Rework createdb to correctly allow for only one directory or (new) ts…

…v input, in additonal to loose files
steineggerlab · Mar 4, 2024 · e1394aa · e1394aa
1 parent 0c3b7f2
commit e1394aa
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Showing 2 changed files with 50 additions and 13 deletions.
diff --git a/src/FoldseekBase.cpp b/src/FoldseekBase.cpp
@@ -16,11 +16,19 @@ void (*validatorUpdate)(void) = updateValdiation;
 
 std::vector<Command> foldseekCommands = {
         {"createdb",             structcreatedb,                &localPar.structurecreatedb,    COMMAND_MAIN,
-                "Convert PDB/mmCIF/tar[.gz]/DB files to a db",
-                "Convert PDB/mmCIF/tar[.gz]/DB files to a db",
+                "Convert PDB/mmCIF/tar[.gz]/DB files or directory/TSV to a structure DB",
+                "# Process multiple files\n"
+                "foldseek createdb examples/1tim.pdb.gz examples/8tim.pdb.gz DB\n"
+                "# Process a directory containing PDB|mmCIF[.gz]|tar[.gz]|DB recursively, only one directory can be given\n"
+                "foldseek createdb examples/ DB\n"
+                "# Process a TSV file with a list of PDB|mmCIF[.gz]|tar[.gz]|DB, only one TSV can be given\n"
+                "foldseek createdb examples.tsv DB\n"
+                "# Process a directory or tar file and filter based on file name\n"
+                "# Note: --file-include and --file-exclude only apply to directory or tar input\n"
+                "foldseek createdb examples/ --file-include \"pdb.gz$\"\n",
                 "Martin Steinegger <martin.steinegger@snu.ac.kr>",
-                "<i:PDB|mmCIF[.gz]|tar|DB> ... <i:PDB|mmCIF[.gz]|tar|DB> <o:sequenceDB>",
-                CITATION_FOLDSEEK, {{"PDB|mmCIF[.gz]|stdin|tar|DB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA | DbType::VARIADIC,
+                "<i:directory|.tsv>|<i:PDB|mmCIF[.gz]|tar[.gz]|DB> ... <i:PDB|mmCIF[.gz]|tar|DB> <o:sequenceDB>",
+                CITATION_FOLDSEEK, {{"PDB|mmCIF[.gz]|stdin|tar[.gz]|DB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA | DbType::VARIADIC,
 #ifdef HAVE_GCS
                                             &DbValidator::flatfileStdinGenericUri
 #else

diff --git a/src/strucclustutils/structcreatedb.cpp b/src/strucclustutils/structcreatedb.cpp
@@ -250,10 +250,21 @@ int structcreatedb(int argc, const char **argv, const Command& command) {
     std::string outputName = par.filenames.back();
     par.filenames.pop_back();
 
-
     PatternCompiler include(par.fileInclude.c_str());
     PatternCompiler exclude(par.fileExclude.c_str());
-    if (par.filenames.size() == 1 && FileUtil::directoryExists(par.filenames.back().c_str())) {
+
+    for (size_t i = 1; i < par.filenames.size(); ++i) {
+        if (FileUtil::directoryExists(par.filenames[i].c_str()) || Util::endsWith(".tsv", par.filenames[i].c_str())) {
+            Debug(Debug::ERROR) << "Only one directory or tsv file (" << par.filenames[i] << ") or a list of files can be given\n";
+            EXIT(EXIT_FAILURE);
+        }
+    }
+
+    if (FileUtil::directoryExists(par.filenames[0].c_str())) {
+        if (par.filenames.size() > 1) {
+            Debug(Debug::ERROR) << "Only one directory can be given\n";
+            EXIT(EXIT_FAILURE);
+        }
         std::vector<std::string> dirs;
         dirs.push_back(par.filenames.back());
         par.filenames.pop_back();
@@ -266,22 +277,40 @@ int structcreatedb(int argc, const char **argv, const Command& command) {
             }
             while (dirent* entry = readdir(handle)) {
                 std::string filename(entry->d_name);
-
-                if (filename != "." && filename !="..") {
+                if (filename != "." && filename != "..") {
                     std::string fullpath = dir + "/" + filename;
                     struct stat info;
                     stat(fullpath.c_str(), &info);
-		    if (info.st_mode & S_IFDIR) {
+                    if (info.st_mode & S_IFDIR) {
                         dirs.push_back(fullpath);
-                    } else {
-                        if (include.isMatch(filename.c_str()) == true && exclude.isMatch(filename.c_str()) == false) {
-                            par.filenames.push_back(fullpath);
-                        }
+                    } else if (include.isMatch(filename.c_str()) == true && exclude.isMatch(filename.c_str()) == false) {
+                        par.filenames.push_back(fullpath);
                     }
                 }
             }
             closedir(handle);
         }
+    } else if (Util::endsWith(".tsv", par.filenames[0])) {
+        if (par.filenames.size() > 1) {
+            Debug(Debug::ERROR) << "Only one tsv file can be given\n";
+            EXIT(EXIT_FAILURE);
+        }
+        std::string tsv = par.filenames.back();
+        par.filenames.pop_back();
+
+        FILE* file = FileUtil::openFileOrDie(tsv.c_str(), "r", true);
+        char* line = NULL;
+        size_t len = 0;
+        ssize_t read;
+        while ((read = getline(&line, &len, file)) != -1) {
+            if (line[read - 1] == '\n') {
+                line[read - 1] = '\0';
+                read--;
+            }
+            par.filenames.push_back(line);
+        }
+        free(line);
+        fclose(file);
     }
 
     Debug(Debug::INFO) << "Output file: " << outputName << "\n";