Commit 159cebc0 authored by Mathieu Giraud's avatar Mathieu Giraud

tests: re-update some tests, filter for complete recombinations

These tests were previously launched without '-i', on purpose.
parent 58df8009
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 5 -K -g $VIDJIL_DIR/germline $VIDJIL_DIR/data/multi-short.fa ; head -n 17 out/multi-short.affects
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 5 -K -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL $VIDJIL_DIR/data/multi-short.fa ; head -n 17 out/multi-short.affects
# Testing .affects output (-K)
$ First sequence (TRA), display sequence
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DIR/data/multi-short.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRG,TRD,IGH,IGK,IGL $VIDJIL_DIR/data/multi-short.fa
$ Segment all the seven reads
1:junction detected in 7 reads
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline $VIDJIL_DIR/data/trd-dd2-dd3.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline/homo-sapiens.g:TRD $VIDJIL_DIR/data/trd-dd2-dd3.fa
$ Segment only 2 reads, because there is no -i
$ Segment only 2 reads, because we do not look for incomplete recombinations
1:junction detected in 2 reads
$ TRDV3*01-TRDD3*01 reported as "UNSEG only V/5'"
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline -u $VIDJIL_DIR/data/segmentation-2.fa ; cat ./out///segmentation-2.UNSEG_ambiguous.fa ; cat ./out///segmentation-2.UNSEG_too_few_V_J.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -u $VIDJIL_DIR/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
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline -uuu $VIDJIL_DIR/data/segmentation-2.fa ; cat out/segmentation-2.unsegmented.vdj.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRA,TRB,TRD,TRG,IGH,IGK,IGL -uuu $VIDJIL_DIR/data/segmentation-2.fa ; cat out/segmentation-2.unsegmented.vdj.fa
$ Only one sequence is segmented, but it is too small for a window (too short w)
1: junction detected in 1 reads
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