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vidjil
vidjil
Commits
f421f6d2
Commit
f421f6d2
authored
Feb 28, 2016
by
Mathieu Giraud
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tests: CDR3/JUNCTION, some working sequences
parent
dbcc9d2f
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11 deletions
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algo/tests/clones_lec.should_get
algo/tests/clones_lec.should_get
+5
-1
algo/tests/should-vdj-tests/0000-nck-TRB.should-vdj.fa
algo/tests/should-vdj-tests/0000-nck-TRB.should-vdj.fa
+2
-1
algo/tests/should-vdj-tests/0000-nck-TRD.should-vdj.fa
algo/tests/should-vdj-tests/0000-nck-TRD.should-vdj.fa
+1
-1
algo/tests/should-vdj-tests/0118-lil-IGH-TRG.should-vdj.fa
algo/tests/should-vdj-tests/0118-lil-IGH-TRG.should-vdj.fa
+2
-2
algo/tests/should-vdj-tests/0298-lil-IGH.should-vdj.fa
algo/tests/should-vdj-tests/0298-lil-IGH.should-vdj.fa
+6
-5
algo/tests/should-vdj-tests/1043-IGK.should-vdj.fa
algo/tests/should-vdj-tests/1043-IGK.should-vdj.fa
+1
-1
No files found.
algo/tests/clones_lec.should_get
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f421f6d2
!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
View file @
f421f6d2
...
...
@@ -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
View file @
f421f6d2
...
...
@@ -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
View file @
f421f6d2
...
...
@@ -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
View file @
f421f6d2
# 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
ATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA
AAATAGTG
GCTACGAT
TTGACTAC
TGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGTT
ATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA
AA
ATAGTGGCTACGA
T
TTGACTACT
GGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGTT
# IGHV3-48*01 ...TGTGTATTACTGTGCGAGAGA
...
...
algo/tests/should-vdj-tests/1043-IGK.should-vdj.fa
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f421f6d2
>IGKV1-5*03 9/4/1 IGKJ1*01 [IGK]
>IGKV1-5*03 9/4/1 IGKJ1*01 [IGK]
{CQQYNRLWTF}
CTCCTGCTACTCTGGCTCCCAGGTGCCAAATGTGACATCCAGATGACCCAGTCTCCTTCCACCCTGTCTGCGTCTGTAGGAGACAGAGTCACCATCACCTGCCGGGCCAGTCAGAGTATTAATAACAACTTGGCCTGGTATCAGGAGAAGCCAGGGAAAGCCCCTAAGGTCCTGATCTATAAGGCGTCTAGTTTAGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACCTATTACTGCCAACAATATAATAGACTTTGGACGTTCGGCCAAGGGACCAAGGTGGAAGTCAAACGAACTGTGGCTGCACCATCT
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