Merge pull request #44 from ComparativeGenomicsToolkit/chop

Add some subpath naming support
ComparativeGenomicsToolkit · May 6, 2021 · b34a0f7 · b34a0f7
2 parents 1244493 + 2860c3a
commit b34a0f7
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Showing 2 changed files with 69 additions and 1 deletion.
diff --git a/clip-vg.cpp b/clip-vg.cpp
@@ -56,9 +56,49 @@ static void replace_path_name_substrings(MutablePathMutableHandleGraph* graph, c
 static void forwardize_paths(MutablePathMutableHandleGraph* graph, const string& ref_prefix, bool progress);
 static vector<unordered_set<nid_t>> weakly_connected_components(const HandleGraph* graph);
 
+
+// from path.cpp in vg
+// Check if using subpath naming scheme.  If it is return true,
+// the root path name, and the offset (false otherwise)
+// formats accepted:
+// name[start]  (0-based)
+// name[start-end] (0-based, open-ended like BED, end defaults to 0 in above case)
+static tuple<bool, string, size_t, size_t>parse_subpath_name(const string& path_name) {
+    size_t tag_offset = path_name.rfind("[");
+    if (tag_offset == string::npos || tag_offset + 2 >= path_name.length() || path_name.back() != ']') {
+        return make_tuple(false, "", 0, 0);
+    } else {
+        string offset_str = path_name.substr(tag_offset + 1, path_name.length() - tag_offset - 2);
+        size_t sep_offset = offset_str.find("-");
+        string end_offset_str;
+        if (sep_offset != string::npos && !offset_str.empty() && sep_offset < offset_str.length() - 1) {
+            end_offset_str = offset_str.substr(sep_offset + 1, offset_str.length() - sep_offset - 1);
+            offset_str = offset_str.substr(0, sep_offset);
+        }
+        size_t offset_val;
+        size_t end_offset_val = 0;
+        try {
+           offset_val = std::stol(offset_str);
+           if (!end_offset_str.empty()) {
+               end_offset_val = std::stol(end_offset_str);
+           }
+        } catch(...) {
+            return make_tuple(false, "", 0, 0);
+        }
+        return make_tuple(true, path_name.substr(0, tag_offset), offset_val, end_offset_val);
+    }
+}
+
 // Create a subpath name (todo: make same function in vg consistent (it only includes start))
 static inline string make_subpath_name(const string& path_name, size_t offset, size_t length) {
-    return path_name + "[" + std::to_string(offset) + "-" + std::to_string(offset + length) + "]";
+    tuple<bool, string, size_t, size_t> parsed_name = parse_subpath_name(path_name);
+    size_t cur_offset = 0;
+    const string* cur_name = &path_name;
+    if (get<0>(parsed_name)) {
+        cur_offset = get<2>(parsed_name);
+        cur_name = &get<1>(parsed_name);
+    }
+    return *cur_name + "[" + std::to_string(cur_offset + offset) + "-" + std::to_string(cur_offset + offset + length) + "]";
 }
 
 int main(int argc, char** argv) {

diff --git a/hal2vg.cpp b/hal2vg.cpp
@@ -96,6 +96,8 @@ static void pinch_to_handle(const Genome* genome,
 
 static void chop_graph(MutablePathMutableHandleGraph& graph, size_t maxNodeLength);
 
+static void resolve_subpath_naming(string& path_name);
+
 int main(int argc, char** argv) {
     CLParser optionsParser;
     initParser(&optionsParser);
@@ -641,6 +643,11 @@ void pinch_to_handle(const Genome* genome,
         int64_t seqID = nameToID.find(seqName)->second;
         stPinchThread* thread = stPinchThreadSet_getThread(threadSet, seqID);
 
+        // cactus_graphmap_split can make paths like contig_sub_1_3.  here we convert that
+        // into a format vg can (sometimes) understand contig[1-3].
+        // (the reason we go through this is that assembly hubs can't handle any special characters apparently)
+        resolve_subpath_naming(seqName);
+
         // create the path
         path_handle_t pathHandle = graph.create_path_handle(seqName);
         string pathString;
@@ -763,3 +770,24 @@ void chop_graph(MutablePathMutableHandleGraph& graph, size_t maxNodeLength) {
         graph.divide_handle(handle, offsets);
     }
 }
+
+void resolve_subpath_naming(string& path_name) {
+    size_t sp = path_name.rfind("_sub_");
+    if (sp != string::npos) {
+        size_t up = path_name.rfind("_");
+        if (up != string::npos && up > sp + 1) {
+            int64_t start;
+            int64_t end;
+            try {
+                start = stol(path_name.substr(sp + 5, up - sp - 5));
+                end = stol(path_name.substr(up + 1));
+            } catch (...) {
+                return;
+            }
+            stringstream new_name;
+            new_name << path_name.substr(0, sp) << "[" << start << "-" << end << "]";
+            path_name = new_name.str();
+        }
+    }
+    return;
+}