Commit 778ad84e authored by Mathieu Giraud's avatar Mathieu Giraud

tests: update tests for -w 50

parent 2d80348c
!LAUNCH: ../../vidjil -G ../../germline/TRG -c clones ../../data/segment_lec.fa
$ Extract 40bp windows (TRG)
1:found . 40-windows
$ Extract 50bp windows (TRG)
1:found . 50-windows
$ Find the good number of windows
1: found 2 .* in 4 segments .* inside 7 sequences
......
......@@ -7,5 +7,5 @@ $ Same number of 'V' affectations in both reads
2:143
$ Only one window
1:==> found 1 60-window
1:==> found 1 ..-window
......@@ -4,4 +4,4 @@ $ Skip the good number of reads
1:Processing every 131th read
$ Analyze the good number of reads
1: found 100 60-windows in 100 segments .100.. inside 100 sequences
1: found 100 ..-windows in 100 segments .100.. inside 100 sequences
!LAUNCH: ../../vidjil -G ../../germline/IGH -r 5 -b data ../../data/Stanford_S22.fasta ; cat out/data.vidjil | python ../../tools/format_json.py -1
!LAUNCH: ../../vidjil -G ../../germline/IGH -w 60 -r 5 -b data ../../data/Stanford_S22.fasta ; cat out/data.vidjil | python ../../tools/format_json.py -1
$ Number of reads
e1:"total": [13153]
......
!LAUNCH: ../../vidjil -r 5 -o out2 -u -U -v -G ../../germline/IGH ../../data/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa ; grep UNSEG out2/Stanford_S22.unsegmented.vdj.fa
!LAUNCH: ../../vidjil -w 60 -r 5 -o out2 -u -U -v -G ../../germline/IGH ../../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)
......
!LAUNCH: ../../vidjil -G ../../germline/IGH ../../data/Stanford_S22.fasta ; python ../../tools/fuse.py out/Stanford_S22.vidjil out/Stanford_S22.vidjil -o out/fused.data ; cat out/fused.data | python ../../tools/format_json.py -1
!LAUNCH: ../../vidjil -w 60 -G ../../germline/IGH ../../data/Stanford_S22.fasta ; python ../../tools/fuse.py out/Stanford_S22.vidjil out/Stanford_S22.vidjil -o out/fused.data ; cat out/fused.data | python ../../tools/format_json.py -1
$ Points list
e1:"original_names": ["../../data/Stanford_S22.fasta", "../../data/Stanford_S22.fasta"]
......
......@@ -11,5 +11,4 @@ $ Parses germline/IGHJ.fa
1: 701 bp in 13 sequences
$ Find the good number of windows in Stanford S22 (contiguous seed 14)
1: found 10921 60-windows in 13114 segments
1: found 10743 50-windows in 13114 segments
!LAUNCH: ../../vidjil -G ../../germline/IGH -r 5 -l ../../data/Stanford_S22.label ../../data/Stanford_S22.fasta
!LAUNCH: ../../vidjil -w 60 -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 -x 100 -G ../../germline/IGH ../../data/Stanford_S22.fasta
$ Analyze the good number of sequences in Stanford S22
1: found 98 60-windows in 99 segments .99.. inside 100 sequences
1: found 98 ..-windows in 99 segments .99.. inside 100 sequences
......@@ -16,5 +16,5 @@ $ Find approximately the good number of sequences for e-value computation
1: approx. 131.. sequences
$ Find the good number of windows in Stanford S22
1: found 10935 60-windows in 13138 segments
1: found 10732 50-windows in 13138 segments
......@@ -13,5 +13,8 @@ $ Keep the same number of windows
0:==> keep
$ Same segmentation for the main clone
2:clone.001.*0 114 118 131 137 180
2:clone.001.*0 31 38 57 66 111
$ Same representative for the main clone
2:clone.001.* 112 bp .45. of 247 bp.
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