Commit df4fa16b authored by Mathieu Giraud's avatar Mathieu Giraud

tests: breaking change in should, put !OUTPUT_FILE before commands

parent 13f555e2
!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline -r 1 -1 -2 -K bug4225-j.fa
!OUTPUT_FILE: out/bug4225-j.affects
!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline -r 1 -1 -2 -K bug4225-j.fa
$ Find only +k and ? affects before the stretch of _ for all loci
16: seed .*(\+k| \?){28}( _)+$
!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline -r 1 -4 -K ../data/chimera-fake-half.fa
!OUTPUT_FILE: out/chimera-fake-half.affects
!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline -r 1 -4 -K ../data/chimera-fake-half.fa
$ Find only +B and ? affects on the TRB and unexpected lines
2: seed .* _(\+B| \?){48} _
!REQUIRES: python $VIDJIL_DIR/tools/check_python_version.py
!LAUNCH: $VIDJIL_DIR/$EXEC -x 100 -r 1 -z 5 -w 60 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/vidjil-to-fasta.py -o out/S22.fasta out/Stanford_S22.vidjil ;
!OUTPUT_FILE: out/S22.fasta
!LAUNCH: $VIDJIL_DIR/$EXEC -x 100 -r 1 -z 5 -w 60 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/vidjil-to-fasta.py -o out/S22.fasta out/Stanford_S22.vidjil ;
$ 5 representative sequences in the FASTA output file
5:>
!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DATA/cdr3-stopcodon.fa
!OUTPUT_FILE: out/cdr3-stopcodon.vidjil
!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DATA/cdr3-stopcodon.fa
$ Two identical junctions in JSON
2: "CATWDRKNYYKKLF"
......
......@@ -2,8 +2,8 @@
## Now a productive sequence, with a stop codon after a TRGJ gene
## We now use -J ../TRGJ.fa, see #3147
!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -3 -V $VIDJIL_DIR/germline/homo-sapiens/TRGV.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRGJ.fa $VIDJIL_DATA/productive_stop_after_J.fa
!OUTPUT_FILE: out/productive_stop_after_J.vidjil
!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -3 -V $VIDJIL_DIR/germline/homo-sapiens/TRGV.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRGJ.fa $VIDJIL_DATA/productive_stop_after_J.fa
$ Clone name
1: "TRGV9.01 0/CA/0 TRGJP.01"
......
!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/productive_stop_before_V.fa
!OUTPUT_FILE: out/productive_stop_before_V.vidjil
!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/productive_stop_before_V.fa
$ first clone name
1: "IGHV1-69.06 2/AACCCCCAACAAAGC/4 IGHD3-3.01 9/CCCATAAGTACCGT/1 IGHJ6.02"
......
......@@ -18,8 +18,8 @@ $ There is a warning on multiple candidate assignations
$ The warning is also found on stdout
1:\[warning\] \(W69\) Several genes with equal probability
!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -g $VIDJIL_DIR/germline/homo-sapiens.g:TRB $VIDJIL_DATA/trb-only-VJ.fa
!OUTPUT_FILE: out/trb-only-VJ.vidjil
!LAUNCH: $VIDJIL_DIR/$EXEC -c designations -g $VIDJIL_DIR/germline/homo-sapiens.g:TRB $VIDJIL_DATA/trb-only-VJ.fa
$ With -c designation, the recombination is properly designated, without any D
1:"name": "TRBJ2-3.01"
......
!LAUNCH: $VIDJIL_DIR/$EXEC -x 100 -r 1 -y 1 -z 0 -w 10 --out-clone-files -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta 2>&1
!OUTPUT_FILE: out/seq/clone.fa-1
### !EXIT_CODE: 1
!LAUNCH: $VIDJIL_DIR/$EXEC -x 100 -r 1 -y 1 -z 0 -w 10 --out-clone-files -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta 2>&1
$ We should find a window
1:[ACGT]{10}
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