tests: update tests

beaed38d · Mathieu Giraud · bb3a5cfc · beaed38d · beaed38d · beaed38d
Commit beaed38d authored Jan 31, 2017 by Mathieu Giraud
37 changed files
--- a/algo/tests/should-get-tests/ambiguous_representative2.should-get
+++ b/algo/tests/should-get-tests/ambiguous_representative2.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -c clones -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/test_representatives.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -c clones -G $VIDJIL_DIR/germline/homo-sapiens/IGH $VIDJIL_DIR/data/test_representatives.fa

 $ Three clones should be found
 1:3 clones

--- a/algo/tests/should-get-tests/clones_lec.should-get
+++ b/algo/tests/should-get-tests/clones_lec.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -G $VIDJIL_DIR/germline/TRG -c clones -A -3 $VIDJIL_DIR/data/segment_lec.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -G $VIDJIL_DIR/germline/homo-sapiens/TRG -c clones -A -3 $VIDJIL_DIR/data/segment_lec.fa

 $ Extract 50bp windows (TRG)
 1:found . 50-windows

--- a/algo/tests/should-get-tests/clones_simul.should-get
+++ b/algo/tests/should-get-tests/clones_simul.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -G $VIDJIL_DIR/germline/IGH -y 3 -z 1 -r 1 $VIDJIL_DIR/data/clones_simul.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -G $VIDJIL_DIR/germline/homo-sapiens/IGH -y 3 -z 1 -r 1 $VIDJIL_DIR/data/clones_simul.fa

 $ Junction extractions
 1:found 25 50-windows in 66 reads

--- a/algo/tests/should-get-tests/clones_simul_cluster.should-get
+++ b/algo/tests/should-get-tests/clones_simul_cluster.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -G $VIDJIL_DIR/germline/IGH -y 3 -z 0 -r 1 -n 5 $VIDJIL_DIR/data/clones_simul.fa ; cat out/clones_simul.vidjil
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -G $VIDJIL_DIR/germline/homo-sapiens/IGH -y 3 -z 0 -r 1 -n 5 $VIDJIL_DIR/data/clones_simul.fa ; cat out/clones_simul.vidjil

 $ Window extractions
 2:found 25 50-windows in 66 reads

--- a/algo/tests/should-get-tests/common-V-D.should-get
+++ b/algo/tests/should-get-tests/common-V-D.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -KA -z 0 -s \\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\# -G $VIDJIL_DIR/germline/IGH  $VIDJIL_DIR/data/common-V-D.fa  ; cat out/common-V-D.affects
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -KA -z 0 -s \\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\# -G $VIDJIL_DIR/germline/homo-sapiens/IGH  $VIDJIL_DIR/data/common-V-D.fa  ; cat out/common-V-D.affects

 $ Segments the sequence
 1: SEG  .* -> .* 1 

--- a/algo/tests/should-get-tests/gzip.should-get
+++ b/algo/tests/should-get-tests/gzip.should-get
 !NO_LAUNCHER:
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/clones_simul.fa > out-fa ;  $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -G $VIDJIL_DIR/germline/IGH -b clones_simul $VIDJIL_DIR/data/clones_simul.fa.gz > out-fa-gz ; diff -s -I '\#' -I 'index' -I 'data/clones_simul' out-fa out-fa-gz ; echo 'Diff: '\\$?; wc -l out-fa-gz
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -G $VIDJIL_DIR/germline/homo-sapiens/IGH $VIDJIL_DIR/data/clones_simul.fa > out-fa ;  $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -G $VIDJIL_DIR/germline/homo-sapiens/IGH -b clones_simul $VIDJIL_DIR/data/clones_simul.fa.gz > out-fa-gz ; diff -s -I '\#' -I 'index' -I 'data/clones_simul' out-fa out-fa-gz ; echo 'Diff: '\\$?; wc -l out-fa-gz

 $ Identical output
 1:Diff: 0

--- a/algo/tests/should-get-tests/large-N.should-get
+++ b/algo/tests/should-get-tests/large-N.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -G $VIDJIL_DIR/germline/IGH -r 1 $VIDJIL_DIR/data/large_N.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -G $VIDJIL_DIR/germline/homo-sapiens/IGH -r 1 $VIDJIL_DIR/data/large_N.fa

 $ Find a huge insertion in the segmentation
 1:>clone-001.*/[ACGT]{100}
--- a/algo/tests/should-get-tests/large-r.should-get
+++ b/algo/tests/should-get-tests/large-r.should-get
-!LAUNCH: (for i in {1..100000}; do echo '>read' ; echo ccgtgtattactgtgcgagagagctgaatacttccagcactg ; done ;) > same-igh-100k.fa ; $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -G $VIDJIL_DIR/germline/IGH -r 5000  -w 15  same-igh-100k.fa; rm -f same-igh-100k.fa
+!LAUNCH: (for i in {1..100000}; do echo '>read' ; echo ccgtgtattactgtgcgagagagctgaatacttccagcactg ; done ;) > same-igh-100k.fa ; $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -G $VIDJIL_DIR/germline/homo-sapiens/IGH -r 5000  -w 15  same-igh-100k.fa; rm -f same-igh-100k.fa

 $ Find a unique clone with all reads
 1:>clone-001--IGH--0100000--100.--window

--- a/algo/tests/should-get-tests/no-cdr3-json.should_get
+++ b/algo/tests/should-get-tests/no-cdr3-json.should_get
 # The sequences are on TRG, no CDR3 should be found with IGH

-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -3 -V $VIDJIL_DIR/germline/IGHV.fa -D $VIDJIL_DIR/germline/IGHD.fa -J $VIDJIL_DIR/germline/IGHJ.fa $VIDJIL_DIR/algo/tests/should-vdj-tests/cdr3-indels.should-vdj.fa; cat out/cdr3-indels.should-vdj.vidjil
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -3 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa $VIDJIL_DIR/algo/tests/should-vdj-tests/cdr3-indels.should-vdj.fa; cat out/cdr3-indels.should-vdj.vidjil

 $ No CDR3 should be found
 0:TRGV.* [{].*[}]

--- a/algo/tests/should-get-tests/overlap-stdout.should-get
+++ b/algo/tests/should-get-tests/overlap-stdout.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -G $VIDJIL_DIR/germline/IGH -A $VIDJIL_DIR/data/overlap-d-j.fa | grep -v web | tail -4 | tr -d '\\\\n' | wc -c
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -G $VIDJIL_DIR/germline/homo-sapiens/IGH -A $VIDJIL_DIR/data/overlap-d-j.fa | grep -v web | tail -4 | tr -d '\\\\n' | wc -c

 $ Exported sequence has all the bases
 1:116

--- a/algo/tests/should-get-tests/quality-json.should-get
+++ b/algo/tests/should-get-tests/quality-json.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c clones -A -G $VIDJIL_DIR/germline/TRG -A  $VIDJIL_DIR/data/segment_lec.fq > /dev/null ; cat out/segment_lec.vidjil
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c clones -A -G $VIDJIL_DIR/germline/homo-sapiens/TRG -A  $VIDJIL_DIR/data/segment_lec.fq > /dev/null ; cat out/segment_lec.vidjil

 $ Window
 1:"id": "GGGGTCTATTACTGTGCCACCTGGGCCTTATTATAAGAAACTCTTTGGCA"

--- a/algo/tests/should-get-tests/representative-N.should-get
+++ b/algo/tests/should-get-tests/representative-N.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -G $VIDJIL_DIR/germline/TRG ../should-vdj-tests/ext-nucleotides-N.should-vdj.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -G $VIDJIL_DIR/germline/homo-sapiens/TRG ../should-vdj-tests/ext-nucleotides-N.should-vdj.fa

 $ Segments on TRG
 1: TRG .* -> .* 1

--- a/algo/tests/should-get-tests/revcomp.should-get
+++ b/algo/tests/should-get-tests/revcomp.should-get
-!LAUNCH: $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 9 -G $VIDJIL_DIR/germline/IGH  -K -c clones $VIDJIL_DIR/data/revcomp.fa ; grep 'X.X.X' out/revcomp.affects | sed 's/[^X]//g'  | sort -u ; grep '#>'  out/revcomp.affects | sed 's/.*SEG.../e-value:/' | cut -f 1 -d' '
+!LAUNCH: $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 9 -G $VIDJIL_DIR/germline/homo-sapiens/IGH  -K -c clones $VIDJIL_DIR/data/revcomp.fa ; grep 'X.X.X' out/revcomp.affects | sed 's/[^X]//g'  | sort -u ; grep '#>'  out/revcomp.affects | sed 's/.*SEG.../e-value:/' | cut -f 1 -d' '

 $ Segments both reads, normal and reverse
 1:junction detected in 2 reads

--- a/algo/tests/should-get-tests/segment_S22.should-get
+++ b/algo/tests/should-get-tests/segment_S22.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -G $VIDJIL_DIR/germline/IGH -c segment $VIDJIL_DIR/data/segment_S22.fa | grep '^>' ; cat out/segment_S22.vidjil | python $VIDJIL_DIR/tools/format_json.py -1
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -G $VIDJIL_DIR/germline/homo-sapiens/IGH -c segment $VIDJIL_DIR/data/segment_S22.fa | grep '^>' ; cat out/segment_S22.vidjil | python $VIDJIL_DIR/tools/format_json.py -1

 $ First sequence Stanford
 #                            164        175                 195     203

--- a/algo/tests/should-get-tests/segmentation-D-read-number.should-get
+++ b/algo/tests/should-get-tests/segmentation-D-read-number.should-get
@@ -11,14 +11,14 @@
  echo '>seq'\\$i; echo ggctggagtgggtttcatacattagtagtaatagtggtgccatatactacgcagactctgtgaagggccgattcaccatctccagaaacaatgccaaggactcactgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgcgagagcgatcccccggtattactatgatact\\$(cat /dev/urandom | LC_CTYPE=C tr -dc 'acgt' | head -c 4)ggcccaaacgactactggggccagggaaccctggtcaccgtctcctcag; \
 done;\
 cat $VIDJIL_DIR/data/buggy-D.fa) > \\$file1; \
-$VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -G $VIDJIL_DIR/germline/IGH \\$file1; \
+$VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -G $VIDJIL_DIR/germline/homo-sapiens/IGH \\$file1; \
 file2=$(mktemp); \
 (for i in {1..5}; do \
  echo '>seq'\\$i; echo ggctggagtgggtttcatacattagtagtaatagtggtgccatatactacgcagactctgtgaagggccgattcaccatctccagaaacaatgccaaggactcactgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgcgagagcgatcccccggtattactatgatact\\$(cat /dev/urandom | LC_CTYPE=C tr -dc 'acgt' | head -c 4)ggcccaaacgactactggggccagggaaccctggtcaccgtctcctcag; \
 done;\
 cat $VIDJIL_DIR/data/buggy-D.fa) > \\$file2; \
-$VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -G $VIDJIL_DIR/germline/IGH \\$file2;\
-$VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/buggy-D.fa)
+$VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -G $VIDJIL_DIR/germline/homo-sapiens/IGH \\$file2;\
+$VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -d -r 1 -w 60 -z 100 -G $VIDJIL_DIR/germline/homo-sapiens/IGH $VIDJIL_DIR/data/buggy-D.fa)

 $ Three times the same window
 3: TGTGCGGGATCTTCGTCCTCTTATCATAATAATGGTTTTTTGGCGGGGGAGTCATGGGGC

--- a/algo/tests/should-get-tests/sequences_of_interest.should_get
+++ b/algo/tests/should-get-tests/sequences_of_interest.should_get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -G $VIDJIL_DIR/germline/IGH -W ACCGGTATTACT -W CAGCTGCTCCCC -W TGGGCCACTC -W ATCAACGCTGGCAATGGTAACACTAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATACGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTCTGTATTACTGTGCGAGAGTGCGCAGCAGCTGGTCTGATGCTTTTGATTATCTGG $VIDJIL_DIR/data/clones_simul.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -G $VIDJIL_DIR/germline/homo-sapiens/IGH -W ACCGGTATTACT -W CAGCTGCTCCCC -W TGGGCCACTC -W ATCAACGCTGGCAATGGTAACACTAAATATTCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGGACACATACGCGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAAGACACGGCTCTGTATTACTGTGCGAGAGTGCGCAGCAGCTGGTCTGATGCTTTTGATTATCTGG $VIDJIL_DIR/data/clones_simul.fa

 $ ACCGGTATTACT is found (in window and representative and in the command line)
 3:ACCGGTATTACT

--- a/algo/tests/should-get-tests/stanford-X100-sampled.should-get
+++ b/algo/tests/should-get-tests/stanford-X100-sampled.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -X 100 -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -X 100 -G $VIDJIL_DIR/germline/homo-sapiens/IGH $VIDJIL_DIR/data/Stanford_S22.fasta

 $ Skip the good number of reads
 1:Processing every 131th read

--- a/algo/tests/should-get-tests/stanford-debug.should-get
+++ b/algo/tests/should-get-tests/stanford-debug.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -\# FA -k 16 -z 0 -w 60 -r 5 -o out2 -uuu -U -v -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa ; grep UNSEG out2/Stanford_S22.unsegmented.vdj.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -\# FA -k 16 -z 0 -w 60 -r 5 -o out2 -uuu -U -v -G $VIDJIL_DIR/germline/homo-sapiens/IGH $VIDJIL_DIR/data/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa ; grep UNSEG out2/Stanford_S22.unsegmented.vdj.fa
 # Testing uncommon and debug options 

 $ verbose (-v)

--- a/algo/tests/should-get-tests/stanford-detailed.should-get
+++ b/algo/tests/should-get-tests/stanford-detailed.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 2 -r 5 -a -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/Stanford_S22.fasta ; cat out/seq/clone.fa-2
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 2 -r 5 -a -G $VIDJIL_DIR/germline/homo-sapiens/IGH $VIDJIL_DIR/data/Stanford_S22.fasta ; cat out/seq/clone.fa-2
 # Testing detailed clone output (-a)

 $ Detailed clone output (out/seq/clone.fa-2), germline

--- a/algo/tests/should-get-tests/stanford-fuse.should-get
+++ b/algo/tests/should-get-tests/stanford-fuse.should-get
 !REQUIRES: python $VIDJIL_DIR/tools/check_python_version.py
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 0 -w 60 -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/fuse.py out/Stanford_S22.vidjil out/Stanford_S22.vidjil -o out/fused.data ; cat out/fused.data | python $VIDJIL_DIR/tools/format_json.py -1
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 0 -w 60 -G $VIDJIL_DIR/germline/homo-sapiens/IGH $VIDJIL_DIR/data/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/fuse.py out/Stanford_S22.vidjil out/Stanford_S22.vidjil -o out/fused.data ; cat out/fused.data | python $VIDJIL_DIR/tools/format_json.py -1

 $ Points list
 e1:"original_names": ["../../..//data/Stanford_S22.fasta", "../../..//data/Stanford_S22.fasta"]

--- a/algo/tests/should-get-tests/stanford-json.should-get
+++ b/algo/tests/should-get-tests/stanford-json.should-get
 !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
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -3 -z 1 -G $VIDJIL_DIR/germline/homo-sapiens/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"

--- a/algo/tests/should-get-tests/stanford-k14.should-get
+++ b/algo/tests/should-get-tests/stanford-k14.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -k 14 -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -k 14 -G $VIDJIL_DIR/germline/homo-sapiens/IGH $VIDJIL_DIR/data/Stanford_S22.fasta
 !LOG: stanford-k14.log

 $ Find the good number of windows in Stanford S22 (contiguous seed 14)

--- a/algo/tests/should-get-tests/stanford-labels-FaW.should-get
+++ b/algo/tests/should-get-tests/stanford-labels-FaW.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -t 0 -G $VIDJIL_DIR/germline/IGH -FaW GAGAGGTTACTATGATAGTAGTGGTTATTACGGGGTAGGGCAGTACTACT $VIDJIL_DIR/data/Stanford_S22.fasta ; cat out/seq/clone.fa-1
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -t 0 -G $VIDJIL_DIR/germline/homo-sapiens/IGH -FaW GAGAGGTTACTATGATAGTAGTGGTTATTACGGGGTAGGGCAGTACTACT $VIDJIL_DIR/data/Stanford_S22.fasta ; cat out/seq/clone.fa-1

 $ Keep only one windows, the one given by -W, with only 5 reads (it is actually the second clone in Stanford_S22.fasta)
 1: keep 1 windows in 5 reads

--- a/algo/tests/should-get-tests/stanford-labels-W.should-get
+++ b/algo/tests/should-get-tests/stanford-labels-W.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 0 -G $VIDJIL_DIR/germline/IGH -r 5 -W GAGAGATGGACGGGATACGTAAAACGACATATGGTTCGGGGTTTGGTGCT $VIDJIL_DIR/data/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 0 -G $VIDJIL_DIR/germline/homo-sapiens/IGH -r 5 -W GAGAGATGGACGGGATACGTAAAACGACATATGGTTCGGGGTTTGGTGCT $VIDJIL_DIR/data/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil

 $ Some clone has only one read, bypassing the -r 5 option, and the good label
 1: clone-00..*0001-.* -W

--- a/algo/tests/should-get-tests/stanford-labels.should-get
+++ b/algo/tests/should-get-tests/stanford-labels.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 0 -G $VIDJIL_DIR/germline/IGH -r 5 -l $VIDJIL_DIR/data/Stanford_S22.label $VIDJIL_DIR/data/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 0 -G $VIDJIL_DIR/germline/homo-sapiens/IGH -r 5 -l $VIDJIL_DIR/data/Stanford_S22.label $VIDJIL_DIR/data/Stanford_S22.fasta ; cat out/Stanford_S22.vidjil

 $ Some clone has only one read, bypassing the -r 5 option, and the good label
 1: clone-00..*0001-.* my-clone

--- a/algo/tests/should-get-tests/stanford-segment-x100-first.should-get
+++ b/algo/tests/should-get-tests/stanford-segment-x100-first.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -x 2 -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -x 2 -G $VIDJIL_DIR/germline/homo-sapiens/IGH $VIDJIL_DIR/data/Stanford_S22.fasta

 $ Segments the good number of sequences in Stanford S22 
 2: >lcl

--- a/algo/tests/should-get-tests/stanford-vidjil-to-fasta.should_get
+++ b/algo/tests/should-get-tests/stanford-vidjil-to-fasta.should_get
 !REQUIRES: python $VIDJIL_DIR/tools/check_python_version.py
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -z 5 -w 60 -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/vidjil-to-fasta.py  -o out/S22.fasta out/Stanford_S22.vidjil ;
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -z 5 -w 60 -G $VIDJIL_DIR/germline/homo-sapiens/IGH $VIDJIL_DIR/data/Stanford_S22.fasta ; python $VIDJIL_DIR/tools/vidjil-to-fasta.py  -o out/S22.fasta out/Stanford_S22.vidjil ;
 !OUTPUT_FILE: out/S22.fasta

 $ 5 representative sequences in the FASTA output file

--- a/algo/tests/should-get-tests/stanford-w100.should-get
+++ b/algo/tests/should-get-tests/stanford-w100.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -y 0 -s '#####-#####' -w 100 -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -y 0 -s '#####-#####' -w 100 -G $VIDJIL_DIR/germline/homo-sapiens/IGH $VIDJIL_DIR/data/Stanford_S22.fasta
 !LOG: stanford-w100.log

 $ Find the good number of "too short sequences" for windows of size 100

--- a/algo/tests/should-get-tests/stanford-x100-first.should-get
+++ b/algo/tests/should-get-tests/stanford-x100-first.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -x 100 -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/Stanford_S22.fasta
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -y 0 -x 100 -G $VIDJIL_DIR/germline/homo-sapiens/IGH $VIDJIL_DIR/data/Stanford_S22.fasta

 $ Analyze the good number of sequences in Stanford S22 
 1: found .* of 100 reads
--- a/algo/tests/should-get-tests/stanford.should-get
+++ b/algo/tests/should-get-tests/stanford.should-get
-!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
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -z 0 -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -s \\\\#\\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\#\\\\# $VIDJIL_DIR/data/Stanford_S22.fasta

 $ Germlines are custom
 1: custom germlines
@@ -9,7 +9,7 @@ $ Parses IGHV.fa germline
 $ Parses IGHD.fa germline
 1: 1070 bp in  44 sequences

-$ Parses germline/IGHJ.fa
+$ Parses germline/homo-sapiens/IGHJ.fa
 1: 701 bp in  13 sequences

 $ Find the good index load

--- a/algo/tests/should-get-tests/trb-only-VJ.should-get
+++ b/algo/tests/should-get-tests/trb-only-VJ.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -G $VIDJIL_DIR/germline/TRB $VIDJIL_DIR/data/trb-only-VJ.fa ; cat out/trb-only-VJ.vidjil
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -G $VIDJIL_DIR/germline/homo-sapiens/TRB $VIDJIL_DIR/data/trb-only-VJ.fa ; cat out/trb-only-VJ.vidjil

 $ Segments the read on TRB (the information is given twice, stdout + .vidjil)
 2: TRB .* -> .* 1

--- a/algo/tests/should-get-tests/trd-dd2-dd3.should-get
+++ b/algo/tests/should-get-tests/trd-dd2-dd3.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -k 8 -w 20 -V $VIDJIL_DIR/germline/TRDV.fa -V $VIDJIL_DIR/germline/TRDD2_upstream.fa -J $VIDJIL_DIR/germline/TRDD3_downstream.fa -J $VIDJIL_DIR/germline/TRDJ.fa $VIDJIL_DIR/data/trd-dd2-dd3.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 10 -k 8 -w 20 -V $VIDJIL_DIR/germline/homo-sapiens/TRDV.fa -V $VIDJIL_DIR/germline/homo-sapiens/TRDD2_upstream.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRDD3_downstream.fa -J $VIDJIL_DIR/germline/homo-sapiens/TRDJ.fa $VIDJIL_DIR/data/trd-dd2-dd3.fa

 $ Segment all 8 reads, thanks to TRDD2 and TRDD3
 1: junction detected in 8 reads .100..

--- a/algo/tests/should-get-tests/vidjil-error-w-small.should-get
+++ b/algo/tests/should-get-tests/vidjil-error-w-small.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -w 10 -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/Stanford-S22.fa 2>&1
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -w 10 -G $VIDJIL_DIR/germline/homo-sapiens/IGH $VIDJIL_DIR/data/Stanford-S22.fa 2>&1
 !EXIT_CODE: 1

 $ Error, too small -w

--- a/algo/tests/should-get-tests/vidjil-warning-A.should-get
+++ b/algo/tests/should-get-tests/vidjil-warning-A.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/toy_V.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -G $VIDJIL_DIR/germline/homo-sapiens/IGH $VIDJIL_DIR/data/toy_V.fa

 $ Warning, -A
 1:WARNING

--- a/algo/tests/should-get-tests/vidjil-warning-z.should-get
+++ b/algo/tests/should-get-tests/vidjil-warning-z.should-get
 !NO_LAUNCHER:
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 200 -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/trd-dd2-dd3.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 200 -G $VIDJIL_DIR/germline/homo-sapiens/IGH $VIDJIL_DIR/data/trd-dd2-dd3.fa

 $ Warning, -z
 1:WARNING

--- a/algo/tests/should-get-tests/vidjil_long_segment.should-get
+++ b/algo/tests/should-get-tests/vidjil_long_segment.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -G $VIDJIL_DIR/germline/IGH $VIDJIL_DIR/data/long-segmentation.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -G $VIDJIL_DIR/germline/homo-sapiens/IGH $VIDJIL_DIR/data/long-segmentation.fa

 $ Sequence should be segmented by k-mer segmenter
 e1:SEG_+ -> 1 
--- a/algo/tests/should-get-tests/vidjil_revcomp_s22.should-get
+++ b/algo/tests/should-get-tests/vidjil_revcomp_s22.should-get
-!LAUNCH: $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -G $VIDJIL_DIR/germline/IGH -% 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DIR/data/Stanford_S22.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' | sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22.log && $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -G $VIDJIL_DIR/germline/IGH -% 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DIR/data/Stanford_S22.rc.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' |  sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22_rc.log && diff out/Stanford_S22{,.rc}.vidjil | grep GGG && diff vidjil_s22.log vidjil_s22_rc.log
+!LAUNCH: $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -G $VIDJIL_DIR/germline/homo-sapiens/IGH -% 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DIR/data/Stanford_S22.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' | sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22.log && $LAUNCHER $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -G $VIDJIL_DIR/germline/homo-sapiens/IGH -% 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DIR/data/Stanford_S22.rc.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' |  sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22_rc.log && diff out/Stanford_S22{,.rc}.vidjil | grep GGG && diff vidjil_s22.log vidjil_s22_rc.log
 !EXIT_CODE: 1

 $ Same number segmented