Commit dac8244f authored by Mathieu Giraud's avatar Mathieu Giraud

tests: merging some related test files

parent 9d391a47
!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 windows in 66 reads
$ No clustering
1:==> 25 clones
$ Clone 1 output
1:Clone #001 .* 29 reads
$ Clone 2 output
1:Clone #002 .* 14 reads
$ Clone 3 output (sequencing error)
1:Clone #003 .* 1 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 windows in 66 reads
$ No clustering
1:==> 25 clones
$ Clone 1 output
1:Clone #001 .* 29 reads
$ Clone 2 output
1:Clone #002 .* 14 reads
$ Clone 3 output (sequencing error)
1:Clone #003 .* 1 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 0 -r 1 --cluster-epsilon 5 $VIDJIL_DATA/clones_simul.fa ; cat out/clones_simul.vidjil
$ Window extractions
......
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -y 0 -x 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
$ Analyze the good number of sequences in Stanford S22
1: found .* of 100 reads
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -y 0 -x 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
$ Analyze the good number of sequences in Stanford S22
1: found .* of 100 reads
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -y 0 -X 100 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta
$ Skip the good number of reads
......
!NO_LAUNCHER:
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -H
$ License
1:vidjil-algo is free software
$ Check default costs
1:analysis.* "4, -6, -10, -1, -10"
1:clustering .* "1, -4, -4, 0, 0"
$ Show seeds
1: 9c.#########
1: 13s.#######-######
$ Display advanced options
: , experimental options
: custom Cost
$ Correct number of options
54:^..-
......@@ -16,3 +16,25 @@ $ Do not display advanced options
$ Correct number of regular options
24:^..-
!NO_LAUNCHER:
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -H
$ License
1:vidjil-algo is free software
$ Check default costs
1:analysis.* "4, -6, -10, -1, -10"
1:clustering .* "1, -4, -4, 0, 0"
$ Show seeds
1: 9c.#########
1: 13s.#######-######
$ Display advanced options
: , experimental options
: custom Cost
$ Correct number of options
54:^..-
......@@ -29,3 +29,31 @@ $ Compute the diversity. All windows have only one read, full diversity.
1: E = 1.000
1: Ds = 1.000
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DATA/multi-short.fa
$ Segment all the seven reads
1:junction detected in 7 reads
$ Segment one read on TRA
1:TRA .* -> .* 1
$ Segment one read on TRB
1:TRB .* -> .* 1
$ Segment one read on TRG
1:TRG .* -> .* 1
$ Segment one read on TRD
1:TRD .* -> .* 1
$ Segment one read on IGH
1:IGH .* -> .* 1
$ Segment one read on IGK
1:IGK .* -> .* 1
$ Segment one read on IGL
1:IGL .* -> .* 1
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DATA/multi-short.fa
$ Segment all the seven reads
1:junction detected in 7 reads
$ Segment one read on TRA
1:TRA .* -> .* 1
$ Segment one read on TRB
1:TRB .* -> .* 1
$ Segment one read on TRG
1:TRG .* -> .* 1
$ Segment one read on TRD
1:TRD .* -> .* 1
$ Segment one read on IGH
1:IGH .* -> .* 1
$ Segment one read on IGK
1:IGK .* -> .* 1
$ Segment one read on IGL
1:IGL .* -> .* 1
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -u $VIDJIL_DATA/segmentation-2.fa ; cat ./out///segmentation-2.UNSEG_ambiguous.fa ; cat ./out///segmentation-2.UNSEG_too_few_V_J.fa
$ The proper unsegmentation cause is given
1: UNSEG too short -> .* 1
1: UNSEG strand -> .* 1
1: UNSEG too few V/J -> .* 3
1: UNSEG only V/5' -> .* 1
1: UNSEG only J/3' -> .* 1
1: UNSEG ambiguous -> .* 1
1: UNSEG too short w -> .* 1
$ The UNSEG ambiguous read is reported in the .UNSEG_ambiguous.fa file (-u)
1: >ambiguous .* UNSEG ambiguous
$ The UNSEG too few V/J reads are *not* reported in any .fa file (-u)
0: >too_few_vj-..* UNSEG too few V/J
......@@ -23,3 +23,22 @@ $ The proper unsegmentation cause is given in the .unsegmented.vdj.fa file (-uuu
1: >too_short_w .* UNSEG too short w
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -u $VIDJIL_DATA/segmentation-2.fa ; cat ./out///segmentation-2.UNSEG_ambiguous.fa ; cat ./out///segmentation-2.UNSEG_too_few_V_J.fa
$ The proper unsegmentation cause is given
1: UNSEG too short -> .* 1
1: UNSEG strand -> .* 1
1: UNSEG too few V/J -> .* 3
1: UNSEG only V/5' -> .* 1
1: UNSEG only J/3' -> .* 1
1: UNSEG ambiguous -> .* 1
1: UNSEG too short w -> .* 1
$ The UNSEG ambiguous read is reported in the .UNSEG_ambiguous.fa file (-u)
1: >ambiguous .* UNSEG ambiguous
$ The UNSEG too few V/J reads are *not* reported in any .fa file (-u)
0: >too_few_vj-..* UNSEG too few V/J
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