Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
vidjil
vidjil
Commits
a4d405f7
Commit
a4d405f7
authored
May 27, 2020
by
Mathieu Giraud
Browse files
tests: tdd, update test, actual start V positions and codes
parent
98e37b14
Changes
2
Hide whitespace changes
Inline
Side-by-side
algo/tests/data/productive_stop_before_V.fa
View file @
a4d405f7
# These
sequences have stop codon
before the start of the V gene
#
result
should be productive
# These
two recombinations start
before the start of the V gene
, including a stop codon in that zone.
#
They
should be productive
>IGHV1-69*06 2/AACCCCCAACAAAGC/4 IGHD3-3*01 9/CCCATAAGTACCGT/1 IGHJ6*02 [IGH]
CTGGAGGTTCCTCTTTGTGGTGGCAGCAGCTACAGGTAAGGGGCTTCCTAGTCCTAAGGCTGAGGAAGGGATCCTGGTTTAGTTAAAGAGGATTTTATTCACCCCTGTGTCCTGTCCACAGGTGTCCAGTCCCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCCTATCTTTGGTACAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAAACCCCCAACAAAGCTACGATTTTTGGAGTGGTCCCATAAGTACCGTTTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAGGTAAG
# start of the V gene @133
# end of the J gene @534
>132/0 IGHV1-69*06 2/AACCCCCAACAAAGC/4 IGHD3-3*01 9/CCCATAAGTACCGT/1 IGHJ6*02 40/GGTAAG [IGH]
CTGGAGGTTCCTCTTTGTGGTGGCAGCAGCTACAGGTAAGGGGCTTCCTAGTCCTAAGGCTGAGGAAGGGATCCTGGTTTAGTTAAAGAGGATTTTATTCACCCCTGTGTCCTGTCCACAGGTGTCCAGTCC
CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCCTATCTTTGGTACAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAAACCCCCAACAAAGCTACGATTTTTGGAGTGGTCCCATAAGTACCGTTTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG
GTAAG
# start of the V gene @146
>145/0 IGHV3-74*01 0/GACCG/6 IGHD1-7*01 0/GC/10 IGHJ4*02 [IGH]
AGCTGGGTTTTCCTTGTTGCTATTTTAAAAGGTGATTCATGGAGAATTGGAGATGTGGAGTGTGAATGGACATGGGTGAGATAAGCAGTGGATGTGTGTGGCAGTTTCTGACCAGGGTGTCTCTGTGTTTGCAGGTGTCTCGTGT
GAGGTGCTTCTGGTGGAGTCCGGGGGAGGCTTAGTTAAGGCGGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAATTACTGGATGCACTGGGTCCGCCAAGTTCCAGGGAAGGGCCTGGAGTGGGTCTCACGTATTAACAGCGATGGGAGCGCCATAAGGTACGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGGACACACTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTTTATTATTGTGCAAGAGAGACCGACTGGAATTACGCCTACTGGGGCCAGGGAACCCTGGTC
# actual sequence was continuing after J
# ... ACCGTCTCCT CAGGTAAG
>IGHV3-74*01 0/GACCG/6 IGHD1-7*01 0/GC/10 IGHJ4*02 [IGH]
AGCTGGGTTTTCCTTGTTGCTATTTTAAAAGGTGATTCATGGAGAATTGGAGATGTGGAGTGTGAATGGACATGGGTGAGATAAGCAGTGGATGTGTGTGGCAGTTTCTGACCAGGGTGTCTCTGTGTTTGCAGGTGTCTCGTGTGAGGTGCTTCTGGTGGAGTCCGGGGGAGGCTTAGTTAAGGCGGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAATTACTGGATGCACTGGGTCCGCCAAGTTCCAGGGAAGGGCCTGGAGTGGGTCTCACGTATTAACAGCGATGGGAGCGCCATAAGGTACGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGGACACACTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTTTATTATTGTGCAAGAGAGACCGACTGGAATTACGCCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAGGTAAG
algo/tests/should-get-tests/productive_stop_before_V.should
View file @
a4d405f7
...
...
@@ -2,15 +2,27 @@
!OUTPUT_FILE: out/productive_stop_before_V.vidjil
$ first clone name
1: "IGHV1-69
*
06 2/AACCCCCAACAAAGC/4 IGHD3-3
*
01 9/CCCATAAGTACCGT/1 IGHJ6
*
02"
1: "IGHV1-69
.
06 2/AACCCCCAACAAAGC/4 IGHD3-3
.
01 9/CCCATAAGTACCGT/1 IGHJ6
.
02"
$ second clone name
1: "IGHV3-74
*
01 0/GACCG/6 IGHD1-7
*
01 0/GC/10 IGHJ4
*
02"
1: "IGHV3-74
.
01 0/GACCG/6 IGHD1-7
.
01 0/GC/10 IGHJ4
.
02"
$ We should get 6 start position in vidjil (2 by segments)
6: "start"
# There are 10 = 2x5 segments (V, D, J, cdr3 and junction)
$ We should get 6 stop position in vidjil (2 by segments)
6: "stop"
$ Correct number of start positions
10: "start"
$ Correct start position of IGHV1-69*06
1: "start": 133
$ Correct stop position of IGHJ6*02
1: "stop": 534
$ Correct start position of IGHV3-74*01
1: "start": 146
$ Correct number of stop positions (10-1, no stop positions for J on the second sequence)
9: "stop"
$ The two sequences are productive
f2: "productive": true
$ But only one productive
2: "productive": true
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment