From 778ad84e030309857bf9387b82e7d7202d4f3807 Mon Sep 17 00:00:00 2001 From: Mathieu Giraud Date: Thu, 16 Apr 2015 09:14:12 +0200 Subject: [PATCH] tests: update tests for -w 50 --- algo/tests/clones_lec.should_get | 4 ++-- algo/tests/revcomp.should_get | 2 +- algo/tests/stanford-X100-sampled.should_get | 2 +- algo/tests/stanford-data.should_get | 2 +- algo/tests/stanford-debug.should_get | 2 +- algo/tests/stanford-fuse.should_get | 2 +- algo/tests/stanford-k14.should_get | 3 +-- algo/tests/stanford-labels.should_get | 2 +- algo/tests/stanford-x100-first.should_get | 2 +- algo/tests/stanford.should_get | 2 +- algo/tests/vidjil_revcomp_s22.should_get | 5 ++++- 11 files changed, 15 insertions(+), 13 deletions(-) diff --git a/algo/tests/clones_lec.should_get b/algo/tests/clones_lec.should_get index 3c9056b0a..e1e9a2495 100644 --- a/algo/tests/clones_lec.should_get +++ b/algo/tests/clones_lec.should_get @@ -1,7 +1,7 @@ !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 diff --git a/algo/tests/revcomp.should_get b/algo/tests/revcomp.should_get index 099ab1b48..91b0df703 100644 --- a/algo/tests/revcomp.should_get +++ b/algo/tests/revcomp.should_get @@ -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 diff --git a/algo/tests/stanford-X100-sampled.should_get b/algo/tests/stanford-X100-sampled.should_get index 41afe1647..dbb9893fa 100644 --- a/algo/tests/stanford-X100-sampled.should_get +++ b/algo/tests/stanford-X100-sampled.should_get @@ -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 diff --git a/algo/tests/stanford-data.should_get b/algo/tests/stanford-data.should_get index d7e3b4e0f..0839c34c2 100644 --- a/algo/tests/stanford-data.should_get +++ b/algo/tests/stanford-data.should_get @@ -1,4 +1,4 @@ -!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] diff --git a/algo/tests/stanford-debug.should_get b/algo/tests/stanford-debug.should_get index 933e3f2cd..edd03fa00 100644 --- a/algo/tests/stanford-debug.should_get +++ b/algo/tests/stanford-debug.should_get @@ -1,4 +1,4 @@ -!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) diff --git a/algo/tests/stanford-fuse.should_get b/algo/tests/stanford-fuse.should_get index c0072fa17..c85292ec0 100644 --- a/algo/tests/stanford-fuse.should_get +++ b/algo/tests/stanford-fuse.should_get @@ -1,4 +1,4 @@ -!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"] diff --git a/algo/tests/stanford-k14.should_get b/algo/tests/stanford-k14.should_get index 600989f9f..7411d8981 100644 --- a/algo/tests/stanford-k14.should_get +++ b/algo/tests/stanford-k14.should_get @@ -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 diff --git a/algo/tests/stanford-labels.should_get b/algo/tests/stanford-labels.should_get index 886aa943e..b8ddec56f 100644 --- a/algo/tests/stanford-labels.should_get +++ b/algo/tests/stanford-labels.should_get @@ -1,4 +1,4 @@ -!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 diff --git a/algo/tests/stanford-x100-first.should_get b/algo/tests/stanford-x100-first.should_get index 6ab2eba53..522069305 100644 --- a/algo/tests/stanford-x100-first.should_get +++ b/algo/tests/stanford-x100-first.should_get @@ -1,4 +1,4 @@ !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 diff --git a/algo/tests/stanford.should_get b/algo/tests/stanford.should_get index 2a844cfe4..1cb4a3a8e 100644 --- a/algo/tests/stanford.should_get +++ b/algo/tests/stanford.should_get @@ -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 diff --git a/algo/tests/vidjil_revcomp_s22.should_get b/algo/tests/vidjil_revcomp_s22.should_get index d1dc01a15..21787e364 100644 --- a/algo/tests/vidjil_revcomp_s22.should_get +++ b/algo/tests/vidjil_revcomp_s22.should_get @@ -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. -- GitLab