Commit 0f24c9ba authored by Mathieu Giraud's avatar Mathieu Giraud

tests: remove '-d' options

Additionally, one test has a different output due to a previously forgotten '-d' option.
parent 965463ce
!LAUNCH: ../../vidjil -k 14 -w 50 -c clones -G ../../germline/IGH -y 3 -z 1 -r 1 -d ../../data/clones_simul.fa
!LAUNCH: ../../vidjil -k 14 -w 50 -c clones -G ../../germline/IGH -y 3 -z 1 -r 1 ../../data/clones_simul.fa
$ Junction extractions
1:found 25 50-windows in 66 segments
......
!LAUNCH: ../../vidjil -k 14 -w 50 -c clones -G ../../germline/IGH -y 3 -z 1 -r 1 -n 5 -d ../../data/clones_simul.fa
!LAUNCH: ../../vidjil -k 14 -w 50 -c clones -G ../../germline/IGH -y 3 -z 1 -r 1 -n 5 ../../data/clones_simul.fa
$ Window extractions
1:found 25 50-windows in 66 segments
......
......@@ -3,5 +3,5 @@
$ Identical output
1:Diff: 0
$ Testing out-fa-gz has approximately 69 lines
1: [67]. out-fa-gz
$ Testing out-fa-gz has approximately 80 lines
1: [78]. out-fa-gz
!LAUNCH: ../../vidjil -G ../../germline/IGH -d -c segment ../../data/segment_S22.fa | grep '^>'
!LAUNCH: ../../vidjil -G ../../germline/IGH -c segment ../../data/segment_S22.fa | grep '^>'
$ First sequence Stanford
# 164 175 195 203
......
!LAUNCH: ../../vidjil -G ../../germline/IGH -r 5 -d -b data ../../data/Stanford_S22.fasta ; cat out/data.vidjil | sh format-json.sh
!LAUNCH: ../../vidjil -G ../../germline/IGH -r 5 -b data ../../data/Stanford_S22.fasta ; cat out/data.vidjil | sh format-json.sh
$ Number of reads
1:"total" : [ 13153 ] ,
......
!LAUNCH: ../../vidjil -d -r 5 -o out2 -u -U -v -G ../../germline/IGH ../../data/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa out2/Stanford_S22.unsegmented.fa
!LAUNCH: ../../vidjil -r 5 -o out2 -u -U -v -G ../../germline/IGH ../../data/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa out2/Stanford_S22.unsegmented.fa
# Testing uncommon and debug options
$ verbose (-v)
......
!LAUNCH: ../../vidjil -d -r 5 -a -G ../../germline/IGH ../../data/Stanford_S22.fasta ; cat out/seq/clone.fa-2
!LAUNCH: ../../vidjil -r 5 -a -G ../../germline/IGH ../../data/Stanford_S22.fasta ; cat out/seq/clone.fa-2
# Testing detailed clone output (-a)
$ Detailed clone output (out/seq/clone.fa-2), germline
......
!LAUNCH: ../../vidjil -G ../../germline/IGH -d ../../data/Stanford_S22.fasta ; python ../../server/fuse.py out/Stanford_S22.vidjil out/Stanford_S22.vidjil -o out/fused.data ; cat out/fused.data | sh format-json.sh
!LAUNCH: ../../vidjil -G ../../germline/IGH ../../data/Stanford_S22.fasta ; python ../../server/fuse.py out/Stanford_S22.vidjil out/Stanford_S22.vidjil -o out/fused.data ; cat out/fused.data | sh format-json.sh
$ Points list
f1:"point": [ "", "" ]
......
!LAUNCH: ../../vidjil -k 14 -G ../../germline/IGH -d ../../data/Stanford_S22.fasta
!LAUNCH: ../../vidjil -k 14 -G ../../germline/IGH ../../data/Stanford_S22.fasta
!LOG: stanford-k14.log
$ Parses IGHV.fa germline
......
!LAUNCH: ../../vidjil -G ../../germline/IGH -d -r 5 -l ../../data/Stanford_S22.label ../../data/Stanford_S22.fasta
!LAUNCH: ../../vidjil -G ../../germline/IGH -r 5 -l ../../data/Stanford_S22.label ../../data/Stanford_S22.fasta
$ Keep the good number of windows, including one window labeled in Stanford_S22.label
1: keep 3 windows
......
!LAUNCH: ../../vidjil -s '#####-#####' -w 100 -G ../../germline/IGH -d ../../data/Stanford_S22.fasta
!LAUNCH: ../../vidjil -s '#####-#####' -w 100 -G ../../germline/IGH ../../data/Stanford_S22.fasta
!LOG: stanford-w100.log
$ Parses IGHV.fa germline
......
!LAUNCH: ../../vidjil -V ../../germline/IGHV.fa -D ../../germline/IGHD.fa -J ../../germline/IGHJ.fa -d -s \\\\#\\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\#\\\\# ../../data/Stanford_S22.fasta
!LAUNCH: ../../vidjil -V ../../germline/IGHV.fa -D ../../germline/IGHD.fa -J ../../germline/IGHJ.fa -s \\\\#\\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\#\\\\# ../../data/Stanford_S22.fasta
$ Parses IGHV.fa germline
f1: 99341 bp in 341 sequences
......
!LAUNCH: ../../vidjil -k 9 -G ../../germline/IGH -d -% 0.001 -r 4 -c clones ../../data/Stanford_S22.fasta > vidjil_s22.log && ../../vidjil -k 9 -G ../../germline/IGH -d -% 0.001 -r 4 -c clones ../../data/Stanford_S22.rc.fasta > vidjil_s22_rc.log && diff vidjil_s22.log vidjil_s22_rc.log
!LAUNCH: ../../vidjil -k 9 -G ../../germline/IGH -% 0.001 -r 4 -c clones ../../data/Stanford_S22.fasta > vidjil_s22.log && ../../vidjil -k 9 -G ../../germline/IGH -% 0.001 -r 4 -c clones ../../data/Stanford_S22.rc.fasta > vidjil_s22_rc.log && diff vidjil_s22.log vidjil_s22_rc.log
$ Same number segmented
0:==> segmented
......
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