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Commit 101e2d3c authored by Mathieu Giraud's avatar Mathieu Giraud

tests: update and add tests, species

parent 426a2da1
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline -g $VIDJIL_DIR/germline/isotypes.data -i $VIDJIL_DIR/data/isotypes.fa
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline -g $VIDJIL_DIR/germline/isotypes.germlines -i $VIDJIL_DIR/data/isotypes.fa
$ Report the correct species
1: Homo sapiens .9606.
$ Segment the three reads
1: junction detected in 3 reads
......
!REQUIRES: python $VIDJIL_DIR/tools/check_python_version.py
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -3 -z 1 -G $VIDJIL_DIR/germline/IGH -w 60 -r 5 -e 10 -b data $VIDJIL_DIR/data/Stanford_S22.fasta > /dev/null ; cat out/data.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
$ Custom germlines
1:"species": "custom germlines"
$ Number of reads
e1:"total": [13153]
......
!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -z 0 -V $VIDJIL_DIR/germline/IGHV.fa -D $VIDJIL_DIR/germline/IGHD.fa -J $VIDJIL_DIR/germline/IGHJ.fa -s \\\\#\\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\#\\\\# $VIDJIL_DIR/data/Stanford_S22.fasta
$ Germlines are custom
1: custom germlines
$ Parses IGHV.fa germline
1: 102221 bp in 350 sequences
......
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