Commit d4725752 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

tests: update

parent 2a098ac3
!LAUNCH: $VIDJIL_DIR/$EXEC -c segment -g ../../../germline/homo-sapiens.g:IGH bug20131218.fa
!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -g ../../../germline/homo-sapiens.g:IGH bug20131218.fa
# The number of deletions in the D is larger than the D length itself.
$ Bug with the number of deletions in the D.
!LAUNCH: $VIDJIL_DIR/$EXEC -E 1 -d -g $VIDJIL_DIR/germline -c segment bug2249.fa
!LAUNCH: $VIDJIL_DIR/$EXEC -E 1 -d -g $VIDJIL_DIR/germline -c designations bug2249.fa
$ Should not have a TRDD2 (length 9) with 8 deletions (first seq)
f0:7 TRDD2.01 1
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c segment -g $VIDJIL_DIR/germline/homo-sapiens.g $VIDJIL_DATA/3344-bad-filtering.fa
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -g $VIDJIL_DIR/germline/homo-sapiens.g $VIDJIL_DATA/3344-bad-filtering.fa
$ Check that proper filtering is used
1: IGHV4-31.02
!REQUIRES: python $VIDJIL_DIR/tools/
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --alternative-genes 3 -c segment -x 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta > /dev/null ; cat out/Stanford_S22.vidjil | python $VIDJIL_DIR/tools/ -1
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --alternative-genes 3 -c designations -x 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta > /dev/null ; cat out/Stanford_S22.vidjil | python $VIDJIL_DIR/tools/ -1
$ Presence of alternative:
1: "3alt"
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c segment -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DATA/cdr3-stopcodon.fa
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DATA/cdr3-stopcodon.fa
!OUTPUT_FILE: out/cdr3-stopcodon.vidjil
$ Two identical junctions in JSON
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c segment -3 -E 1.0 -g $VIDJIL_DIR/germline ../should-vdj-tests/Demo-X5.should-vdj.fa
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -3 -E 1.0 -g $VIDJIL_DIR/germline ../should-vdj-tests/Demo-X5.should-vdj.fa
$ Detects a CDR3 on regular V(D)J recombinations
1: IGH SEG.* [{].*[}]
......@@ -12,7 +12,7 @@
# '-c windows'
0:Extracting windows
# '-c segment', one time
# '-c designations', one time
1:Segmenting V.D.J
# '-c germlines'
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -3 -c segment -g $VIDJIL_DIR/germline/mus-musculus.g $VIDJIL_DATA/example_mouse.fa
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -3 -c designations -g $VIDJIL_DIR/germline/mus-musculus.g $VIDJIL_DATA/example_mouse.fa
$ Segment sequence on IGK
!LAUNCH: $VIDJIL_DIR/$EXEC -c segment $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH,IGK,IGL $VIDJIL_DATA/multi-complete.fa ; cat out/multi-complete.vidjil | python $VIDJIL_DIR/tools/ -1
!LAUNCH: $VIDJIL_DIR/$EXEC -c designations $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH,IGK,IGL $VIDJIL_DATA/multi-complete.fa ; cat out/multi-complete.vidjil | python $VIDJIL_DIR/tools/ -1
$ Segment the Ig recombinations
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -g $VIDJIL_DIR/germline $VIDJIL_DATA/multi-tiny.fa
$ Do not segment any of the seven reads
# The sequences are on TRG, no CDR3 should be found with IGH
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c segment -3 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa ../should-vdj-tests/cdr3-indels.should-vdj.fa; cat out/cdr3-indels.should-vdj.vidjil
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -3 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa ../should-vdj-tests/cdr3-indels.should-vdj.fa; cat out/cdr3-indels.should-vdj.vidjil
$ No CDR3 should be found
0:TRGV.* [{].*[}]
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -3 -g $VIDJIL_DIR/germline $VIDJIL_DATA/no-cdr3.fa
$ No CDR3 should be found
0:seq1.* IGH SEG.* [{].*[}]
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c segment -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -A $VIDJIL_DATA/overlap-d-j.fa | grep -v out | tail -4 | tr -d '\n' | wc -c
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -A $VIDJIL_DATA/overlap-d-j.fa | grep -v out | tail -4 | tr -d '\n' | wc -c
$ Exported sequence has all the bases
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -c segment $VIDJIL_DATA/segment_S22.fa | grep '^>' ; cat out/segment_S22.vidjil | python $VIDJIL_DIR/tools/ -1
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -c designations $VIDJIL_DATA/segment_S22.fa | grep '^>' ; cat out/segment_S22.vidjil | python $VIDJIL_DIR/tools/ -1
$ First sequence Stanford
# 164 175 195 203
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -v -g $VIDJIL_DIR/germline -c segment $VIDJIL_DATA/segment_simul.fa | grep '^[>#]'
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -v -g $VIDJIL_DIR/germline -c designations $VIDJIL_DATA/segment_simul.fa | grep '^[>#]'
$ First sequence, easy segmentation (no error, few deletions at the windows, small N)
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c segment -x 2 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -x 2 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
$ Segments the good number of sequences in Stanford S22
2: >lcl
......@@ -14,7 +14,7 @@ cd $VIDJIL_DIR
# '-c windows'
1:Extracting windows
# '-c segment'
# '-c designations'
1:Segmenting V.D.J
# '-c germlines'
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c segment -g $VIDJIL_DIR/germline/homo-sapiens.g $VIDJIL_DATA/what-V.fa
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -c designations -g $VIDJIL_DIR/germline/homo-sapiens.g $VIDJIL_DATA/what-V.fa
$ V1*01 is recognized three times
3: VJ .* TRGV1.01
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