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vidjil
vidjil
Commits
745b47db
Commit
745b47db
authored
Feb 06, 2016
by
Mathieu Giraud
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tests: test segmentation details in json
parent
6c2d6a72
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algo/tests/stanford-json.should_get
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745b47db
!REQUIRES: python ../../tools/check_python_version.py
!LAUNCH: ../../vidjil -z 1 -G ../../germline/IGH -w 60 -r 5 -e 10 -b data ../../data/Stanford_S22.fasta ; cat out/data.vidjil | python ../../tools/format_json.py -1
!LAUNCH: ../../vidjil -z 1 -G ../../germline/IGH -w 60 -r 5 -e 10 -b data ../../data/Stanford_S22.fasta
> /dev/null
; cat out/data.vidjil | python ../../tools/format_json.py -1
$ Number of reads
e1:"total": [13153]
...
...
@@ -13,6 +13,27 @@ $ Most abundant window
$ Segmentation
1:"name": "IGHV3-23.05 6/ACCCGGGAGGAACAATAT/9 IGHD6-13.01 0//5 IGHJ4.02"
$ Segmentation details - V
1:"5": "IGHV3-23.05",
1:"5end": 54,
1:"5del": 6,
$ Segmentation details - D
1:"4delLeft": 9,
1:"4start": 73,
1:"4": "IGHD6-13.01",
1:"4end": 84,
1:"4delRight": 0,
$ Segmentation details - J
1:"3del": 5,
1:"3start": 85,
1:"3": "IGHJ4.02",
$ Segmentation details - N1, N2
1:"N1": 18,
1:"N2": 0,
$ Second sequence has a DNA sequence provided
1:"id": "CTGTGCGAGAGGTTACTATGATAGTAGTGGTTATTACGGGGTAGGGCAGTACTACTACTA".*"sequence": "[ACGT]+",
...
...
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