add code to remove temporary files

README.md

@@ -247,6 +247,8 @@ Let's try an example, NC_012624.fna.
 
 <a name="Release"></a>
 ## Release History 
+- 1.7.2.2.2
+  - add code to remove temporary files (created by tempfile.NamedTemporaryFile()) once blastn search completes in case that large amounts of temporary files consume too much space. (Thanks Biancamaria for the suggestion)
 - 1.7.2.2
   - ISEScan can output .csv (columns are separated by `,`) and .tsv (columns are separated by `tab`) result files, which are much easier for users to parse the results (Thanks oschwengers for his suggestion)
   - add command options `--seqfile` and `--output` to remove the positional parmater `seqfile`, `proteome` and `hmm` (Thanks oschwengers for his suggestion)

isescan.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 # ISEScan version
-version = '1.7.2.2.1'
+version = '1.7.2.2.2'
 
 import argparse
 import os

pred.py

@@ -1434,6 +1434,8 @@ def getFullIS4seqOnStream(args):
 	query = orfExtSeqFile
 	blastOut4orfExt, err = tools.doBlastn2seqOnStream(nthread, query, fp.name, strand='both', task='megablast', 
 			perc_ident=constants.SIM4ISO)
+	tools.deleteFile(fp.name)
+
 	if len(err) > 0:
 		#e = 'Blastn ISs in {} against {}: {}'.format(seqid, db, err)
 		e = 'Blastn ISs in {} against {}: {}'.format(seqid, seqid, err)

tools.py

@@ -864,6 +864,15 @@ def seq2blastdb(seqFile, db):
 	do_cmd = shlex.split(' '.join(cmdline))
 	subprocess.check_call(do_cmd, shell=False, universal_newlines=False, stdout=subprocess.DEVNULL)
 
+# delete the file pointing by full path f.
+# f: /path/to/file, a character string
+def deleteFile(f):
+	cmd = 'rm'
+	cmdline = [cmd, f]
+	do_cmd = shlex.split(' '.join(cmdline))
+	subprocess.check_call(do_cmd, shell=False, universal_newlines=False, stdout=subprocess.DEVNULL)
+
+
 # Search all IS elements (Tpase) ORFs against IS element (Tpase ORF) database.
 # command: blastn -query /home/data/insertion_sequence/output4FragGeneScan1.19_illumina_5/NC_002754.1.fna.ffn \
 #		-db /home/data/insertion_sequence/blastdb/NC_002754.1.fna.ffn -out blast.6 \