Commit 64dcc963 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

tests: update tests

parent 54946cae
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -t 0 -g $VIDJIL_DIR/germline -2 $VIDJIL_DIR/data/chimera-fake.fa
$ The KmerSegmenter segments the three chimera reads on PSEUDO_MAX12 germline (-2)
1:xxx .* -> .* 3
1:unexpected .* -> .* 3
$ The FineSegmenter gives the locus information (-2)
1:Unexpected .*TRAV.*/.*TRBV
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DIR/data/chimera-fake-D.fa
$ The KmerSegmenter segments the chimera reads on PSEUDO_MAX12 germline (-2)
f1:xxx .* -> .* 2
f1:unexpected .* -> .* 2
$ The FineSegmenter gives the locus information (-2)
f1:Unexpected [+]IGHD/[+]TRBJ
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DIR/data/chimera-fake-VJ.fa
$ The KmerSegmenter segments the five chimera reads on PSEUDO_MAX12 germline (-2)
1:xxx .* -> .* 5
1:unexpected .* -> .* 5
$ The FineSegmenter gives the locus information (-2)
1:Unexpected [+]TRBV/[+]TRGJ
......
......@@ -2,7 +2,7 @@
# TODO: a more precise modeling should give a e-value computation that could make this work even with -e 1
$ The KmerSegmenter segments the six chimera reads on PSEUDO_MAX1U germline (-4)
1:xxx .* -> .* 6
1:unexpected .* -> .* 6
$ The FineSegmenter gives the locus information (-4)
1:Unexpected .*TRAV.*/.\?
......
......@@ -9,13 +9,13 @@ $ Do not segment the TR recombinations
4:TR.* UNSEG
$ Report the unsegmented sequences in the json output
1: "germline": "zzz", "id": "TRA
1: "germline": "zzz", "id": "TRB
1: "germline": "zzz", "id": "TRG
1: "germline": "zzz", "id": "TRD
1: "germline": "not analyzed", "id": "TRA
1: "germline": "not analyzed", "id": "TRB
1: "germline": "not analyzed", "id": "TRG
1: "germline": "not analyzed", "id": "TRD
$ Count the unsegmented sequences in the json output
1: "zzz": .4.
1: "not analyzed": .4.
$ Count the segmented sequences in the json output
1: "segmented": .3.
......
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