Commit df4954bb authored by Mathieu Giraud's avatar Mathieu Giraud

tests: update tests, 'segments' -> 'reads'

parent e8452843
...@@ -4,7 +4,7 @@ $ Extract 50bp windows (TRG) ...@@ -4,7 +4,7 @@ $ Extract 50bp windows (TRG)
1:found . 50-windows 1:found . 50-windows
$ Find the good number of 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 $ Find the good statistics on TRG
1: TRG .* -> .* 7 .* 84.0 .* 2 .* 2.0 1: TRG .* -> .* 7 .* 84.0 .* 2 .* 2.0
......
!LAUNCH: ../../vidjil -k 14 -w 50 -c clones -G ../../germline/IGH -y 3 -z 1 -r 1 ../../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 $ Junction extractions
1:found 25 50-windows in 66 segments 1:found 25 50-windows in 66 reads
$ No clustering $ No clustering
1:==> 25 clones 1:==> 25 clones
......
!LAUNCH: ../../vidjil -k 14 -w 50 -c clones -G ../../germline/IGH -y 3 -z 1 -r 1 -n 5 ../../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 $ Window extractions
1:found 25 50-windows in 66 segments 1:found 25 50-windows in 66 reads
$ Some clustering $ Some clustering
1:==> 2 clusters 1:==> 2 clusters
......
...@@ -4,4 +4,4 @@ $ Skip the good number of reads ...@@ -4,4 +4,4 @@ $ Skip the good number of reads
1:Processing every 131th read 1:Processing every 131th read
$ Analyze the good number of reads $ 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
...@@ -11,4 +11,4 @@ $ Parses germline/IGHJ.fa ...@@ -11,4 +11,4 @@ $ Parses germline/IGHJ.fa
1: 701 bp in 13 sequences 1: 701 bp in 13 sequences
$ Find the good number of windows in Stanford S22 (contiguous seed 14) $ 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
...@@ -8,4 +8,4 @@ $ Find the good number of segmented sequences (including "too short sequences") ...@@ -8,4 +8,4 @@ $ Find the good number of segmented sequences (including "too short sequences")
1: junction detected in 13148 reads .100%. 1: junction detected in 13148 reads .100%.
$ Find the good number of windows of size 100 in Stanford S22 $ 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
!LAUNCH: ../../vidjil -x 100 -G ../../germline/IGH ../../data/Stanford_S22.fasta !LAUNCH: ../../vidjil -x 100 -G ../../germline/IGH ../../data/Stanford_S22.fasta
$ Analyze the good number of sequences in Stanford S22 $ 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
...@@ -16,5 +16,5 @@ $ Find approximately the good number of sequences for e-value computation ...@@ -16,5 +16,5 @@ $ Find approximately the good number of sequences for e-value computation
1: approx. 131.. sequences 1: approx. 131.. sequences
$ Find the good number of windows in Stanford S22 $ 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
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