Solves multiprocessing pandora map --discover issue with GATB graph…

… creation (closes #195)
iqbal-lab-org · Nov 15, 2019 · 951717a · 951717a
1 parent bd4dbee
commit 951717a
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Showing 7 changed files with 66 additions and 64 deletions.
diff --git a/include/denovo_discovery/denovo_discovery.h b/include/denovo_discovery/denovo_discovery.h
@@ -21,7 +21,7 @@ class DenovoDiscovery {
     DenovoDiscovery(const uint_least8_t& kmer_size, const double& read_error_rate,
         const uint8_t max_insertion_size = 15);
 
-    void find_paths_through_candidate_region(CandidateRegion& candidate_region);
+    void find_paths_through_candidate_region(CandidateRegion& candidate_region, const fs::path &denovo_output_directory);
 
     double calculate_kmer_coverage(
         const uint32_t& read_covg, const uint32_t& ref_length) const;

diff --git a/include/denovo_discovery/local_assembly.h b/include/denovo_discovery/local_assembly.h
@@ -58,7 +58,7 @@ bool string_ends_with(std::string const& query, std::string const& ending);
 
 std::string reverse_complement(const std::string& forward);
 
-void remove_graph_file();
+void remove_graph_file (const fs::path &prefix);
 
 std::vector<std::string> generate_start_kmers(
     const std::string& sequence, const uint16_t& k, uint32_t num_to_generate);

diff --git a/src/denovo_discovery/denovo_discovery.cpp b/src/denovo_discovery/denovo_discovery.cpp
@@ -1,14 +1,15 @@
 #include "denovo_discovery/denovo_discovery.h"
 
 void DenovoDiscovery::find_paths_through_candidate_region(
-    CandidateRegion& candidate_region)
+    CandidateRegion& candidate_region, const fs::path &denovo_output_directory)
 {
     const auto read_covg { candidate_region.pileup.size() };
     const auto length_of_candidate_sequence {
         candidate_region.max_likelihood_sequence.length()
     };
     const double expected_kmer_covg { calculate_kmer_coverage(
         read_covg, length_of_candidate_sequence) };
+    const fs::path GATB_graph_filepath (denovo_output_directory / "GATB_graph");
 
     BOOST_LOG_TRIVIAL(debug) << "Running local assembly for: "
                              << candidate_region.get_name() << " - interval ["
@@ -32,10 +33,11 @@ void DenovoDiscovery::find_paths_through_candidate_region(
     LocalAssemblyGraph graph;
 
     try {
+        const std::string GATB_graph_filepath_as_string = GATB_graph_filepath.string();
         Graph gatb_graph
             = LocalAssemblyGraph::create(new BankStrings(candidate_region.pileup),
-                "-kmer-size %d -abundance-min %d -verbose 0 -nb-cores 1", kmer_size,
-                min_covg_for_node_in_assembly_graph);
+                "-kmer-size %d -abundance-min %d -verbose 0 -nb-cores 1 -out %s", kmer_size,
+                min_covg_for_node_in_assembly_graph, GATB_graph_filepath_as_string.c_str());
         if (clean_assembly_graph) {
             clean(gatb_graph);
         }
@@ -44,7 +46,7 @@ void DenovoDiscovery::find_paths_through_candidate_region(
     } catch (gatb::core::system::Exception& error) {
         BOOST_LOG_TRIVIAL(debug) << "Couldn't create GATB graph."
                                  << "\n\tEXCEPTION: " << error.getMessage();
-        remove_graph_file();
+        remove_graph_file(GATB_graph_filepath);
         return;
     }
 
@@ -76,7 +78,7 @@ void DenovoDiscovery::find_paths_through_candidate_region(
                     start_node, end_node, max_path_length, expected_kmer_covg);
 
                 if (abandoned) {
-                    remove_graph_file();
+                    remove_graph_file(GATB_graph_filepath);
                     return;
                 }
 
@@ -105,7 +107,7 @@ void DenovoDiscovery::find_paths_through_candidate_region(
                                   .append(candidate_region.right_flanking_sequence);
                     }
 
-                    remove_graph_file();
+                    remove_graph_file(GATB_graph_filepath);
                     return;
                 }
             }
@@ -114,7 +116,7 @@ void DenovoDiscovery::find_paths_through_candidate_region(
     BOOST_LOG_TRIVIAL(debug) << "Could not find any combination of start and end "
                                 "k-mers. Skipping local assembly for "
                              << candidate_region.get_name();
-    remove_graph_file();
+    remove_graph_file(GATB_graph_filepath);
 }
 
 DenovoDiscovery::DenovoDiscovery(const uint_least8_t& kmer_size,

diff --git a/src/denovo_discovery/local_assembly.cpp b/src/denovo_discovery/local_assembly.cpp
@@ -245,10 +245,10 @@ void LocalAssemblyGraph::build_paths_between(const std::string& start_kmer,
     }
 }
 
-void remove_graph_file()
+void remove_graph_file (const fs::path &prefix)
 {
-    const fs::path p { "dummy.h5" };
-    fs::remove(p);
+    const fs::path h5_file(prefix.string() + ".h5");
+    fs::remove(h5_file);
 }
 
 void clean(Graph& graph, const uint16_t& num_cores)

diff --git a/src/map_main.cpp b/src/map_main.cpp
@@ -487,7 +487,7 @@ int pandora_map(int argc, char *argv[]) {
 
         for (auto &element : candidate_regions) {
             auto &candidate_region {element.second};
-            denovo.find_paths_through_candidate_region(candidate_region); //TODO: this is hard to parallelize due to GATB's temp files
+            denovo.find_paths_through_candidate_region(candidate_region, denovo_output_directory); //TODO: this is hard to parallelize due to GATB's temp files
             candidate_region.write_denovo_paths_to_file(denovo_output_directory);
         }
     }

diff --git a/test/denovo_discovery/denovo_discovery_test.cpp b/test/denovo_discovery/denovo_discovery_test.cpp
@@ -109,7 +109,7 @@ TEST(FindPathsThroughCandidateRegionTest, emptyPileupReturnsEmpty)
     CandidateRegion candidate_region { Interval(0, 1), "test" };
     candidate_region.max_likelihood_sequence = "ATGCGCTGAGAGTCGGACT";
 
-    denovo.find_paths_through_candidate_region(candidate_region);
+    denovo.find_paths_through_candidate_region(candidate_region, ".");
 
     const DenovoPaths expected;
     const auto& actual { candidate_region.denovo_paths };
@@ -126,7 +126,7 @@ TEST(FindPathsThroughCandidateRegionTest, kmerSizeBiggerThanCandidateReturnsEmpt
     candidate_region.max_likelihood_sequence = "ATGCGCTGAGAGTCGGACT";
     candidate_region.pileup = { "FOO", "BAR" };
 
-    denovo.find_paths_through_candidate_region(candidate_region);
+    denovo.find_paths_through_candidate_region(candidate_region, ".");
 
     const DenovoPaths expected;
     const auto& actual { candidate_region.denovo_paths };
@@ -144,7 +144,7 @@ TEST(FindPathsThroughCandidateRegionTest,
     candidate_region.max_likelihood_sequence = "ATGCGCTGAGAGTCGGACT";
     candidate_region.pileup = { "FOO", "BAR" };
 
-    denovo.find_paths_through_candidate_region(candidate_region);
+    denovo.find_paths_through_candidate_region(candidate_region, ".");
 
     const DenovoPaths expected;
     const auto& actual { candidate_region.denovo_paths };
@@ -161,7 +161,7 @@ TEST(FindPathsThroughCandidateRegionTest, startKmersDontExistInGraphReturnEmpty)
     candidate_region.max_likelihood_sequence = "GGGGGGGGGGAGTCGGACT";
     candidate_region.pileup = { "ATGCGCTGAGAGTCGGACT", "ATGCGCTGAGAGTCGGACT" };
 
-    denovo.find_paths_through_candidate_region(candidate_region);
+    denovo.find_paths_through_candidate_region(candidate_region, ".");
 
     const DenovoPaths expected;
     const auto& actual { candidate_region.denovo_paths };
@@ -178,7 +178,7 @@ TEST(FindPathsThroughCandidateRegionTest, endKmersDontExistInGraphReturnEmpty)
     candidate_region.max_likelihood_sequence = "ATGCGCTGAGCCCCCCCCC";
     candidate_region.pileup = { "ATGCGCTGAGAGTCGGACT", "ATGCGCTGAGAGTCGGACT" };
 
-    denovo.find_paths_through_candidate_region(candidate_region);
+    denovo.find_paths_through_candidate_region(candidate_region, ".");
 
     const DenovoPaths expected;
     const auto& actual { candidate_region.denovo_paths };
@@ -196,7 +196,7 @@ TEST(FindPathsThroughCandidateRegionTest, endKmerExistsInStartKmersFindPathAndCy
     candidate_region.max_likelihood_sequence = "ATGCGCTGAGATGCGCTGA";
     candidate_region.pileup = { "ATGCGCTGACATGCGCTGA", "ATGCGCTGACATGCGCTGA" };
 
-    denovo.find_paths_through_candidate_region(candidate_region);
+    denovo.find_paths_through_candidate_region(candidate_region, ".");
 
     const DenovoPaths expected { "ATGCGCTGACATGCGCTGA", "ATGCGCTGACATGCGCTGACATGCGCTGA",
         "ATGCGCTGACATGCGCTGACATGCGCTGACATGCGCTGA",
@@ -220,7 +220,7 @@ TEST(FindPathsThroughCandidateRegionTest,
     candidate_region.pileup
         = { "ATGCGCTGAGAGTCGGACT", "ATGCGCTGAGAGTCGGACT", "AAATAAA", "GCGGCGCGGCC" };
 
-    denovo.find_paths_through_candidate_region(candidate_region);
+    denovo.find_paths_through_candidate_region(candidate_region, ".");
 
     const DenovoPaths expected { "ATGCGCTGAGAGTCGGACT" };
     const auto& actual { candidate_region.denovo_paths };
@@ -237,7 +237,7 @@ TEST(FindPathsThroughCandidateRegionTest, twoIdenticalReadsReturnOnePath)
     candidate_region.max_likelihood_sequence = "ATGCGCTGAGAGTCGGACT";
     candidate_region.pileup = { "ATGCGCTGAGAGTCGGACT", "ATGCGCTGAGAGTCGGACT" };
 
-    denovo.find_paths_through_candidate_region(candidate_region);
+    denovo.find_paths_through_candidate_region(candidate_region, ".");
 
     const DenovoPaths expected { "ATGCGCTGAGAGTCGGACT" };
     const auto& actual { candidate_region.denovo_paths };
@@ -255,7 +255,7 @@ TEST(
     candidate_region.max_likelihood_sequence = "ATGCGCTGAGAGTCGGACT";
     candidate_region.pileup = { "ATGCGCTGAGAGTCGGACT", "ATGCGCTGATAGTCGGACT" };
 
-    denovo.find_paths_through_candidate_region(candidate_region);
+    denovo.find_paths_through_candidate_region(candidate_region, ".");
 
     const DenovoPaths expected;
     const auto& actual { candidate_region.denovo_paths };
@@ -274,7 +274,7 @@ TEST(FindPathsThroughCandidateRegionTest,
     candidate_region.pileup
         = { "ATGCGCTGAGAGTCGGACT", "ATGCGCTGAGAGTCGGACT", "ATGCGCTGATAGTCGGACT" };
 
-    denovo.find_paths_through_candidate_region(candidate_region);
+    denovo.find_paths_through_candidate_region(candidate_region, ".");
 
     const DenovoPaths expected { "ATGCGCTGAGAGTCGGACT" };
     const auto& actual { candidate_region.denovo_paths };
@@ -292,7 +292,7 @@ TEST(FindPathsThroughCandidateRegionTest, twoPossiblePathsWithGoodCovgReturnsTwo
     candidate_region.pileup = { "ATGCGCTGAGAGTCGGACT", "ATGCGCTGAGAGTCGGACT",
         "ATGCGCTGATAGTCGGACT", "ATGCGCTGATAGTCGGACT" };
 
-    denovo.find_paths_through_candidate_region(candidate_region);
+    denovo.find_paths_through_candidate_region(candidate_region, ".");
     std::sort(
         candidate_region.denovo_paths.begin(), candidate_region.denovo_paths.end());