Commit 6ef7daff authored by Mathieu Giraud's avatar Mathieu Giraud

should-get-tests/: update

parent ad996aa4
......@@ -12,10 +12,10 @@ $ Find the good statistics on TRG
$ Find the good length statistics
1: SEG -> .* 84.0
$ Four segmented on forward
$ Four detected on forward
1:SEG_\+ -> 4
$ Three segmented on reverse (Junc#01 doesn't have its rc)
$ Three detected on reverse (Junc#01 doesn't have its rc)
1:SEG_- -> 3
$ No too short window
......
!LAUNCH: $VIDJIL_DIR/$EXEC -r 1 -k 4 -w 20 -z 0 -c clones -V $VIDJIL_DATA/toy_V.fa -J $VIDJIL_DATA/toy_J.fa $VIDJIL_DATA/ambiguous_representative.fa
$ Short reads properly segmented
$ Short reads properly detected
1:SEG_+.* -> .* 4
$ Window found
......
!LAUNCH: $VIDJIL_DIR/$EXEC --header-sep FA -k 16 -z 0 -w 60 -r 5 -o out2 -uuu -U -v -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa $VIDJIL_DATA/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa ; grep UNSEG out2/Stanford_S22.unsegmented.vdj.fa
!LAUNCH: $VIDJIL_DIR/$EXEC --header-sep FA -k 16 -z 0 -w 60 -r 5 -o out2 -uuu -U -v -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa $VIDJIL_DATA/Stanford_S22.fasta ; tail out2/Stanford_S22.detected.vdj.fa ; grep UNSEG out2/Stanford_S22.undetected.vdj.fa
# Testing uncommon and debug options
$ verbose (-v)
2:auditioned sequences
$ segmented.fa (-U)
$ detected.fa (-U)
2:>lcl.FLN1.* VJ .* seed custom SEG_[+]
$ unsegmented.fa (-u)
$ undetected.fa (-u)
3:>lcl.FLN1.* UNSEG
$ fasta header stops before FA
......
......@@ -11,5 +11,5 @@ $ With default seeds the J is not found as it is too short
$ With different seeds we don't have the same seed for the IGHV and IGHJ
1: IGH .* ######-###### .* ########
$ The sequence is segmented
$ The sequence is detected
1: SEG -> 1
......@@ -9,7 +9,7 @@ $ From homo-sapiens.g
$ Number of reads
1:"total": \[13153\]
$ Number of segmented reads
$ Number of detected reads
1:"segmented": \[13153\]
$ Most abundant window
......
......@@ -3,13 +3,13 @@
!LAUNCH: diff out/Stanford_S22{,.rc}.vidjil | grep GGG && diff vidjil_s22.log vidjil_s22_rc.log
!EXIT_CODE: 1
$ Same number segmented
0:==> segmented
$ Same number detected
0:==> detected
$ Same number of windows found
0:==> found
$ Same number unsegmented
$ Same number undetected
0:UNSEG.*->
$ Keep the same number of windows
......
......@@ -6,7 +6,7 @@ $ Just one window found
$ Just one clone found
1:==> 1 clones
$ Two reads segmented on TRA+D
$ Two reads detected on TRA+D
1:TRA.D -> 2
$ One clone for the two reads, Vd1/Ja29
......
......@@ -3,6 +3,6 @@
$ Segment 6 reads, thanks to -i
1:junction detected in 6 reads
$ 4 reads are segmented on TRD+ (with -w 10, otherwise the reads are too short)
$ 4 reads are detected on TRD+ (with -w 10, otherwise the reads are too short)
1: TRD[+] .*->.* 4
!LAUNCH: $VIDJIL_DIR/$EXEC -y 0 --trim 1 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -x 100 $VIDJIL_DATA/Stanford_S22.fasta
$ No read segmented as we have no germline because of the --trim
$ No read detected as we have no germline because of the --trim
1: UNSEG too few V/J -> 100
!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -uuu $VIDJIL_DATA/segmentation-2.fa ; cat out/segmentation-2.unsegmented.vdj.fa
!LAUNCH: $VIDJIL_DIR/$EXEC -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -uuu $VIDJIL_DATA/segmentation-2.fa ; cat out/segmentation-2.undetected.vdj.fa
$ Only one sequence is segmented, but it is too small for a window (too short w)
$ Only one sequence is detected, but it is too small for a window (too short w)
1: junction detected in 1 reads
1: found 0 windows in 0 reads
......@@ -13,7 +13,7 @@ $ The proper unsegmentation cause is given
1: UNSEG ambiguous -> .* 1
1: UNSEG too short w -> .* 1
$ The proper unsegmentation cause is given in the .unsegmented.vdj.fa file (-uuu)
$ The proper cause is given in the .undetected.vdj.fa file (-uuu)
1: >too_short .* UNSEG too short
1: >strand .* UNSEG strand
3: >too_few_vj-..* UNSEG too few V/J
......
......@@ -17,7 +17,7 @@ $ Some changed windows are lighlty shortened
63: w95/-10
29: w90/-10
$ Find the good number of segmented sequences (including "too short sequences")
$ Find the good number of detected sequences (including "too short sequences")
1: junction detected in 13153 reads .100%.
$ Find the good number of windows in Stanford S22
......
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