Fixed conflicts in version change

malnirav · Sep 15, 2017 · 67ed8cd · 67ed8cd
2 parents 45f158f + 3eda55e
commit 67ed8cd
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,12 +1,7 @@
 Package: hiReadsProcessor
 Title: Functions to process LM-PCR reads from 454/Illumina data
-<<<<<<< HEAD
 Version: 1.13.0
 Date: 2016-05-05
-=======
-Version: 1.3.0
-Date: 2015-04-02
->>>>>>> origin/master
 Author: Nirav V Malani <[email protected]>
 Maintainer: Nirav V Malani <[email protected]>
 Description: hiReadsProcessor contains set of functions which allow

diff --git a/R/hiReadsProcessor.R b/R/hiReadsProcessor.R
@@ -489,11 +489,7 @@ replicateReads <- function(dnaSet, counts = NULL) {
     if(is.null(names(dnaSet))) {
       stop("No names attribute found in dnaSet object")
     }
-<<<<<<< HEAD
     counts <- as.numeric(sub(".+counts=(\\d+)", "\\1", names(dnaSet)))
-=======
-    counts <- as.numeric(sub(".+counts=(\\d+).*","\\1", names(dnaSet)))
->>>>>>> origin/master
     if(all(is.na(counts))) {
       warning("No counts=\\d+ marker found at the end of definition line or ",
               "names attribute in dnaSet object. Defaulting to count=1")

diff --git a/inst/tests/runTests.R b/inst/tests/runTests.R
@@ -0,0 +1,8 @@
+## unit tests will not be done if testthat is not available
+if(require("testthat", quietly = TRUE)) {
+    library(hiReadsProcessor)
+    data(FLX_seqProps)
+    test_package("hiReadsProcessor")    
+} else {
+    warning("cannot run unit tests -- package 'testthat' is not available")
+}
diff --git a/inst/tests/tests/test_coreFeatures.R b/inst/tests/tests/test_coreFeatures.R
@@ -0,0 +1,77 @@
+test_that("all core function tests", {
+
+#### extractor tests ####
+samplename <- "Roth-MLV3p-CD4TMLVWell6-Tsp509I"
+subjectSeqs <- extractSeqs(seqProps, feature='genomicLinkered', sector = "1", 
+                           samplename = samplename)[[1]][[1]]
+subjectSeqs <- head(subjectSeqs)
+expect_equal(as.character(subjectSeqs), 
+             structure(c("CCTTCTACCACTGTCTTCAATT", "GGAGAATCCTTTTGTTATTTCCTGGAAATGCTTGAATCATAGATGAGTCTCTTCCTGCGTCCGTGTATTTCAGCTGCAGTTTCCAAGTGTGTAATAGTGCTGTCCACAAGGAATAGCTGCTGTTACTGTAAATT", "CTATGCCCTTCTGCGAGGTCAGAAAGGGCACGCACTCACACCCGTCCCACCTTCAATT", "ATATGAGTAGGACAGTTGGCAGATGAAATT", "TTATGAAGCCCGTTCTTCAGAAAGGTTTATAGCACTTTCGTTAAACCTCCTTCCTGTTCAAAATGCAGCGCACTAGAGTATTTTTCCCCAATCCACCGTTAAGCGGCTTCTTCTTAAGCAGGACTGTTTTGGGTCTCTTGGTTGCTACCCCTACTACACCCTACTAATATGTTGCACAAAGCGACGGGGAACCCCTTCTCCCCCAAACGATGTGCGTGGAAACACACAATGTCCCACTCTCTCCATTCCCAGAAACCTAGACTCTCCCCTCAAATACCTTTCCTGGCTCATCTACAGCACTAAGGTCTCAAGGTAGGGGCAAAAGCCCGCGACGATT", "GAACATCTCACCCGGATTTTTTACTGACTCCACTAAAATT"), .Names = c("GQKHUJB01AS3TK", "GQKHUJB01A92GD", "GQKHUJB01AXJRO", "GQKHUJB01A3C99", "GQKHUJB01BCP6X", "GQKHUJB01AL0CB")))
+
+subjectSeqs <- extractFeature(seqProps, feature='decoded', sector = "1", 
+                              samplename = samplename)[[1]][[1]]
+subjectSeqs <- head(subjectSeqs)
+expect_equal(as.character(subjectSeqs), 
+             structure(c("TGATTGACTACCCGTCAGCGGGGGTCTTTCACCTTCTACCACTGTCTTCAATTGTCCCTTAAGCGGAGCCC", "TGATTGACTACCCGTCAGCGGGGGGTCTTTCAGGAGAATCCTTTTGTTATTTCCTGGAAATGCTTGAATCATAGATGAGTCTCTTCCTGCGTCCGTGTATTTCAGCTGCAGTTTCCAAGTGTGTAATAGTGCTGTCCACAAGGAATAGCTGCTGTTACTGTAAATTGTCCCTTAAGCGGAGCCC", "TGATTGACTACCCGTCAGCGGGGGTCTTTCACTATGCCCTTCTGCGAGGTCAGAAAGGGCACGCACTCACACCCGTCCCACCTTCAATTGTCCCTTAAGCGGAGCCC", "TGATTGACTACCCGTCAGCGGGGGTCTTTCAATATGAGTAGGACAGTTGGCAGATGAAATTGTCCCTTAAGCGGAGCCC", "TGATTGACTACCCGTCAGCGGGGGGTCTTTCATTATGAAGCCCGTTCTTCAGAAAGGTTTATAGCACTTTCGTTAAACCTCCTTCCTGTTCAAAATGCAGCGCACTAGAGTATTTTTCCCCAATCCACCGTTAAGCGGCTTCTTCTTAAGCAGGACTGTTTTGGGTCTCTTGGTTGCTACCCCTACTACACCCTACTAATATGTTGCACAAAGCGACGGGGAACCCCTTCTCCCCCAAACGATGTGCGTGGAAACACACAATGTCCCACTCTCTCCATTCCCAGAAACCTAGACTCTCCCCTCAAATACCTTTCCTGGCTCATCTACAGCACTAAGGTCTCAAGGTAGGGGCAAAAGCCCGCGACGATTGTCCCTTAAGCGGA", "TGATTGACTACCCGTCAGCGGGGGTCTTTCAGAACATCTCACCCGGATTTTTTACTGACTCCACTAAAATTGTCCCTTAAGCGGAGCCC"), .Names = c("GQKHUJB01AS3TK", "GQKHUJB01A92GD", "GQKHUJB01AXJRO", "GQKHUJB01A3C99", "GQKHUJB01BCP6X", "GQKHUJB01AL0CB")))
+
+patternSeq <- extractFeature(seqProps, feature = 'primerltrsequence' , sector = "1",
+                             samplename = samplename)
+patternSeq <- patternSeq[[1]][[1]]
+expect_equal(patternSeq, "TGATTGACTACCCGTCAGCGG")
+
+#### test pairwise alignments to primers ####
+res <- pairwiseAlignSeqs(subjectSeqs, patternSeq, qualityThreshold = 0.85)
+expect_that(res, is_identical_to(
+  new("IRanges", start = c(1L, 1L, 1L, 1L, 1L, 1L) , 
+      width = c(21L, 21L, 21L, 21L, 21L, 21L), 
+      NAMES = c("GQKHUJB01AS3TK", "GQKHUJB01A92GD", "GQKHUJB01AXJRO", 
+                "GQKHUJB01A3C99", "GQKHUJB01BCP6X", "GQKHUJB01AL0CB"), 
+      elementType = "integer", elementMetadata = NULL, metadata = list())))
+
+#### test pairwise alignments to linkers ####
+patternSeq <- extractFeature(seqProps, feature='linkersequence' ,sector = "1", 
+                             samplename = samplename)
+patternSeq <- patternSeq[[1]][[1]]
+expect_equal(patternSeq, "GTCCCTTAAGCGGAGCCCT")
+
+res <- pairwiseAlignSeqs(subjectSeqs, patternSeq, qualityThreshold=0.55,
+                         side="middle")
+expect_that(res, is_identical_to(
+  new("IRanges", 
+      start = c(54L, 167L, 90L, 62L, 370L, 72L), 
+      width = c(18L, 18L, 18L, 18L, 14L, 18L), 
+      NAMES = c("GQKHUJB01AS3TK", "GQKHUJB01A92GD", "GQKHUJB01AXJRO", 
+                "GQKHUJB01A3C99", "GQKHUJB01BCP6X", "GQKHUJB01AL0CB"),
+      elementType = "integer", elementMetadata = NULL , metadata = list())))
+
+#### test pairwise alignments to linkers with primerID ####
+ids <- c("GGTTCTACGT", "AGGAGTATGA", "TGTCGGTATA", "GTTATAAAAC", "AGGCTATATC", 
+         "ATGGTTTGTT")
+subjectSeqs <- xscat(subjectSeqs, xscat(ids,"TTTTTTTTTTT"))
+patternSeq <- "AAGCGGAGCCCNNNNNNNNNNTTTTTTTTTTT"
+res <- primerIDAlignSeqs(subjectSeqs, patternSeq, doAnchored = TRUE)
+expect_that(res, is_identical_to(
+  new("CompressedIRangesList", elementType = "IRanges", elementMetadata = NULL,
+      metadata = list(), 
+      partitioning = new("PartitioningByEnd", end = c(5L, 10L), 
+                         NAMES = c("hits", "primerIDs"), elementType = "integer"
+                         , elementMetadata = NULL, metadata = list()), 
+      unlistData = new("IRanges", 
+                       start = c(61L, 174L, 97L, 69L, 79L, 72L, 185L, 108L, 
+                                 80L, 90L), 
+                       width = c(32L, 32L, 32L, 32L, 32L, 10L, 10L, 10L, 10L, 
+                                 10L),
+                       NAMES = c("read 1", "read 2", "read 3", "read 4", 
+                                 "read 6", "read 1", "read 2", "read 3", 
+                                 "read 4", "read 6"), elementType = "integer",
+                       elementMetadata = NULL, metadata = list()
+                      ))))
+
+#### test writers & readers ####
+psl <- head(extractFeature(seqProps, feature='psl', sector = "1", 
+                           samplename = samplename)[[1]][[1]])
+expect_that(write.psl(psl), prints_text("out.psl"))
+expect_that(file.remove("out.psl"), is_true())
+
+#### test utils ####
+})