update software

Author: yangfangs

physpetool/phylotree/consensustree.py

@@ -42,7 +42,7 @@ def docontree(input, output, rule):
     # prepare a dir store result
     if not os.path.exists(output):
         os.mkdir(output)
-    consensuseCmd = raxmlpath + "/raxmlHPC-PTHREADS-AVX " + " -J " + rule + " -m GTRCAT -z " + input + " -w " + output + " -n T1"
+    consensuseCmd = raxmlpath + "/raxmlHPC " + " -J " + rule + " -m GTRCAT -z " + input + " -w " + output + " -n T1"
     subprocess.call(consensuseCmd, shell=True)
 
 def do_astral(input,output):

physpetool/phylotree/doraxml.py

@@ -52,7 +52,7 @@ def doraxml(inputfile, outputfile, raxmlpara, thread):
     raxmlpath = getlocalpath()
     if not os.path.exists(outputfile):
         os.mkdir(outputfile)
-    strs = raxmlpath + "/raxmlHPC-PTHREADS-AVX " + "-T " + threadtostr + " " + raxmlpararet
+    strs = raxmlpath + "/raxmlHPC " + "-T " + threadtostr + " " + raxmlpararet
     # cmd command
     cmd = strs + " -s " + inputfile + " -w " + outputfile
     subprocess.call(cmd, shell=True)

physpetool/physpe/autobuild.py

@@ -389,8 +389,8 @@ def starting_esrna(in_put, out_put,
     out_retrieve = retrieve16srna(ssu_input, out_put,args_db)
     end = time.time()
     auto_build_log.info('Retrieving SSU rRNA sequences used time: {} Seconds'.format(end - start))
-    if not recovery_dic == {}:
-        recovery(out_retrieve, recovery_dic)
+    if not recovery_dic == []:
+        recovery_silva(out_retrieve, recovery_dic, ssu_input)
     retrieve_srna_path = os.path.join(out_retrieve, 'rna_sequence.fasta')
 
     fw = open(retrieve_srna_path, 'a')