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MGEScan · Feb 11, 2016 · f99341f · f99341f
1 parent 944fe5c
commit f99341f
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Showing 4 changed files with 21 additions and 13 deletions.
diff --git a/mgescan/cmd.py b/mgescan/cmd.py
@@ -17,7 +17,7 @@
 import os, sys
 from docopt import docopt
 from multiprocessing import Process
-from subprocess import Popen, PIPE
+from subprocess import check_call, Popen, PIPE
 from mgescan import utils
 from mgescan.split import Split
 import shutil
@@ -195,11 +195,17 @@ def run_cmd(self, cmd):
         cmd = cmd % vars(self)
         if self.debug:
             print (cmd)
-        p = Popen(cmd.split(), stdout=PIPE, stderr=PIPE)
-        std_msgs = p.communicate()
-        if self.debug:
-            print std_msgs
-	return p
+        #p = Popen(cmd.split(), stdin=PIPE, stdout=PIPE, stderr=PIPE)
+        #std_msgs = p.communicate()
+        try:
+            retcode = check_call(cmd.split())
+            if retcode < 0:
+                print >>sys.stderr, "%s was terminated by signal" % cmd, -retcode
+            else:
+                print >>sys.stderr, "Returned", retcode
+        except OSError as e:
+            print >>sys.stderr, "Failed:", e
+	return retcode
 
 def main():
     arguments = docopt(__doc__, version='MGEScan 0.0.3')

diff --git a/mgescan/ltr/toGFF.py b/mgescan/ltr/toGFF.py
@@ -13,7 +13,7 @@
 
 if len(sys.argv) < 3:
     print sys.argv[0], "LTRout new-GFF-file"
-        sys.exit()
+    sys.exit()
 
 infile = open(sys.argv[1], "r")
 outfile = open(sys.argv[2], "w")

diff --git a/mgescan/nonltr/post_process2.pl b/mgescan/nonltr/post_process2.pl
@@ -347,9 +347,6 @@ sub get_domain_dna_seq{
 		#system("hmmsearch  --noali --domtblout ".$hmm_dir."tbl ".$_[1]."3 ".$_[0]." > /dev/null");
 		my $command = ("hmmsearch  --noali --domtblout ".$tmpfile." ".$_[1]."3 ".$_[0]." > /dev/null");
 		print $command if ($debug);
-		if ($debug && not prompt_yn("Continue?")) {
-			exit;
-		}
 		system($command);
 		#my $hmm_command = "cat ".$hmm_dir."tbl";
 		#my $hmm_result = `$hmm_command`;
@@ -472,9 +469,6 @@ sub vote_hmmsearch{
 			my $command = ("hmmsearch --noali --domtblout ".$tmpfile." ".$_[1].$line[$i].".".$_[2].".hmm3 ".$_[0]." > /dev/null");
 			system($command);
 			print $command if ($debug);
-			if ($debug && not prompt_yn("Continue?")) {
-				exit;
-			}
 			#my $command = "cat ".$hmm_dir."tbl";
 			#my $hmm_result = `$command`;
 			local $/ = undef;

diff --git a/mgescan/nonltr/run_hmm.pl b/mgescan/nonltr/run_hmm.pl
@@ -79,6 +79,9 @@
 	# MGEScan -m ./hmm/chr.hmm -s ./aaa/NC_003070.9.fa -r ./test/f/pos/NC_003070.9.fa.rt.pos -a ./test/f/pos/NC_003070.9.fa.ape.pos -o ./test/f/out1/NC_003070.9.fa -p ./ -d ./test/f/out1/ -v 3
 	$command = $pdir."hmm/MGEScan -m ".$pdir."hmm/chr.hmm -s ".$dna_file." -r ".$domain_rt_pos_file." -a ".$domain_ape_pos_file." -o ".$out_file." -p ".$pdir." -d ".$out1_dir." -v ".$hmmerv;
 	print $command."\n" if ($debug);
+	if ($debug && not prompt_yn("Continue?")) {
+		exit;
+	}
 	system($command); 
 }
 
@@ -117,6 +120,11 @@ sub get_signal_domain{
 	if ($hmmerv == 3){
 		#system("hmmconvert ".${$_[1]}." > ".${$_[1]}."c");
 		my $hmm_command = "hmmsearch  -E 0.00001 --noali --domtblout ".$tmpfile." ".${$_[1]}."3 ".${$_[0]}." > /dev/null";
+		print $hmm_command if ($debug);
+		if ($debug && not prompt_yn("Continue?")) {
+			exit;
+		}
+
 		system($hmm_command);
 		#$hmm_command = "cat ".$tmpfile;
 		local $/ = undef;