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vidjil
vidjil
Commits
96ba9051
Commit
96ba9051
authored
Feb 16, 2017
by
Mathieu Giraud
Browse files
Merge branch 'dev' into feature/evalue-d
parents
28229b78
513e978b
Changes
4
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algo/tests/should-get-tests/example_mouse.should-get
0 → 100644
View file @
96ba9051
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -g $VIDJIL_DIR/germline/mus-musculus.g $VIDJIL_DIR/data/example_mouse.fa
$ Segment sequence on IGK
1:segIGK.*IGKV.*IGKJ
$ Segment sequence on IGH
1:segIGH.*IGHV.*IGHD.*IGHJ
$ Segment sequence on IGL
1:segIGL.*IGLV.*IGLJ
algo/tests/should-vdj-to-tap.py
View file @
96ba9051
...
...
@@ -217,8 +217,8 @@ def should_result_to_tap(should_pattern, result, tap_id):
should_regex
=
should_pattern_to_regex
(
should_pattern
)
# match = should_regex.search(result)
match
=
os
.
system
(
"echo '%s' | grep -E '%s' > /dev/null 2>&1"
\
%
(
result
.
replace
(
"'"
,
"
\\
'"
),
should_regex
.
pattern
.
replace
(
"'"
,
"
\\
'"
)))
%
(
result
.
replace
(
"'"
,
"
'
\\
'
'
"
),
should_regex
.
pattern
.
replace
(
"'"
,
"
'
\\
'
'
"
)))
found
=
(
match
==
0
)
globals
()[
'global_stats'
][
locus
]
+=
1
...
...
data/example_mouse.fa
0 → 100644
View file @
96ba9051
>segIGK
GGGAGTCATTCTTGGTCAGGAGACGTTGTAGAAATGAGACCGTCTATTCAGTTCCTGGGG
CTCTTGTTGTTCTGGCTTCATGGTGCTCAGTGTGACATCCAGATGACACAGTCTCCATCC
TCACTGTCTGCATCTCTGGGAGGCAAAGTCACCATCACTTGCAAGGCAAGCCAAGACATT
AACAAGTATATAGCTTGGTACCAACACAAGCCTGGAAAAGGTCCTAGGCTGCTCATACAT
TACACATCTACATTACAGCCAGGCATCCCATCAAGGTTCAGTGGAAGTGGGTCTGGGAGA
GATTATTCCTTCAGCATCAGCAACCTGGAGCCTGAAGATATTGCAACTTATTATTGTCTA
CAGTATGATAATCTGTGGACGTTCGGTGGAGGCACCAAGCTGGAAATCAAACGGGCTGAT
GCTGCACCAACTGTATCCATCTTCCCACCATCCAGTG
>segIGH
GGGAAGACATTTGGGAAGGACTGACTCTCTGAGGAGACTGTGAGAGTGGTGCCTTGGCCCCAGTAGTCAAAGTAGCTACTACCGTAGTAATCGTATCTTGCACAATAATAGACCGCAGAGTCCTCAGATGTCAGGCTGCTGAGCTGCATGTAGGCTGTGCTGGAGGGTTTGTCTACAGTCAGTGTGGCCTTGCTCTTGAACTTCTCATTGTACTTAGTACCACCACTATTAGGATCAATCCTTCCAATCCACTCAAGGCCTCGTCCAGGCCTCTGCTTCACCCAGTGCATCCAGTAGCTGGTGAAGGTGTAGCCAGAAGCCTTGCAGGACAGCTTCACTGAAGCCCCAGGCTTCACAAGCTCAGCCCCAGGCTGCTGCAGTTGGACCTGGGAGTGGACACCTGTAGCTGTTGCTACCAAGAAGAGGATGATACAGCTCCATCCCATAGTGAGGTCCTGTGTGCTCAGTAACTGTAAAGAGAACAGTGATCTCAACCCGTATTTATGAAGTGAAGTATT
>segIGL
GAGAGTGGGAGTGGACTTGGGCTGACCTAGGACAGTGACCTTGGTTCCACTGCCGAAAATAAATGGTTGCTGTACCATAGAGCACAGAAATATATTGCCTCATCCTCAGTCTGTGCCCCTGTGATGGTGAGGGCAGCCTTGTCTCCAATCAGGGAGCCTGAGAATCTGGCAGGAACACCTGGAGCTCGGTTGTTGGTACCACCTATTAGACCAGTGAATAAATGATCTGGTTTTTCTTGGACCCAGTTGGCATAGTTACTAGTTGTAACAGCCCCAGTACTTGAGCGACAAGTGAGTGTGACTGTTTCACCAGGTGATGTGGTGAGTGCAGATTCGTGAGTCACAACAGCCTGGGAAATGGCCCCTGAGCTGAGAGCCAGGAGAGAGAGTATAAGTGAAATCCAGGCCATAATTCACAAACCAGGTCTATTCTTTTCAATATTGGTCCCCCGTAGATCGGTGTATTCACATTGTC
\ No newline at end of file
germline/germline_id
View file @
96ba9051
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