added find_isoform

src/main-functions/find_isoform.cpp

@@ -0,0 +1,79 @@
+#include "find_isoform.h"
+
+#include <string>
+#include <unordered_map>
+#include <vector>
+#include <utility>
+
+#include "../classes/GFFData.h"
+#include "../classes/GeneAnnotationParser.h"
+#include "../classes/junctions.h"
+#include "../classes/Pos.h"
+#include "get_transcript_seq.h"
+#include "group_bam2isoform.h"
+
+void
+find_isoform
+(
+ 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)
+{
+ Rcpp::Rcout << "#### Reading Gene Annotations\n";
+
+ GFFData gene_annotation = parse_gff_file(gff3);
+
+ std::unordered_map<std::string, Junctions>
+ transcript_to_junctions = map_transcripts_to_junctions(
+ gene_annotation.transcript_to_exon
+ );
+
+ gene_annotation.gene_to_transcript = remove_similar_tr(
+ gene_annotation.gene_to_transcript,
+ gene_annotation.transcript_to_exon,
+ 10
+ );
+
+ std::unordered_map<std::string, std::vector<exon>>
+ gene_dict = get_gene_flat(
+ gene_annotation.gene_to_transcript,
+ gene_annotation.transcript_to_exon
+ );
+
+ std::unordered_map<std::string, std::vector<GeneBlocks>>
+ chr_to_blocks = get_gene_blocks(
+ gene_dict, 
+ gene_annotation.chr_to_gene,
+ gene_annotation.gene_to_transcript
+ );
+
+ // GROUP_BAM2ISOFORM
+ group_bam2isoform(
+ genome_bam,
+ isoform_gff3,
+ tss_tes_stat,
+ gene_dict,
+ transcript_to_junctions,
+ gene_annotation.transcript_dict,
+ chr_to_blocks,
+ genomefa,
+ isoform_parameters,
+ raw_splice_isoform
+ );
+
+ GFFData isoform_annotation = parse_gff_file(isoform_gff3);
+
+ // get_transcript_seq
+ get_transcript_seq(
+ genomefa,
+ transcript_fa,
+ isoform_annotation,
+ gene_annotation
+ ); // - This does not modify values that are used later (it modifies chr_to_blocks, but only transcript_dict_i and transcript_dict are used later.)
+ return;
+}

src/main-functions/find_isoform.h

@@ -0,0 +1,22 @@
+#ifndef FIND_ISOFORM_H
+#define FIND_ISOFORM_H
+
+#include <Rcpp.h>
+
+#include <string>
+
+#include "../classes/Pos.h"
+
+void
+find_isoform
+(
+ 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);
+
+#endif // FIND_ISOFORM_H