1. seqTools
  2. tests
  3. test_seqTools.r
Browse code

Update version 1.9.1

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqTools@128664 bc3139a8-67e5-0310-9ffc-ced21a209358

Wolfgang Kaisers authored on 13/04/2017 16:00:27
Showing1 changed files
tests/test_seqTools.r
History View file @2b2568d
... ... 
@@ -1,8 +1,24 @@
1 1
2 
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
3 
+## Load prerequisites
4 
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
5 
+
2 6 
 library(seqTools)
3 7
4 
-filename <- "test_seqTools.r"
8 
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
9 
+## Initialize example data
10 
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
11 
+
12 
+basedir<-system.file("extdata",package="seqTools")
13 
+
14 
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
15 
+## Run tests
16 
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
17 
+
18 
+filename <- "test_seqTools.R"
5 19 
 basedir <- system.file("extdata", package = "seqTools")
20 
+load(file.path(basedir,"test_res.RData"))
21 
+
6 22
7 23 
 ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
8 24 
 ## countDnaKmers
... ... 
@@ -10,7 +26,7 @@ basedir <- system.file("extdata", package = "seqTools")
10 26
11 27 
 if(!identical(countDnaKmers("ACGT", k = 1, start = 3:1, width = 1), cdk_ACGT))
12 28 
     stop("[countDnaKmers] Test 1 '", filename, "' FAILED!")
13 
-
29 
+
14 30 
 if(!identical(countDnaKmers("ACGT", k = 1, start = 3, width = 1), cdk_ACGT_one))
15 31 
     stop("[countDnaKmers] Test 2 '", filename, "' FAILED!")
16 32
... ... 
@@ -27,49 +43,6 @@ if(!identical(
27 43 
     stop("[revCountDnaKmers] Test 1 '", filename, "' FAILED!")
28 44
29 45
30 
-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
31 
-## kmerCount.fastqq
32 
-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
33 
-
34 
-fq <- fastqq(file.path(basedir, "test_l5_N.fq"), k = 2)
35 
-if(!identical(kmerCount(fq), kmer_l5_N))
36 
-    stop("[kmerCount.fastqq] Test 1 '", filename, "' FAILED!")
37 
-
38 
-fq<-fastqq(file.path(basedir, "test_l6.fq"), k = 2)
39 
-if(!identical(kmerCount(fq), kmer_l6))
40 
-    stop("[kmerCount.fastqq] Test 2 '", filename, "' FAILED!")
41 
-
42 
-fq<-fastqq(file.path(basedir, "test_l6_multi_line.fq"), k = 2)
43 
-if(!identical(kmerCount(fq), kmer_l6_ml))
44 
-    stop("[kmerCount.fastqq] Test 3 '", filename, "' FAILED!")
45 
-
46 
-fq<-fastqq(file.path(basedir, "test_l10_20_40.fq"),k = 2)
47 
-if(!identical(kmerCount(fq), kmer_l10_20))
48 
-    stop("[kmerCount.fastqq] Test 4 '", filename, "' FAILED!")
49 
-
50 
-fq<-fastqq(file.path(basedir, "test_l10_atcg.fq"), k = 2)
51 
-if(!identical(kmerCount(fq), kmer_l10_atcg))
52 
-    stop("[kmerCount.fastqq] Test 5 '", filename, "' FAILED!")
53 
-
54 
-fq<-fastqq(file.path(basedir, "test_l10_ATCGN.fq"), k = 2)
55 
-if(!identical(kmerCount(fq), kmer_l10_ATCGN))
56 
-    stop("[kmerCount.fastqq] Test 6 '", filename, "' FAILED!")
57 
-
58 
-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
59 
-## ascii2char, char2ascii
60 
-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
61 
-
62 
-if(!identical(ascii2char(97:101, multiple = FALSE), "abcde"))
63 
-    stop("[ascii2char] Test 1 '", filename, "' FAILED!")
64 
-
65 
-if(!identical(ascii2char(97:101, multiple = TRUE), letters[1:5]))
66 
-    stop("[ascii2char] Test 2 '", filename, "' FAILED!")
67 
-
68 
-if(!identical(ascii2char(char2ascii("abcde")), "abcde"))
69 
-    stop("[ascii2char] Test 3 '", filename, "' FAILED!")
70 
-
71 
-if(!identical(char2ascii("abcde"), 97:101))
72 
-    stop("[char2ascii] Test 1 '", filename, "' FAILED!")
73 46
74 47 
 ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
75 48 
 ## END OF FILE
Browse code

add seqTools package

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqTools@95415 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 13/10/2014 19:02:34
Showing1 changed files
tests/test_seqTools.r
History View file @e46f15e
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,76 @@
1 
+
2 
+library(seqTools)
3 
+
4 
+filename <- "test_seqTools.r"
5 
+basedir <- system.file("extdata", package = "seqTools")
6 
+
7 
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
8 
+## countDnaKmers
9 
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
10 
+
11 
+if(!identical(countDnaKmers("ACGT", k = 1, start = 3:1, width = 1), cdk_ACGT))
12 
+    stop("[countDnaKmers] Test 1 '", filename, "' FAILED!")
13 
+
14 
+if(!identical(countDnaKmers("ACGT", k = 1, start = 3, width = 1), cdk_ACGT_one))
15 
+    stop("[countDnaKmers] Test 2 '", filename, "' FAILED!")
16 
+
17 
+if(!identical(
18 
+        countDnaKmers("ATTNAC", k = 2, start = 1:3, width = 1), cdk_ATTNAC))
19 
+    stop("[countDnaKmers] Test 3 '", filename, "' FAILED!")
20 
+
21 
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
22 
+## revCountDnaKmers
23 
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
24 
+
25 
+if(!identical(
26 
+        revCountDnaKmers("ACGTACGT", k = 2, start = 6:4, width = 2), rck_ACGT))
27 
+    stop("[revCountDnaKmers] Test 1 '", filename, "' FAILED!")
28 
+
29 
+
30 
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
31 
+## kmerCount.fastqq
32 
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
33 
+
34 
+fq <- fastqq(file.path(basedir, "test_l5_N.fq"), k = 2)
35 
+if(!identical(kmerCount(fq), kmer_l5_N))
36 
+    stop("[kmerCount.fastqq] Test 1 '", filename, "' FAILED!")
37 
+
38 
+fq<-fastqq(file.path(basedir, "test_l6.fq"), k = 2)
39 
+if(!identical(kmerCount(fq), kmer_l6))
40 
+    stop("[kmerCount.fastqq] Test 2 '", filename, "' FAILED!")
41 
+
42 
+fq<-fastqq(file.path(basedir, "test_l6_multi_line.fq"), k = 2)
43 
+if(!identical(kmerCount(fq), kmer_l6_ml))
44 
+    stop("[kmerCount.fastqq] Test 3 '", filename, "' FAILED!")
45 
+
46 
+fq<-fastqq(file.path(basedir, "test_l10_20_40.fq"),k = 2)
47 
+if(!identical(kmerCount(fq), kmer_l10_20))
48 
+    stop("[kmerCount.fastqq] Test 4 '", filename, "' FAILED!")
49 
+
50 
+fq<-fastqq(file.path(basedir, "test_l10_atcg.fq"), k = 2)
51 
+if(!identical(kmerCount(fq), kmer_l10_atcg))
52 
+    stop("[kmerCount.fastqq] Test 5 '", filename, "' FAILED!")
53 
+
54 
+fq<-fastqq(file.path(basedir, "test_l10_ATCGN.fq"), k = 2)
55 
+if(!identical(kmerCount(fq), kmer_l10_ATCGN))
56 
+    stop("[kmerCount.fastqq] Test 6 '", filename, "' FAILED!")
57 
+
58 
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
59 
+## ascii2char, char2ascii
60 
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
61 
+
62 
+if(!identical(ascii2char(97:101, multiple = FALSE), "abcde"))
63 
+    stop("[ascii2char] Test 1 '", filename, "' FAILED!")
64 
+
65 
+if(!identical(ascii2char(97:101, multiple = TRUE), letters[1:5]))
66 
+    stop("[ascii2char] Test 2 '", filename, "' FAILED!")
67 
+
68 
+if(!identical(ascii2char(char2ascii("abcde")), "abcde"))
69 
+    stop("[ascii2char] Test 3 '", filename, "' FAILED!")
70 
+
71 
+if(!identical(char2ascii("abcde"), 97:101))
72 
+    stop("[char2ascii] Test 1 '", filename, "' FAILED!")
73 
+
74 
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
75 
+## END OF FILE
76 
+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##