new --ungapped alignment opt; fixed tmp path use to avoid retaining m…

…akeblastdb files

c-SSTAR

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = '2.0.0'
+__version__ = '2.1.0'
 
 import argparse
 import gzip
@@ -52,6 +52,9 @@ def parse_args():
         '--min-identity', type=require_float_1_to_100,
         metavar='FLOAT', default=95,
         help='minimum alignment nucleotide identity [%(default)s]')
+    aln.add_argument(
+        '--ungapped', action='store_true', default=False,
+        help='store ungapped-only alignments for BLASTn [off]')
     opt = parser.add_argument_group('I/O Options')
     opt.add_argument(
         '--basename', type=str, metavar='STR',
@@ -72,6 +75,9 @@ def parse_args():
         '--report', default=None, metavar='FILE',
         help='summary tab-delimited report [stdout]')
     msc = parser.add_argument_group('Misc Options')
+    msc.add_argument(
+        '--debug', default=False, action='store_true',
+        help='turn on debugging')
     msc.add_argument(
         '-h', '--help', action='help',
         help='show this help message and exit')
@@ -291,7 +297,7 @@ def main():
         'command -v blastn', shell=True).rstrip())
     logging.info(subprocess.check_output(
         'blastn -version | tail -n 1', shell=True).rstrip())
-    tmp_query_idx = os.path.join(outdir, base_genome)
+    tmp_query_idx = os.path.join(tmp, base_genome)
     sys_call('makeblastdb -in {} -out {} -dbtype nucl'.format(
         infile_query, tmp_query_idx))
     for x in ['.nin', '.nsq', '.nhr']:
@@ -302,14 +308,16 @@ def main():
                 ' search\n{} file empty\n'.
                 format(os.path.join(outdir, base_genome + x)))
             sys.exit(1)
-    sys_call(
-        'blastn -task blastn -query {} -db {} -out {} -evalue 1e-5'
-        ' -max_target_seqs 1 -perc_identity {} -culling_limit 1'
-        ' -outfmt "6 qseqid sseqid pident length mismatch gaps qstart qend'
-        ' sstart send evalue bitscore qlen slen sseq" -num_threads {}'.
-        format(infile_db, tmp_query_idx,
-               os.path.join(outdir, base_genome + '.blastn.tsv'),
-               min_identity, args.cpus))
+    cmd = ('blastn -task blastn -query {} -db {} -out {} -evalue 1e-5'
+           ' -max_target_seqs 1 -perc_identity {} -culling_limit 1'
+           ' -outfmt "6 qseqid sseqid pident length mismatch gaps qstart qend'
+           ' sstart send evalue bitscore qlen slen sseq" -num_threads {}'.
+           format(infile_db, tmp_query_idx,
+                  os.path.join(outdir, base_genome + '.blastn.tsv'),
+                  min_identity, args.cpus))
+    if args.ungapped:
+        cmd += ' -ungapped'
+    sys_call(cmd)
     shutil.rmtree(tmp)
     empty = require_file_exists_and_test_empty(
         os.path.join(outdir, base_genome + '.blastn.tsv'))