Change createdb.cpp so that it takes in ".txt" file containing paths of different fasta files

src/MMseqsBase.cpp

@@ -11,6 +11,10 @@ std::vector<Command> baseCommands = {
                 "Sensitive homology search",
                 "# Search multiple FASTA against FASTA (like BLASTP, TBLASTN, BLASTX, BLASTN --search-type 3, TBLASTX --search-type 2)\n"
                 "mmseqs easy-search examples/QUERY.fasta examples/QUERY.fasta examples/DB.fasta result.m8 tmp\n\n"
+                "# Search multiple query fasta files against target fasta files using a tsv file containing filepaths\n"
+                "echo -e \"dir1/QUERY1.fasta\\ndir2/QUERY2.fasta\" > examples/queries.tsv\n"
+                "echo -e \"dir3/TARGET1.fasta\\ndir4/TARGET2.fasta\" > examples/targets.tsv\n"
+                "mmseqs easy-search examples/queries.tsv examples/targets.tsv result.m8 tmp\n\n"
                 "# Iterative profile search from stdin (like PSI-BLAST)\n"
                 "cat examples/QUERY.fasta | mmseqs easy-search stdin examples/DB.fasta result.m8 tmp --num-iterations 2\n\n"
                 "# Profile search against small databases (e.g. PFAM, eggNOG)\n"
@@ -125,7 +129,10 @@ std::vector<Command> baseCommands = {
                 "# Create a seqDB from stdin\n"
                 "cat seq.fasta | mmseqs createdb stdin sequenceDB\n\n"
                 "# Create a seqDB by indexing existing FASTA/Q (for single line fasta entries only)\n"
-                "mmseqs createdb seq.fasta sequenceDB --createdb-mode 1\n",
+                "mmseqs createdb seq.fasta sequenceDB --createdb-mode 1\n\n"
+                "# Create a seqDB from a tsv file containing filepaths of multiple FASTA files in each line\n"
+                "echo -e \"dir1/bacteria.fasta\\ndir2/archea.fasta.gz\" > filepaths.tsv\n"
+                "mmseqs createdb filepaths.tsv sequenceDB\n",
                 "Martin Steinegger <[email protected]>",
                 "<i:fastaFile1[.gz|.bz2]> ... <i:fastaFileN[.gz|.bz2]>|<i:stdin> <o:sequenceDB>",
                 CITATION_MMSEQS2, {{"fast[a|q]File[.gz|bz2]|stdin", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA | DbType::VARIADIC, &DbValidator::flatfileStdinAndGeneric },

src/util/createdb.cpp

@@ -19,6 +19,28 @@ int createdb(int argc, const char **argv, const Command& command) {
     std::vector<std::string> filenames(par.filenames);
     std::string dataFile = filenames.back();
     filenames.pop_back();
+    if (Util::endsWith(".tsv", filenames[0])) {
+	    if (filenames.size() > 1) {
+		    Debug(Debug::ERROR) << "Only one tsv file can be given\n";
+		    EXIT(EXIT_FAILURE);
+	    }
+	    std::string tsv = filenames.back();
+	    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--;
+		    }
+		    filenames.push_back(line);
+	    }
+	    free(line);
+	    fclose(file);
+    }
 
     for (size_t i = 0; i < filenames.size(); i++) {
         if (FileUtil::directoryExists(filenames[i].c_str()) == true) {