[med-svn] [parsnp] 01/02: Some plain debugging was helpful to understand how parsnp works - leave this as a deactivated patch

[Andreas Tille]

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tille pushed a commit to branch master
in repository parsnp.

commit 4dde0e6ba3f105dd45c94eb9f5d89364f073058b
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jul 21 09:02:20 2016 +0200

    Some plain debugging was helpful to understand how parsnp works - leave this as a deactivated patch
---
 debian/patches/debug.patch | 75 ++++++++++++++++++++++++++++++++++++++++++++++
 debian/patches/series      |  1 +
 2 files changed, 76 insertions(+)

diff --git a/debian/patches/debug.patch b/debian/patches/debug.patch
new file mode 100644
index 0000000..87785a7
--- /dev/null
+++ b/debian/patches/debug.patch
@@ -0,0 +1,75 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 20 Apr 2016 10:31:32 +0200
+Description: Some plain debugging was helpful to understand how parsnp works
+ leave this as a deactivated patch
+
+--- a/Parsnp.py
++++ b/Parsnp.py
+@@ -936,6 +936,7 @@ if __name__ == "__main__":
+     #3)run parsnp (cores, grid?)
+     print "-->Running Parsnp multi-MUM search and libMUSCLE aligner.."
+     if not os.path.exists(outputDir+os.sep+"blocks"):
++        print "DEBUG: mkdir", outputDir+os.sep+"blocks"
+         os.mkdir(outputDir+os.sep+"blocks")
+     command = ""
+     run_parsnp = 1
+@@ -951,14 +952,16 @@ if __name__ == "__main__":
+                     command = "/usr/lib/parsnp/parsnp %sparsnpAligner.ini"%(outputDir+os.sep)
+                 else:
+                     command = "/usr/lib/parsnp/parsnp %spsnn.ini"%(outputDir+os.sep)
++                print "DEBUG not inifile_exists -> command:", command
+             else:
+                 if not os.path.exists(inifile):
+                     sys.stderr.write("Error: ini file %s does not exist!\n"%(inifile))
+                     sys.exit(1)
+                 command = "/usr/lib/parsnp/parsnp %s"%(inifile)
++                print "DEBUG inifile_exists -> command:", command
+             run_command(command)
+         
+-
++            print "DEBUG command successful:", command
+             if not os.path.exists(outputDir+os.sep+"parsnpAligner.xmfa"):
+ 
+                 successful_run = False
+@@ -971,6 +974,7 @@ if __name__ == "__main__":
+                 runcnt +=1
+                 break
+         os.system("mv "+outputDir+os.sep+"parsnpAligner.xmfa "+outputDir+os.sep+"parsnp.xmfa")
++    print "DEBUG 'if run_parsnp' is done"
+     xmfafile = open(outputDir+os.sep+"parsnp.xmfa",'r')
+         
+     file2hdr_dict = {}
+@@ -995,6 +999,7 @@ if __name__ == "__main__":
+         sys.exit(1)
+ 
+     #update thresholds
++    print "DEBUG update thresholds"
+     if coverage <= 0.01:
+         sys.stderr.write( "  |->["+ERROR_RED+"ERROR"+ENDC+"]"+": aligned regions cover less than 1% of reference genome, something is not right.. please adjust params and rerun. If problem persists please contact developers (treangen at gmail.com)"+ENDC)
+         sys.exit(1)
+--- a/src/parsnp.cpp
++++ b/src/parsnp.cpp
+@@ -517,6 +517,7 @@ void Aligner::writeOutput(string psnp,ve
+     test.append("/parsnpAligner.log");
+     lcbdir.append("/blocks/");
+     lcbprefix.append("/blocks/b");
++cerr << "DEBUG: Try to create testfile " << test.c_str() << endl;
+     try
+     {
+         ofstream testfile ( test.c_str() );
+@@ -525,12 +526,13 @@ void Aligner::writeOutput(string psnp,ve
+     }
+     catch ( char const * str )
+     {
+-        string command = "mkdir ";
++cerr << "DEBUG: Opening testfile " << test.c_str() << " failed - try to create directory " << this->outdir << endl;
++        string command = "mkdir -p ";
+         command.append(this->outdir);
+         int result = system(command.c_str());
+         if ( result )
+         {
+-            cerr << "ParSNP:: error creating output directory, exiting.." << endl;
++            cerr << "ParSNP:: error creating output directory" << this->outdir << ", exiting.." << endl;
+             exit(1);
+         }
+     }
diff --git a/debian/patches/series b/debian/patches/series
index 6ac76e5..9e77cc9 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,3 +4,4 @@ fix_install_path.patch
 avoid_rpath.patch
 add_missing_interpreter_line.patch
 proper_calls_to_tools.patch
+# debug.patch

-- 
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