From df4954bb899a1e4235216f4b0b181076f9c3b9c5 Mon Sep 17 00:00:00 2001 From: Mathieu Giraud Date: Fri, 17 Apr 2015 23:15:38 +0200 Subject: [PATCH] tests: update tests, 'segments' -> 'reads' --- algo/tests/clones_lec.should_get | 2 +- algo/tests/clones_simul.should_get | 2 +- algo/tests/clones_simul_cluster.should_get | 2 +- algo/tests/stanford-X100-sampled.should_get | 2 +- algo/tests/stanford-k14.should_get | 2 +- algo/tests/stanford-w100.should_get | 2 +- algo/tests/stanford-x100-first.should_get | 2 +- algo/tests/stanford.should_get | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/algo/tests/clones_lec.should_get b/algo/tests/clones_lec.should_get index e1e9a2495..04be39d19 100644 --- a/algo/tests/clones_lec.should_get +++ b/algo/tests/clones_lec.should_get @@ -4,7 +4,7 @@ $ Extract 50bp windows (TRG) 1:found . 50-windows $ Find the good number of windows -1: found 2 .* in 4 segments .* inside 7 sequences +1: found 2 .* in 4 reads .* 7 reads $ Find the good statistics on TRG 1: TRG .* -> .* 7 .* 84.0 .* 2 .* 2.0 diff --git a/algo/tests/clones_simul.should_get b/algo/tests/clones_simul.should_get index e73534207..ddf8136d6 100644 --- a/algo/tests/clones_simul.should_get +++ b/algo/tests/clones_simul.should_get @@ -1,7 +1,7 @@ !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 +1:found 25 50-windows in 66 reads $ No clustering 1:==> 25 clones diff --git a/algo/tests/clones_simul_cluster.should_get b/algo/tests/clones_simul_cluster.should_get index 07d506b5f..45a546cb5 100644 --- a/algo/tests/clones_simul_cluster.should_get +++ b/algo/tests/clones_simul_cluster.should_get @@ -1,7 +1,7 @@ !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 +1:found 25 50-windows in 66 reads $ Some clustering 1:==> 2 clusters diff --git a/algo/tests/stanford-X100-sampled.should_get b/algo/tests/stanford-X100-sampled.should_get index dbb9893fa..2afb9281f 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 ..-windows in 100 segments .100.. inside 100 sequences +1: found 100 ..-windows in 100 reads .100. of 100 reads diff --git a/algo/tests/stanford-k14.should_get b/algo/tests/stanford-k14.should_get index 7411d8981..23c482a1d 100644 --- a/algo/tests/stanford-k14.should_get +++ b/algo/tests/stanford-k14.should_get @@ -11,4 +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 10743 50-windows in 13114 segments +1: found 10743 50-windows in 13114 reads diff --git a/algo/tests/stanford-w100.should_get b/algo/tests/stanford-w100.should_get index 97891e937..b301bfb7c 100644 --- a/algo/tests/stanford-w100.should_get +++ b/algo/tests/stanford-w100.should_get @@ -8,4 +8,4 @@ $ Find the good number of segmented sequences (including "too short sequences") 1: junction detected in 13148 reads .100%. $ Find the good number of windows of size 100 in Stanford S22 -1: found 9800 100-windows in 10931 segments +1: found 9800 100-windows in 10931 reads diff --git a/algo/tests/stanford-x100-first.should_get b/algo/tests/stanford-x100-first.should_get index 522069305..30c6daf00 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 ..-windows in 99 segments .99.. inside 100 sequences +1: found 98 ..-windows in 99 reads .99. of 100 reads diff --git a/algo/tests/stanford.should_get b/algo/tests/stanford.should_get index 1cb4a3a8e..194fcc077 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 10732 50-windows in 13138 segments +1: found 10732 50-windows in 13138 reads -- GitLab