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vidjil
vidjil
Commits
015705ce
Commit
015705ce
authored
Feb 25, 2018
by
Mathieu Giraud
Browse files
tools/tests/Makefile, tools/tests/should-get-tests/*: update paths
See
#3039
.
parent
b354cf43
Changes
10
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tools/tests/Makefile
View file @
015705ce
SHOULD
=
$(
wildcard
*
.should-get
)
SHOULD
=
$(
wildcard
should-get-tests/
*
.should-get
)
TAP
=
$
(
SHOULD:.should-get
=
.tap
)
all
:
$(TAP) doctests
fuse-doc.tap
:
fuse-doc.should-get force
should-get-tests/fuse-doc.tap
:
should-get-tests/
fuse-doc.should-get force
$(MAKE)
-C
../../doc analysis-example1.vidjil
../should-to-tap.sh
$<
...
...
tools/tests/should-get-tests/diff-two-files-c.should-get
View file @
015705ce
!LAUNCH: python ../diff.py ../../algo/tests/data/results-two-clones-1-2.vidjil ../../algo/tests/data/results-two-clones-1-3.vidjil -c
!LAUNCH: python
../
../diff.py
../
../../algo/tests/data/results-two-clones-1-2.vidjil
../
../../algo/tests/data/results-two-clones-1-3.vidjil -c
$ Clone id-1 is a common clone, with a different number of reads
1:id-1 .* 800 .* 300
...
...
tools/tests/should-get-tests/diff-two-files.should-get
View file @
015705ce
!LAUNCH: python ../diff.py ../../algo/tests/data/results-two-clones-1-2.vidjil ../../algo/tests/data/results-two-clones-1-3.vidjil
!LAUNCH: python
../
../diff.py
../
../../algo/tests/data/results-two-clones-1-2.vidjil
../
../../algo/tests/data/results-two-clones-1-3.vidjil
$ Clone id-1 has a different number of reads
1:Not the same number or reads: id-1
...
...
tools/tests/should-get-tests/fuse-doc.should-get
View file @
015705ce
!LAUNCH: python ../fuse.py ../../doc/analysis-example1.vidjil ../../doc/analysis-example2.vidjil; cat fused.vidjil | python ../format_json.py -1 -u
!LAUNCH: python
../
../fuse.py
../
../../doc/analysis-example1.vidjil
../
../../doc/analysis-example2.vidjil; cat fused.vidjil | python
../
../format_json.py -1 -u
$ Fuse the two examples (three samples, two identical)
e1:"segmented": [335662, 335662, 410124]
...
...
tools/tests/should-get-tests/fuse-files-no-clones.should-get
View file @
015705ce
!LAUNCH: python ../fuse.py ../../algo/tests/data/no_clones.vidjil ../../algo/tests/data/results-two-clones-1-2.vidjil -o fused_no_clones.vidjil; cat fused_no_clones.vidjil
!LAUNCH: python
../
../fuse.py
../
../../algo/tests/data/no_clones.vidjil
../
../../algo/tests/data/results-two-clones-1-2.vidjil -o fused_no_clones.vidjil; cat fused_no_clones.vidjil
$ Fuse the three files
2: ListWindows: .0, 1000.
...
...
tools/tests/should-get-tests/fuse-three-files.should-get
View file @
015705ce
!LAUNCH: python ../fuse.py ../../algo/tests/data/results-two-clones-1-2.vidjil ../../algo/tests/data/results-two-clones-1-2.vidjil ../../algo/tests/data/results-two-clones-1-2.vidjil ; cat fused.vidjil
!LAUNCH: python
../
../fuse.py
../
../../algo/tests/data/results-two-clones-1-2.vidjil ../../
../
algo/tests/data/results-two-clones-1-2.vidjil
../
../../algo/tests/data/results-two-clones-1-2.vidjil ; cat fused.vidjil
$ Fuse the three files
2: ListWindows: .1000, 1000, 1000.
...
...
tools/tests/should-get-tests/latex.should-get
View file @
015705ce
!LAUNCH: python ../latex.py ../../algo/tests/data/results-two-clones-1-2.vidjil
!LAUNCH: python
../
../latex.py
../
../../algo/tests/data/results-two-clones-1-2.vidjil
$ Display the name of the .vidjil file
2: data/results-two-clones-1-2.vidjil
...
...
tools/tests/should-get-tests/vidjil-to-fasta-with-sequences.should-get
View file @
015705ce
!LAUNCH:
(cd ..;
python vidjil-to-fasta.py -o
tests/
vidjil-to-fasta-with-sequences.fasta ../doc/analysis-example.vidjil > /dev/null; cat
tests/
vidjil-to-fasta-with-sequences.fasta
)
!LAUNCH: python
../../
vidjil-to-fasta.py -o vidjil-to-fasta-with-sequences.fasta
../../
../doc/analysis-example.vidjil > /dev/null; cat vidjil-to-fasta-with-sequences.fasta
$ 19 sequences with a seg field should be found
19:^>
...
...
tools/tests/should-get-tests/vidjil-to-fasta.should-get
View file @
015705ce
!LAUNCH:
(cd ..;
python vidjil-to-fasta.py -o
tests/
vidjil-to-fasta.fasta ../data/no_clones.vidjil > /dev/null; cat
tests/
vidjil-to-fasta.fasta
)
!LAUNCH: python
../../
vidjil-to-fasta.py -o vidjil-to-fasta.fasta
../../
../data/no_clones.vidjil > /dev/null; cat vidjil-to-fasta.fasta
$ No data should be found
0:.
tools/tests/should-get-tests/window-change.should-get
View file @
015705ce
!LAUNCH: (cd .. ; python analysis-windows.py -w 40 ../algo/tests/data/analysis-with-windows.analysis ; python analysis-windows.py -w 60 ../algo/tests/data/analysis-with-windows.analysis.new ; ./diff_json.sh ../algo/tests/data/analysis-with-windows.analysis{,.new.new} -s ; cat ../algo/tests/data/analysis-with-windows.analysis.new)
!LAUNCH: (cd ..
/..
; python analysis-windows.py -w 40 ../algo/tests/data/analysis-with-windows.analysis ; python analysis-windows.py -w 60 ../algo/tests/data/analysis-with-windows.analysis.new ; ./diff_json.sh ../algo/tests/data/analysis-with-windows.analysis{,.new.new} -s ; cat ../algo/tests/data/analysis-with-windows.analysis.new)
$ First and last files are identical
1:are identical
...
...
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