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vidjil
vidjil
Commits
df4954bb
Commit
df4954bb
authored
Apr 17, 2015
by
Mathieu Giraud
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tests: update tests, 'segments' -> 'reads'
parent
e8452843
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algo/tests/clones_lec.should_get
algo/tests/clones_lec.should_get
+1
-1
algo/tests/clones_simul.should_get
algo/tests/clones_simul.should_get
+1
-1
algo/tests/clones_simul_cluster.should_get
algo/tests/clones_simul_cluster.should_get
+1
-1
algo/tests/stanford-X100-sampled.should_get
algo/tests/stanford-X100-sampled.should_get
+1
-1
algo/tests/stanford-k14.should_get
algo/tests/stanford-k14.should_get
+1
-1
algo/tests/stanford-w100.should_get
algo/tests/stanford-w100.should_get
+1
-1
algo/tests/stanford-x100-first.should_get
algo/tests/stanford-x100-first.should_get
+1
-1
algo/tests/stanford.should_get
algo/tests/stanford.should_get
+1
-1
No files found.
algo/tests/clones_lec.should_get
View file @
df4954bb
...
...
@@ -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 sequence
s
1: found 2 .* in 4
reads .* 7 read
s
$ Find the good statistics on TRG
1: TRG .* -> .* 7 .* 84.0 .* 2 .* 2.0
...
...
algo/tests/clones_simul.should_get
View file @
df4954bb
!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
segment
s
1:found 25 50-windows in 66
read
s
$ No clustering
1:==> 25 clones
...
...
algo/tests/clones_simul_cluster.should_get
View file @
df4954bb
!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
segment
s
1:found 25 50-windows in 66
read
s
$ Some clustering
1:==> 2 clusters
...
...
algo/tests/stanford-X100-sampled.should_get
View file @
df4954bb
...
...
@@ -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 sequence
s
1: found 100 ..-windows in 100
reads .100. of 100 read
s
algo/tests/stanford-k14.should_get
View file @
df4954bb
...
...
@@ -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
segment
s
1: found 10743 50-windows in 13114
read
s
algo/tests/stanford-w100.should_get
View file @
df4954bb
...
...
@@ -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
segment
s
1: found 9800 100-windows in 10931
read
s
algo/tests/stanford-x100-first.should_get
View file @
df4954bb
!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 sequence
s
1: found 98 ..-windows in 99
reads .99. of 100 read
s
algo/tests/stanford.should_get
View file @
df4954bb
...
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@@ -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
segment
s
1: found 10732 50-windows in 13138
read
s
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