Commit e8452843 authored by Mathieu Giraud's avatar Mathieu Giraud

tests: update tests, 'segmented' -> 'junction detected in'

parent bea4f443
!LAUNCH: ../../vidjil -g ../../germline -2 -i ../../data/chimera-fake.fa
$ Segment all reads
1:segmented 3 reads
1:junction detected in 3 reads
$ Segment all reads on 'xxx'
1:xxx .* -> .* 3
......
!LAUNCH: ../../vidjil -g ../../germline -i ../../data/chimera-fake.fa
$ Do not segment on any germline, even incomplete
1:segmented 0 reads
1:junction detected in 0 reads
!LAUNCH: ../../vidjil -g ../../germline ../../data/multi-complete.fa
$ Segment all the seven reads
1:segmented 7 reads
1:junction detected in 7 reads
$ Segment one read on TRA
1:TRA .* -> .* 1
......
!LAUNCH: ../../vidjil -g ../../germline -i ../../data/multi-complete.fa
$ Segment all the seven reads
1:segmented 7 reads
1:junction detected in 7 reads
$ Segment one read on TRA
1:TRA .* -> .* 1
......
!LAUNCH: ../../vidjil -g ../../germline -i ../../data/multi-short.fa
$ Segment all the seven reads
1:segmented 7 reads
1:junction detected in 7 reads
$ Segment one read on TRA
1:TRA .* -> .* 1
......
!LAUNCH: ../../vidjil -g ../../germline ../../data/multi-short.fa
$ Segment all the seven reads
1:segmented 7 reads
1:junction detected in 7 reads
$ Segment one read on TRA
1:TRA .* -> .* 1
......
!LAUNCH: $LAUNCHER ../../vidjil -k 9 -G ../../germline/IGH -K -c clones ../../data/revcomp.fa ; grep '#IGH' out/revcomp.affects | sed 's/[^X]//g' | awk '{ print length }'
$ Segments both reads, normal and revers
1:segmented 2 reads
$ Segments both reads, normal and reverse
1:junction detected in 2 reads
$ Same number of 'V' affectations in both reads
2:143
......
......@@ -2,10 +2,10 @@
!LOG: stanford-w100.log
$ Find the good number of "too short sequences" for windows of size 100
1: SEG, no window -> 2217
1: UNSEG too short w -> 2217
$ Find the good number of segmented sequences (including "too short sequences")
1: segmented 13148 reads .100%.
1: junction detected in 13148 reads .100%.
$ Find the good number of windows of size 100 in Stanford S22
1: found 9800 100-windows in 10931 segments
!LAUNCH: ../../vidjil -A -g ../../germline ../../data/trd-dd2-dd3.fa
$ Segment only 2 reads, because there is no -i
1:segmented 2 reads .40..
1:junction detected in 2 reads .40..
$ TRDV3*01-TRDD3*01 reported as "UNSEG too few J"
1:UNSEG too few J .*-> .* 1 .* 63
......
!LAUNCH: ../../vidjil -e 10 -A -i -g ../../germline ../../data/trd-dd2-dd3.fa
$ Segment all 5 reads, thanks to -i
1:segmented 5 reads .100..
1:junction detected in 5 reads .100..
!LAUNCH: ../../vidjil -e 10 -k 8 -w 20 -V ../../germline/TRDV.fa -V ../../germline/TRDD2-01.fa -J ../../germline/TRDD3-01.fa -J ../../germline/TRDJ.fa ../../data/trd-dd2-dd3.fa
$ Segment all 5 reads, thanks to TRDD2 and TRDD3
1: segmented 5 reads .100..
1: junction detected in 5 reads .100..
$ Find the good number of 20-windows
1: found 4 20-windows
......
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