Add easy parsable tsv output to databases

soedinglab · Jul 20, 2022 · 1c739ae · 1c739ae
1 parent ba4e11f
commit 1c739ae
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Showing 2 changed files with 22 additions and 1 deletion.
diff --git a/src/commons/Parameters.cpp b/src/commons/Parameters.cpp
@@ -1303,6 +1303,7 @@ Parameters::Parameters():
 
     databases.push_back(&PARAM_HELP);
     databases.push_back(&PARAM_HELP_LONG);
+    databases.push_back(&PARAM_TSV);
     databases.push_back(&PARAM_REUSELATEST);
     databases.push_back(&PARAM_REMOVE_TMP_FILES);
     databases.push_back(&PARAM_COMPRESSED);

diff --git a/src/workflow/Databases.cpp b/src/workflow/Databases.cpp
@@ -234,6 +234,22 @@ std::string listDatabases(const Command &command, std::vector<DatabaseDownload>
     return description;
 }
 
+std::string listDatabasesTsv(std::vector<DatabaseDownload> &downloads) {
+    std::string description;
+    description.reserve(1024);
+    for (size_t i = 0; i < downloads.size(); ++i) {
+        description.append(downloads[i].name);
+        description.append(1, '\t');
+        description.append(Parameters::getDbTypeName(downloads[i].dbType));
+        description.append(1, '\t');
+        description.append(downloads[i].hasTaxonomy ? "true" : "false");
+        description.append(1, '\t');
+        description.append(downloads[i].url);
+        description.append(1, '\n');
+    }
+    return description;
+}
+
 int databases(int argc, const char **argv, const Command &command) {
     Parameters &par = Parameters::getInstance();
     par.parseParameters(argc, argv, command, false, Parameters::PARSE_ALLOW_EMPTY, 0);
@@ -244,7 +260,11 @@ int databases(int argc, const char **argv, const Command &command) {
     }
     std::string description = listDatabases(command, usedDownloads, par.help);
     if (par.filenames.size() == 0 || par.help) {
-        par.printUsageMessage(command, par.help ? MMseqsParameter::COMMAND_EXPERT : 0, description.c_str());
+        if (par.tsvOut) {
+                Debug(Debug::INFO) << listDatabasesTsv(usedDownloads);
+        } else {
+                par.printUsageMessage(command, par.help ? MMseqsParameter::COMMAND_EXPERT : 0, description.c_str());
+        }
         EXIT(EXIT_SUCCESS);
     }