Fix IndexError in set_vsc_parameters() due to misplaced right paren…

…thesis in string's format method.

Issue:
When the VSG FASTA file was missing, or compressed in the .bz2 format, the program failed to output proper error messages and instead raised an "IndexError: Replacement index 1 out of range for positional args tuple."

Resolution:
The right parenthesis has been correctly placed to ensure the format method is properly closed.

metaphlan/metaphlan.py

@@ -398,18 +398,12 @@ def set_mapping_arguments(index, bowtie2_db):
 
 
 def set_vsc_parameters(index, bowtie2_db):
-    # The corresponding VSG file downloaded from metaphlan_databases site
-    # is actually a bz2 compressed file (as of version vJun23, 202403)
-    # http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/
     vsc_fna = os.path.join(bowtie2_db, "{}_VSG.fna".format(index))
-    vsc_fna_bz2 = "{}.bz2".format(vsc_fna)
     vsc_vinfo = os.path.join(bowtie2_db, "{}_VINFO.csv".format(index))
 
-    if (not os.path.isfile(vsc_fna)) and (not os.path.isfile(vsc_fna_bz2)):
-        sys.stderr.write("Error:\n {0} or {0}.bz2 file not found in bowtie2db folder ({1}). Re-download MetaPhlAn database.".format("{}_VSG.fna".format(index), bowtie2_db))
+    if not os.path.isfile(vsc_fna):
+        sys.stderr.write("Error:\n {} file not found in bowtie2db folder ({}). Re-download MetaPhlAn database.".format("{}_VSG.fna".format(index), bowtie2_db))
         sys.exit(1)
-    else:
-        vsc_fna = vsc_fna if os.path.isfile(vsc_fna) else vsc_fna_bz2
 
     if not os.path.isfile(vsc_vinfo):
         sys.stderr.write("Error:\n {} file not found in bowtie2db folder ({}). Re-download MetaPhlAn database.".format("{}_VINFO.csv".format(index), bowtie2_db))
@@ -1447,14 +1441,6 @@ def main():
     if pars['profile_vsc']:
 
         try:
-            # vsc_fna might be a bz2 compressed file
-            if vsc_fna.endswith(".bz2"):
-                temp_vsc_fna = os.path.join(viralTempFolder, os.path.basename(vsc_fna)[:-4])
-                with bz2.open(vsc_fna, "rt") as infh, open(temp_vsc_fna, "wt") as outfh:
-                    SeqIO.write(SeqIO.parse(infh, "fasta"), outfh, "fasta")
-
-                vsc_fna = temp_vsc_fna
-
             VSCs_markers = SeqIO.index(vsc_fna, "fasta")
         except Exception as e:
             sys.stderr.write('Error: "{}"\nCould not access to {}.\n'.format(e,vsc_fna))