Commit 5eda765e authored by Carsten Kemena's avatar Carsten Kemena

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
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
......
......@@ -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
......
......@@ -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();
}
# 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
# 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
......@@ -81,11 +81,19 @@
[ "$output" == $'Number of sequences included: 9\nNumber 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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