update version

nextgenusfs · May 29, 2018 · 66a89ea · 66a89ea
1 parent 619207a
commit 66a89ea
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Showing 2 changed files with 14 additions and 11 deletions.
diff --git a/bin/amptk-filter.py b/bin/amptk-filter.py
@@ -548,12 +548,12 @@ def __init__(self,prog):
 #get the actual read counts from binary table
 merge = {}
 for index, row in final3.items():
-	merge[index] = []
-	for i in range(0, len(row)):
-		if row[i] == 0:
-			merge[index].append(row[i])
-		else:
-			merge[index].append(SortedTable[index][row.index[i]])
+    merge[index] = []
+    for i in range(0, len(row)):
+        if row[i] == 0:
+            merge[index].append(row[i])
+        else:
+            merge[index].append(SortedTable[index][row.index[i]])
 
 FiltTable = pd.DataFrame(merge, index=list(final3.index))
 FiltTable.index.name = '#OTU ID'
@@ -682,7 +682,7 @@ def __init__(self,prog):
     print("-------------------------------------------------------")
 
     if 'darwin' in sys.platform:
-    	print(colr.WARN + "\nExample of next cmd:" + colr.END + " amptk taxonomy -f %s -i %s -m mapping_file.txt -d ITS2\n" % (otu_new, final_table))
+        print(colr.WARN + "\nExample of next cmd:" + colr.END + " amptk taxonomy -f %s -i %s -m mapping_file.txt -d ITS2\n" % (otu_new, final_table))
     else:
-    	print("\nExample of next cmd: amptk taxonomy -f %s -i %s -m mapping_file.txt -d ITS2\n" % (otu_new, final_table))
+        print("\nExample of next cmd: amptk taxonomy -f %s -i %s -m mapping_file.txt -d ITS2\n" % (otu_new, final_table))
 
diff --git a/bin/amptk.py b/bin/amptk.py
@@ -49,7 +49,7 @@ def download(url, name):
     f.close()
 
 git_version = amptklib.git_version()
-base_version = '1.2.1'
+base_version = '1.2.3'
 if git_version:
     version = base_version+'-'+git_version
 else:
@@ -97,7 +97,7 @@ def download(url, name):
              version	 List version
              citation	 List citation
              
-Written by Jon Palmer (2015-2017) nextgenusfs@gmail.com
+Written by Jon Palmer (2015-2018) nextgenusfs@gmail.com
         """ % version
 
 if len(sys.argv) > 1:
@@ -1096,7 +1096,10 @@ def download(url, name):
     elif sys.argv[1] == 'version' or sys.argv[1] == '--version' or sys.argv[1] == '-version' or sys.argv[1] == '-v':
         print("AMPtk v%s" % version)
     elif sys.argv[1] == 'citation' or sys.argv[1] == '-citation' or sys.argv[1] == '--citation':
-        print("\nPalmer JM, Jusino MA, Banik MT, Lindner DL. 2017. Non-biological synthetic spike-in controls and the\n\tAMPtk software pipeline improve mycobiome data. bioRxiv 213470; doi: 10.1101/213470\n")
+        print("\nPalmer JM, Jusino MA, Banik MT, Lindner DL. 2018. Non-biological synthetic spike-in controls and the\n\tAMPtk software pipeline improve mycobiome data. PeerJ 6:e4925; DOI 10.7717/peerj.4925\n")
+    	print("*** Please also cite the specific tools that you used in AMPtk: ***")
+    	print('\t  USEARCH/UPARSE, VSEARCH, DADA2, LULU, etc.\n')
+
     else:
         print("%s option not recognized" % sys.argv[1])
         print(default_help)