LAUNCH: ../../vidjil -G ../../germline/TRG -c clones -A -3 ../../data/segment_lec.fa
 
 $ Extract 50bp windows (TRG)
 1:found . 50-windows
@@ -12,3 +12,7 @@ $ Find the good statistics on TRG
 $ Find the good length statistics
 3: SEG.* 117.0
 1: UNSEG too short w.* 40.0
+
+$ Find the good CDR3
+1: CATWA#YYKKLF
+1: CAAWRPTGWFKIF
\ No newline at end of file

algo/tests/should-vdj-tests/0000-nck-TRB.should-vdj.fa

@@ -3,7 +3,8 @@ GAGGGTACCACTGACAAAGGAGAAGTCCCCAATGGCTACAATGTCTCCAGATTAAACAAACGGGAGTTCTCGCTCAGGCT
 # AGC commun aux deux segments
 >TRBV7-2*02 0/0/3 TRBJ2-3*01  [TRB]
 TTACCCTTTACTGGTACCGGCAGAGGCTGGGGCAGGGCCTGGAGTTTTTAATTTACTTCCAAGGCAACAGTGCACCAGACAAATCAGGGCTGCCCAGTGATCGCTTCTCTGCAGAGAGGACTGGGGAATCCGTCTCCACTCTGACGATCCAGCGCACACAGCAGGAGGACTCGGCCGTGTATCTCTGTGCCAGCAGCTTTAGCACAGATACGCAGTATTTTGGCCCAGGCACCCGGCTGACAGTGCTCGGTAAGCGGG
->TRBV11-2*01 1/4/0 TRBJ2-7*01  [TRB]
+
+>TRBV11-2*01 1/4/0 TRBJ2-7*01  [TRB]  {CASSLGPSYEQYF}
 AACGGTGTAGTGGATGATTCACAGTTGCCTAAGGATCGATTTTCTGCAGAGAGGCTCAAAGGAGTAGACTCCACTCTCAAGATCCAGCCTGCAAAGCTTGAGGACTCGGCCGTGTATCTCTGTGCCAGCAGCTTAGGTCCCTCGTACGAGCAGTACTTCGGGCCGGGCACCAGGCTC
 
 

algo/tests/should-vdj-tests/0000-nck-TRD.should-vdj.fa

@@ -17,6 +17,6 @@ TGAAATCCGTCGCCTTAACcTtTcaGCCTTACAGCTAGAAgAttcaGCAAAGTACTtTTGTGCTCTtGGGGATCCCGGCC
 >TRDV1 7/5/0 TRDD3 2/5/4 TRDJ1  [TRD] TODO
 AAGCtAGAAgattcAGCAAaGtACttttGtGCtCttGtGCtAACtGGGGGatAAAGAtCGAtAAACtCAtCtttGGAAAAgGAACCCGtGtGACtGtGGAACA
 
->TRDV1 4/13/2 TRDD3 2/8/2 TRDJ1  [TRD]
+>TRDV1 4/13/2 TRDD3 2/8/2 TRDJ1  [TRD]  {CALGVALRNGG*MT!TDKLIF}
 CAAAAAGTGGTCGCTATTCTGTCAACTTCAAGAAAGCAGCGAAATCCGTCGCCTTAACCATTTCAGCCTTACAGCTAGAAGATTCAGCAAAGTACTTTTGTGCTCTTGGGGTAGCTCtTAgGAAtGGGGGATAGAtGACGGACCGATAAACtCATCTTtGGAAAAgGAACCCGtGtGACtGTGGAACa
 

algo/tests/should-vdj-tests/0118-lil-IGH-TRG.should-vdj.fa

@@ -7,10 +7,10 @@ aATTGTAGTAGTACCAGCTGCTATAC
 ggaaTACGATATTTTGACTGGTTA
 CTACTACTACATGGACGTCTGGGGCAAAGGGACCCTGGTCACCGTCTCCTCAGGT
 
->TRGV2*01 1/C/0 TRGJ1*02  [TRG]
+>TRGV2*01 1/C/0 TRGJ1*02  [TRG]  {CATWDG!YYKKLF}
 GGAAGGCCCCACAGCGTCTTCAGTACTATGACTCCTACAACTCCAAGGTTGTGTTGGAATCAGGAGTCAGTCCAGGGAAGTATTATACTTACGCAAGCACAAGGAACAACTTGAGATTGATACTGCGAAATCTAATTGAAAATGACTCTGGGGTCTATTACTGTGCCACCTGGGACGGCTTATTATAAGAAACTCTTTGGCAGTGGAACAACAC
 
->TRGV3*01 0/CC/0 TRGJ1*01  [TRG]
+>TRGV3*01 0/CC/0 TRGJ1*01  [TRG]  {CATWDRPNYYKKLF}
 GGAAGGCCCCACAGCGTCTTCTGTACTATGACGTCTCCACCGCAAGGGATGTGTTGGAATCAGGACTCAGTCCAGGAAAGTATTATACTCATACACCCAGGAGGTGGAGCTGGATATTGAGACTGCAAAATCTAATTGAAAATGATTCTGGGGTCTATTACTGTGCCACCTGGGACAGGCCGAATTATTATAAGAAACTCTTTGGCAGTGGAACAACAC
 
 

algo/tests/should-vdj-tests/0298-lil-IGH.should-vdj.fa

 
 
 # The D/J junction can be seen as 2//7, 3//6, or 4//5
+# 4//5 would imply {CARENSGY!FDYW}
 
->IGHV3-48*01 0/AA/6 IGHD5-12*01 3//6 IGHJ4*02  [IGH]
+>IGHV3-48*01 0/AA/6 IGHD5-12*01 3//6 IGHJ4*02  [IGH]  {CARENSGYD!DYW}
 GGAGTCGGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCC
 TCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGG
 GGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTC
 TGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAA
-ATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAAAATAGTG
-GCTACGAT
-TTGACTAC
-TGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGTT
+ATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA
+AA
+ATAGTGGCTACGA
+TTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGTT
 
 
 # IGHV3-48*01 ...TGTGTATTACTGTGCGAGAGA

algo/tests/should-vdj-tests/1043-IGK.should-vdj.fa

->IGKV1-5*03 9/4/1 IGKJ1*01  [IGK]
+>IGKV1-5*03 9/4/1 IGKJ1*01  [IGK]  {CQQYNRLWTF}
 CTCCTGCTACTCTGGCTCCCAGGTGCCAAATGTGACATCCAGATGACCCAGTCTCCTTCCACCCTGTCTGCGTCTGTAGGAGACAGAGTCACCATCACCTGCCGGGCCAGTCAGAGTATTAATAACAACTTGGCCTGGTATCAGGAGAAGCCAGGGAAAGCCCCTAAGGTCCTGATCTATAAGGCGTCTAGTTTAGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACCTATTACTGCCAACAATATAATAGACTTTGGACGTTCGGCCAAGGGACCAAGGTGGAAGTCAAACGAACTGTGGCTGCACCATCT