More absolute path fixes

bacpop · Jul 2, 2018 · d4e858e · d4e858e
1 parent 1a7bed6
commit d4e858e
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/PopPUNK/mash.py b/PopPUNK/mash.py
@@ -418,9 +418,10 @@ def queryDatabase(qFile, klist, dbPrefix, queryPrefix, self = True, number_plot_
         mash_cmd = mash_exec + " dist -p " + str(threads) + " " + ref_dbname + " " + query_dbname
 
         if no_stream:
-            tmpHandle, tmpName = mkstemp(prefix=dbPrefix, suffix=".tmp", dir="./" + dbPrefix)
+            tmpHandle, tmpName = mkstemp(prefix=os.path.basename(dbPrefix),
+                                         suffix=".tmp", dir="./" + os.path.basename(dbPrefix))
             mash_cmd += " > " + tmpName
-        mash_cmd += " 2> " + dbPrefix + ".err.log"
+        mash_cmd += " 2> " + os.path.basename(dbPrefix) + ".err.log"
         sys.stderr.write(mash_cmd + "\n")
 
         try:

diff --git a/PopPUNK/network.py b/PopPUNK/network.py
@@ -229,8 +229,8 @@ def addQueryToNetwork(rlist, qlist, qfile, G, kmers, assignments, model,
             sys.stderr.write("Found novel query clusters. Calculating distances between them:\n")
 
             # write unassigned queries to file as if a list of references
-            tmpDirName = mkdtemp(prefix=queryDB, suffix="_tmp", dir="./")
-            tmpHandle, tmpFile = mkstemp(prefix=queryDB, suffix="_tmp", dir=tmpDirName)
+            tmpDirName = mkdtemp(prefix=os.path.basename(queryDB), suffix="_tmp", dir="./")
+            tmpHandle, tmpFile = mkstemp(prefix=os.path.basename(queryDB), suffix="_tmp", dir=tmpDirName)
             with open(tmpFile, 'w') as tFile:
                 for query in unassigned:
                     tFile.write(query + '\n')

diff --git a/PopPUNK/prune_db.py b/PopPUNK/prune_db.py
@@ -150,7 +150,7 @@ def main():
             sys.stderr.write("Resketching sequences\n")
 
             # Write names to file
-            tmpHandle, tmpName = mkstemp(prefix=args.output, suffix=".tmp", dir=".")
+            tmpHandle, tmpName = mkstemp(prefix=os.path.basename(args.output), suffix=".tmp", dir=".")
             with open(tmpName, 'w') as tmpRefFile:
                 for newRefSeq in newRefList:
                     tmpRefFile.write(newRefSeq + "\n")