Commit 3c625c8d authored by Mathieu Giraud's avatar Mathieu Giraud

tests: update tests

See #3011.
parent 86339be9
......@@ -4,7 +4,7 @@ $ Load CD-sorting.fa
1:homo-sapiens/CD-sorting.fa .* 28 sequences
$ KmerSegmenter, map reads
1: found 6 50-windows in 8 reads
1: found 6 windows in 8 reads
$ KmerSegmenter, cluster lightly trimmed or mutated reads with original ones
2:Clone .* 2 reads
......
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g -c clones -A -3 $VIDJIL_DATA/segment_lec.fa
$ Extract 50bp windows (TRG)
1:found . 50-windows
$ Extract up to 50bp windows (TRG)
1:windows up to 50bp
$ Find the good number of windows
1: found 4 .* in 7 reads .* 7 reads
......
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 1 -r 1 $VIDJIL_DATA/clones_simul.fa
$ Junction extractions
1:found 25 50-windows in 66 reads
1:found 25 windows in 66 reads
$ No clustering
1:==> 25 clones
......
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 0 -r 1 -n 5 $VIDJIL_DATA/clones_simul.fa ; cat out/clones_simul.vidjil
$ Window extractions
2:found 25 50-windows in 66 reads
2:windows up to 50bp
2:found 25 windows in 66 reads
$ Some clustering
1:==> 2 clusters
......
......@@ -7,7 +7,7 @@ $ Same number of 'V' affectations in both reads
1: XXX
$ Only one window
1:==> found 1 ..-window
1:==> found 1 window
$ Same e-value for both reads
2: e-value:[0-9][.][0-9]+e-..
......@@ -2,7 +2,7 @@
!LOG: stanford-k14.log
$ Find the good number of windows in Stanford S22 (contiguous seed 14)
1: found 10796 50-windows in 13152 reads
1: found 10796 windows in 13152 reads
$ Do not segment any read with SEG_METHOD_ONE on homo-sapiens-cd.g
1: CD .* -> .* 0 .* 0
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -K -e 10 -r 1 -y 0 -s '#####-#####' -w 100 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -b stanford-w100 $VIDJIL_DATA/Stanford_S22.fasta ; grep 'w.*/.* seed' out/stanford-w100.affects; grep -v 'UNSEG strand' out/stanford-w100.vidjil
$ Look for windows up to 100bp
1:windows up to 100bp
$ Find the good number of "too short sequences" for windows of size 100
1: UNSEG too short w -> 0
......@@ -18,7 +21,7 @@ $ Find the good number of segmented sequences (including "too short sequences")
1: junction detected in 13152 reads .100%.
$ Find the good number of windows in Stanford S22
1: found 11835 100-windows in 13152 reads
1: found 11835 windows in 13152 reads
$ Find the correct number of clones with shifted of shortened windows
1243: "Short or shifted window"
......
......@@ -19,7 +19,7 @@ $ Find approximately the good number of sequences for e-value computation
1: approx. 131.. sequences
$ Find the good number of windows in Stanford S22
1: found 10766 50-windows in 13152 reads
1: found 10766 windows in 13152 reads
$ First clone -- find the good number of reads
2:clone-001--.*--0000008
......
......@@ -4,7 +4,8 @@ $ Segment all 8 reads, thanks to TRDD2 and TRDD3
1: junction detected in 8 reads .100..
$ Find the good number of 20-windows
1: found 6 20-windows
1:windows up to 20bp
1: found 6 windows
$ One window is shifted
1: SEG changed w -> 1 60.0
......
......@@ -2,7 +2,7 @@
$ Only one sequence is segmented, but it is too small for a window (too short w)
1: junction detected in 1 reads
1: found 0 50-windows in 0 reads
1: found 0 windows in 0 reads
$ The proper unsegmentation cause is given
1: UNSEG too short -> .* 1
......
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/ -r 1 -c clones $VIDJIL_DATA/revcomp-VdJa.fa
$ Just one window found
1:==> found 1 ..-windows
1:==> found 1 windows
$ Just one clone found
1:==> 1 clones
......
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