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domainWorld
RADS
Commits
5eda765e
Commit
5eda765e
authored
Jul 02, 2018
by
Carsten Kemena
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Merge branch 'develop' into 'master'
fixed collapsing option, added test See merge request
!3
parents
41f70aa1
08194f46
Pipeline
#651
passed with stage
in 3 minutes and 43 seconds
Changes
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6 changed files
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88 additions
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4 deletions
+88
-4
CHANGELOG
CHANGELOG
+3
-0
CMakeLists.txt
CMakeLists.txt
+1
-1
src/DBAccess.cpp
src/DBAccess.cpp
+4
-1
tests/integrationTests/results/collapse-both.txt
tests/integrationTests/results/collapse-both.txt
+35
-0
tests/integrationTests/results/collapse-none.txt
tests/integrationTests/results/collapse-none.txt
+35
-0
tests/integrationTests/runTests.sh
tests/integrationTests/runTests.sh
+10
-2
No files found.
CHANGELOG
View file @
5eda765e
v. 2.3.2
- fixed: query was uncollapsed for next target if collapse was activated
v. 2.3.1
- fixed: query was always collapse independently of parameter
...
...
CMakeLists.txt
View file @
5eda765e
...
...
@@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 2.6)
project
(
RADS C CXX
)
SET
(
MAJOR_VERSION 2
)
SET
(
MINOR_VERSION 3
)
SET
(
PATCH_VERSION
1
)
SET
(
PATCH_VERSION
2
)
SET
(
CMAKE_CXX_FLAGS_COVERAGE
...
...
src/DBAccess.cpp
View file @
5eda765e
...
...
@@ -158,7 +158,10 @@ DBAccess::search(BSDL::AlignmentMatrix<int, BSDL::DSM> &matrix, bool all, bool c
// add all sequences having the same domain arrangement
readSequences_
(
results
.
targets
.
back
().
targetSequences
,
domains
);
queryDA
.
reconstruct
();
}
if
(
collapse
)
queryDA
.
reconstruct
();
results
.
sort
();
}
tests/integrationTests/results/collapse-both.txt
0 → 100644
View file @
5eda765e
# RADS version 2.3.1
# RADS Output v1
# run at Mon Jul 2 16:19:24 2018
#
# query file: -
# database: /local/home/ckeme_01/projects/domainWorld/RADS/tests/integrationTests/annotation
# gap open penalty -50
# gap extension penalty -10
# matrix: /local/home/ckeme_01/.domainWorld/dsm/pfam-31.dsm
# all: false
# collapse: true
# ******************************************************************
# -------------------------------------------------------------------
Results for: manual entered query
Domain arrangement: PF02543 PF02543 PF16861
# score | normalized | SeqID | sequence length | domain arrangement | aln
# -------------------------------------------------------------------
200 1.00 A0A010 530 PF02543 10 63 PF16861 362 524 1
200 1.00 A0A009 530 PF02543 10 63 PF02543 104 312 PF16861 362 524 2
# -------------------------------------------------------------------
List of alignments:
# -------------------------------------------------------------------
1)
Query DA: PF02543 PF16861
Target DA: PF02543 PF16861
2)
Query DA: PF02543 PF16861
Target DA: PF02543 PF16861
tests/integrationTests/results/collapse-none.txt
0 → 100644
View file @
5eda765e
# RADS version 2.3.1
# RADS Output v1
# run at Mon Jul 2 16:20:43 2018
#
# query file: -
# database: /local/home/ckeme_01/projects/domainWorld/RADS/tests/integrationTests/annotation
# gap open penalty -50
# gap extension penalty -10
# matrix: /local/home/ckeme_01/.domainWorld/dsm/pfam-31.dsm
# all: false
# collapse: false
# ******************************************************************
# -------------------------------------------------------------------
Results for: manual entered query
Domain arrangement: PF02543 PF02543 PF16861
# score | normalized | SeqID | sequence length | domain arrangement | aln
# -------------------------------------------------------------------
300 1.00 A0A009 530 PF02543 10 63 PF02543 104 312 PF16861 362 524 1
190 0.69 A0A010 530 PF02543 10 63 PF16861 362 524 2
# -------------------------------------------------------------------
List of alignments:
# -------------------------------------------------------------------
1)
Query DA: PF02543 PF02543 PF16861
Target DA: PF02543 PF02543 PF16861
2)
Query DA: PF02543 PF02543 PF16861
Target DA: ******* PF02543 PF16861
tests/integrationTests/runTests.sh
View file @
5eda765e
...
...
@@ -81,11 +81,19 @@
[
"
$output
"
==
$'Number of sequences included: 9
\n
Number of distinct arrangements 8'
]
run ../../build/rads
-D
PF02543 PF16861
-m
pfam-31.dsm
-d
annotation
-o
test-col-aln.txt
-c
-l
run diff <
(
grep
-v
'#'
test-col-aln.txt
)
<
(
grep
-v
'#'
results/test-col-aln.txt
)
[
$status
==
0
]
rm
annotation.db annotation.da test-col-aln.txt
run ../../build/rads
-D
PF02543 PF02543 PF16861
-m
pfam-31.dsm
-d
annotation
-l
-c
-o
collapse-both.txt
run diff <
(
grep
-v
'#'
collapse-both.txt
)
<
(
grep
-v
'#'
results/collapse-both.txt
)
[
$status
==
0
]
run ../../build/rads
-D
PF02543 PF02543 PF16861
-m
pfam-31.dsm
-d
annotation
-l
-o
collapse-none.txt
run diff <
(
grep
-v
'#'
collapse-none.txt
)
<
(
grep
-v
'#'
results/collapse-none.txt
)
[
$status
==
0
]
rm
annotation.db annotation.da test-col-aln.txt collapse-both.txt collapse-none.txt
}
...
...
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