diff scripts/S03_run_second_blast.py @ 0:90b57ab0bd1d draft default tip

planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/S03_run_second_blast.py	Fri Feb 01 10:23:16 2019 -0500
@@ -0,0 +1,45 @@
+#!/usr/bin/env python
+# coding: utf-8
+# Author : Victor Mataigne
+
+import itertools, argparse, os
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('query_file', help='fasta file (to translate) for query')
+    parser.add_argument('db_file', help='fasta files (already translated) for db')
+    parser.add_argument('file_subname', help='keyword for output file name')
+    parser.add_argument('evalue', help='evalue for blast')
+    parser.add_argument('method', choices=['tblastx', 'diamond'], help='alignment tool (tblastx or diamond)')
+    args = parser.parse_args()
+
+    if args.method == 'diamond':
+        from Bio.Seq import Seq
+        from Bio.Alphabet import IUPAC
+        # Traduire les best hits
+        f_name = 'translated_{}'.format(args.query_file)
+        translated_file = open(f_name, 'w')
+        with open(args.query_file, 'r') as file:
+            for name, seq in itertools.izip_longest(*[file]*2):
+                s = Seq(seq.strip('\n').upper(), IUPAC.ambiguous_dna)
+                translated_file.write(name.strip('\n')+'_orf_1\n')
+                translated_file.write(s.translate()._data+'\n')
+                translated_file.write(name.strip('\n')+'_orf_2\n')
+                translated_file.write(s[1:].translate()._data+'\n')
+                translated_file.write(name.strip('\n')+'_orf_3\n')
+                translated_file.write(s[2:].translate()._data+'\n')
+        translated_file.close()
+
+        os.system('diamond makedb --in %s -d %s >> log_diamond.log' %(args.db_file, args.db_file.split('_')[1]))
+        os.system('diamond blastp -q %s -d %s --max-target-seqs 1 -o matches_blast2_%s -e %s --more-sensitive >> log_diamond.log' %(f_name, args.db_file.split('_')[1], args.file_subname, args.evalue))
+
+    elif args.method == 'tblastx':
+        os.system('formatdb -i %s -p F -o T >> log_tblastx.log' %(args.db_file))
+        os.system('blastall -p tblastx -d %s -i %s -o matches_blast2_%s -T F -e %s -F "mS" -b1 -v1 -K 1 -m 8 >> log_tblastx.log' %(args.db_file, args.query_file, args.file_subname, args.evalue))
+
+    else :
+        print 'Mispecified alignment tool'
+        exit()
+
+if __name__ == "__main__":
+    main()