io tests and pipeline tests

Author: CNuge

R/io.r

@@ -59,7 +59,7 @@ read_fasta = function(x){
   head_line = data[seq(1,length(data), 2)]
   head_line = substr(head_line, 2, nchar(head_line))
 
-  records = data.frame(header = head_line,
+  records = data.frame(header_data = head_line,
                        sequence = data[seq(2,length(data), 2)], 
                        stringsAsFactors = FALSE)
 

R/phmms.r

@@ -12,7 +12,7 @@
 ###############################################################################
 
 ###############################################################################
-#' Nucleotide profile hidden markov model for seqdenoise.
+#' Nucleotide profile hidden markov model for debar.
 #'
 #' This model is stored in the package and was trained on a representitive
 #' sample of the barcode of life database (http://www.boldsystems.org/index.php).
@@ -22,7 +22,7 @@
 ###############################################################################
 
 ###############################################################################
-#' Example coi5p DNA sequence string
+#' Example coi5p DNA sequence string.
 #'
 #' This string of barcode data is used in the package documentation's examples
 #' and within the vignette demonstrating how to use the package.

inst/extdata/small_unittest.fasta

@@ -0,0 +1,4 @@
+>example_read_1
+gttcaacaaatcataaagatattggaattctatactttatatttgctatatgagcaggaataattggatcatctataagaataattattcgccttgaattaggatcatgtggctccttgatcaacaatgaccaaatttacaactccatcatcacaggtcacgcatttattataattttctttatagttatgccattcataattgggggattcggtaactttctagtaccattaataattggatcaccagatatagcttatccccgaataagcaacataagattttgactcctacccccatccattactctattaactctaagaagatttatcaactccggggtaggtacaggatgaacagtatacccaccattagcttctaatttattccatagaggggcatctgtagacttagccattttctctcttcatatcgccagagtctcatctatcataggagccattaatttcatttcaacaattattaacataacacacaaaaattttacaatagataaaattcctttgatagtatgagctatctttatcactgctatcttattattatatatctctaccagttttagctggagctatcaccatattattaactgatcgaaacctcaatacatcatttttcgacccggcggggggtggagacccaattctttatcaacatctattctgattttttggacatccatgaagttta
+>example_read_2
+attcaaccaatcataaagatattggaactctatattttattttcggagcatgatctggaataattggtacagctttaagattaatcatccgaacagaactcggaattcccggatcaataattgggaatgaccaaatctttaatgttattgttacctcacatgcattcatcataatcttcttcatagttataccaattataattgggggattcggaaattgactaatcccaattatattaggagctcctgatatagcatttccacgacttaataatataagattctggttattacctccctccttgtcacttattatttcaagaataatttctgaaagaggagcaggaacaggatgaactgtttatccacccttatcttctaatttagcccatagaggaccaggctgtagacttaacaatttttaggttacatctagcaggaatctcttcgattcttggagcaattaattttattactacaaacatcaatatacgatctagtcttataaaacctgaacgtttaagactattcccatgatcagtttcaatcacagcaattctattactaatctccctacctgtacttgcaggagcaattacaatgcttcttactgaccgaaacattaatacatcattctttgacccagcagggggaggtgacccaattttatatcaacatctattttgattttttggtcaccctgaagttta

inst/extdata/small_unittest.fastq

@@ -0,0 +1,8 @@
+@example_read_1
+gttcaacaaatcataaagatattggaattctatactttatatttgctatatgagcaggaataattggatcatctataagaataattattcgccttgaattaggatcatgtggctccttgatcaacaatgaccaaatttacaactccatcatcacaggtcacgcatttattataattttctttatagttatgccattcataattgggggattcggtaactttctagtaccattaataattggatcaccagatatagcttatccccgaataagcaacataagattttgactcctacccccatccattactctattaactctaagaagatttatcaactccggggtaggtacaggatgaacagtatacccaccattagcttctaatttattccatagaggggcatctgtagacttagccattttctctcttcatatcgccagagtctcatctatcataggagccattaatttcatttcaacaattattaacataacacacaaaaattttacaatagataaaattcctttgatagtatgagctatctttatcactgctatcttattattatatatctctaccagttttagctggagctatcaccatattattaactgatcgaaacctcaatacatcatttttcgacccggcggggggtggagacccaattctttatcaacatctattctgattttttggacatccatgaagttta
++
+~~y~~~~~~Q~~~~~~q~~~~~~~~~`~~~~~~~~~~i~~~~~n~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~F~~U~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~~~~~~~~~d~~~N~~~~~{~~~~~~~z~~~~x~~~~~~d~~~~~~~~~~~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~su~'O~~k~~~~~~~~~~a~~~~~~~~~~~~4~~~~~~u07~~~~~~~~~~~~~~~~~~~~~F~~~~~~~~~~~~{~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~o~~~~~~~~w~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~~~~~~~~~~~~~~~u~~~~~~~~~~~~~~~~~~~o~~~~~~~~~~m~~~~k~~~~~z~p~~~~y~~~~~~~~~~~~~~P~~~J~~~~~~~~~~~~p~V~~~~\~~~~Z`~~~~~~~~~~~~}~~~~~~~~~~~~~w~~~~~~~10~~~~~~~~~~~~~~~U~~~~{?~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~I~~~~~i~~~~~~~~a~~~~~~~~~~c~~~~~o~~~~~~~~~~~~~~~~~~~~~~A~ni~xS~~`F~~~~~~[~
+@example_read_2
+attcaaccaatcataaagatattggaactctatattttattttcggagcatgatctggaataattggtacagctttaagattaatcatccgaacagaactcggaattcccggatcaataattgggaatgaccaaatctttaatgttattgttacctcacatgcattcatcataatcttcttcatagttataccaattataattgggggattcggaaattgactaatcccaattatattaggagctcctgatatagcatttccacgacttaataatataagattctggttattacctccctccttgtcacttattatttcaagaataatttctgaaagaggagcaggaacaggatgaactgtttatccacccttatcttctaatttagcccatagaggaccaggctgtagacttaacaatttttaggttacatctagcaggaatctcttcgattcttggagcaattaattttattactacaaacatcaatatacgatctagtcttataaaacctgaacgtttaagactattcccatgatcagtttcaatcacagcaattctattactaatctccctacctgtacttgcaggagcaattacaatgcttcttactgaccgaaacattaatacatcattctttgacccagcagggggaggtgacccaattttatatcaacatctattttgattttttggtcaccctgaagttta
++
+~Ts~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~u~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~8~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~

man/example_nt_string.Rd

@@ -1,4 +1,4 @@
-test_that("Sequence files are read in properly.", {
+test_that("Sequence files are read, denoised and written properly.", {
 
   fasta_real_file = system.file('extdata/coi_sequel_data_subset.fasta', package = 'debar')
   data1 = read_fasta(fasta_real_file)
@@ -17,5 +17,59 @@ test_that("Sequence files are read in properly.", {
 
   #all.equal(dim(data3), c(250,2))
   expect_equal(all.equal(dim(data3), c(250,2)), TRUE)
+
+  #test writing to fastq file using a temp
+  temp = tempfile()
+  on.exit(unlink(temp))
 
-})
+  #write to a fastq when no quality data
+  x1 = denoise(data1$sequence[[1]], data1$header[[1]], double_pass = FALSE, dir_check = FALSE)
+  write_fastq(x1 , outfile = temp, keep_phred = FALSE, phred_placeholder = "~")
+  
+  #write to fastq with quality data
+  x2 = denoise(data2$sequence[[1]], name = data2$header[[1]], phred = data2$quality[[1]], double_pass = FALSE, dir_check = FALSE)
+  write_fastq(x2 , outfile = temp)
+  
+  #test writing to fasta using a temp
+  temp2 = tempfile()
+  on.exit(unlink(temp2))
+  
+  #write to a fastq when no quality data
+  x3 = denoise(data1$sequence[[1]], data1$header[[1]], double_pass = FALSE, dir_check = FALSE)
+  write_fastq(x3 , outfile = temp2, keep_phred = FALSE, phred_placeholder = "~")
+  
+  #write to fastq with quality data
+  x4 = denoise(data2$sequence[[1]], name = data2$header[[1]], phred = data2$quality[[1]], double_pass = FALSE, dir_check = FALSE)
+  write_fastq(x4 , outfile = temp2)
+  
+  #test the full pipeline on a small sequence datasets
+  # have the 
+  fastq_test_file = system.file('extdata/small_unittest.fastq', package = 'debar')
+  fasta_test_file = system.file('extdata/small_unittest.fasta', package = 'debar')
+  
+  #
+  # Write to a fasta file
+  #
+  temp3 = file.path(tempdir(), "temp_out.fastq")
+  on.exit(unlink(temp3))
+  
+  denoise_file(fastq_test_file, outfile = temp3,  
+                log_file = FALSE, keep_rejects = FALSE, double_pass = FALSE, dir_check = FALSE)
+  
+  denoise_file(fasta_test_file, outfile = temp3, file_type = 'fasta', keep_phred = FALSE, phred_placeholder = "~", 
+              log_file = FALSE, keep_rejects = FALSE, double_pass = FALSE, dir_check = FALSE)
+  
+  
+  #
+  # Write to a fasta file
+  #
+  temp4 = file.path(tempdir(), "temp_out.fasta")  
+  on.exit(unlink(temp4))
+  
+  denoise_file(fasta_test_file, outfile = temp4, file_type = 'fasta', keep_phred = FALSE, phred_placeholder = "~", 
+               log_file = FALSE, keep_rejects = FALSE, double_pass = FALSE, dir_check = FALSE)
+
+  denoise_file(fastq_test_file, outfile = temp4, 
+               log_file = FALSE, keep_rejects = FALSE, double_pass = FALSE, dir_check = FALSE)
+  
+})