Commit f421f6d2 authored by Mathieu Giraud's avatar Mathieu Giraud

tests: CDR3/JUNCTION, some working sequences

parent dbcc9d2f
!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
......@@ -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
......
......@@ -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
......@@ -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
# 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
......
>IGKV1-5*03 9/4/1 IGKJ1*01 [IGK]
>IGKV1-5*03 9/4/1 IGKJ1*01 [IGK] {CQQYNRLWTF}
CTCCTGCTACTCTGGCTCCCAGGTGCCAAATGTGACATCCAGATGACCCAGTCTCCTTCCACCCTGTCTGCGTCTGTAGGAGACAGAGTCACCATCACCTGCCGGGCCAGTCAGAGTATTAATAACAACTTGGCCTGGTATCAGGAGAAGCCAGGGAAAGCCCCTAAGGTCCTGATCTATAAGGCGTCTAGTTTAGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACCTATTACTGCCAACAATATAATAGACTTTGGACGTTCGGCCAAGGGACCAAGGTGGAAGTCAAACGAACTGTGGCTGCACCATCT
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