added group_bam2isoform.cpp testing files

mritchielab · Jul 10, 2023 · 292ca2b · 292ca2b
1 parent ae50f71
commit 292ca2b
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diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -40,3 +40,7 @@ find_barcode <- function(fastq_dir, stats_file, out_fastq, ref_csv, MAX_DIST, UM
  invisible(.Call(`_FLAMES_find_barcode`, fastq_dir, stats_file, out_fastq, ref_csv, MAX_DIST, UMI_LEN))
 }
 
+testfunc <- function(gff3, genome_bam, isoform_gff3, tss_tes_stat, genomefa, transcript_fa, isoform_parameters, raw_splice_isoform) {
+ invisible(.Call(`_FLAMES_testfunc`, gff3, genome_bam, isoform_gff3, tss_tes_stat, genomefa, transcript_fa, isoform_parameters, raw_splice_isoform))
+}
+
diff --git a/R/testfuncs.R b/R/testfuncs.R
@@ -0,0 +1,21 @@
+#' @export
+testfuncR <- function() {
+ # data <- "/stornext/General/data/user_managed/grpu_mritchie_1/Oliver/FLAMESTesting/FLAMESData/FLAMESbulkdata/SIRV/"
+ data <- "/Volumes/MattLab/Oliver/FLAMESTesting/FLAMESData/FLAMESbulkdata/SIRV/"
+ genome_bam <- paste0(data, "FLAMESout/align2genome.bam")
+ gff3 <- paste0(data,"SIRV_isoforms_multi-fasta-annotation_C_170612a.gtf")
+ genomefa <- paste0(data, "SIRV_isoforms_multi-fasta_170612a.fasta")
+ config_file <- paste0(data, "SIRV_config_default.json")
+
+ out = paste0(tempdir(), "/")
+ isoform_gff3 <- paste0(out, "isoform_annotated.gff3")
+ tss_tes_stat <- paste0(out, "tss_tes.bedgraph")
+ transcript_fa <- paste0(out, "transcript_assembly.fa")
+
+ config <- jsonlite::fromJSON(config_file)
+
+ file.exists(c(genome_bam, gff3, genomefa, config_file))
+ testfunc(gff3, genome_bam, isoform_gff3, tss_tes_stat, genomefa, transcript_fa, config$isoform_parameters, "")
+
+ print(out)
+}
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -25,9 +25,27 @@ BEGIN_RCPP
  return R_NilValue;
 END_RCPP
 }
+// testfunc
+void testfunc(const std::string& gff3, const std::string& genome_bam, const std::string& isoform_gff3, const std::string& tss_tes_stat, const std::string& genomefa, const std::string& transcript_fa, const Rcpp::List& isoform_parameters, const std::string& raw_splice_isoform);
+RcppExport SEXP _FLAMES_testfunc(SEXP gff3SEXP, SEXP genome_bamSEXP, SEXP isoform_gff3SEXP, SEXP tss_tes_statSEXP, SEXP genomefaSEXP, SEXP transcript_faSEXP, SEXP isoform_parametersSEXP, SEXP raw_splice_isoformSEXP) {
+BEGIN_RCPP
+ Rcpp::RNGScope rcpp_rngScope_gen;
+ Rcpp::traits::input_parameter< const std::string& >::type gff3(gff3SEXP);
+ Rcpp::traits::input_parameter< const std::string& >::type genome_bam(genome_bamSEXP);
+ Rcpp::traits::input_parameter< const std::string& >::type isoform_gff3(isoform_gff3SEXP);
+ Rcpp::traits::input_parameter< const std::string& >::type tss_tes_stat(tss_tes_statSEXP);
+ Rcpp::traits::input_parameter< const std::string& >::type genomefa(genomefaSEXP);
+ Rcpp::traits::input_parameter< const std::string& >::type transcript_fa(transcript_faSEXP);
+ Rcpp::traits::input_parameter< const Rcpp::List& >::type isoform_parameters(isoform_parametersSEXP);
+ Rcpp::traits::input_parameter< const std::string& >::type raw_splice_isoform(raw_splice_isoformSEXP);
+ testfunc(gff3, genome_bam, isoform_gff3, tss_tes_stat, genomefa, transcript_fa, isoform_parameters, raw_splice_isoform);
+ return R_NilValue;
+END_RCPP
+}
 
 static const R_CallMethodDef CallEntries[] = {
  {"_FLAMES_find_barcode", (DL_FUNC) &_FLAMES_find_barcode, 6},
+ {"_FLAMES_testfunc", (DL_FUNC) &_FLAMES_testfunc, 8},
  {NULL, NULL, 0}
 };