# HG changeset patch
# User public-health-bioinformatics
# Date 1549323254 18000
# Node ID bb1cdfafee5957ef2c5ec02b34f43d54937e50f6
# Parent  0d3dad15541307fb79a7a2c988c15fab6cbbdf9e
planemo upload for repository https://github.com/Public-Health-Bioinformatics/flu_classification_suite commit 6f09c69c51ec3d6bd7487f55384b97155355c456

diff -r 0d3dad155413 -r bb1cdfafee59 assign_clades.py
--- a/assign_clades.py	Thu Jan 17 19:09:30 2019 -0500
+++ b/assign_clades.py	Mon Feb 04 18:34:14 2019 -0500
@@ -27,8 +27,8 @@
 '''Searches record for required amino acids at defined positions. If found, assigns
 clade name to sequence name by appending underscore and clade name to record id.'''
 def call_clade(record):
-    print "---------------------------------------------------------------------"
-    print "Parsing %s for matching flu clade definitions..." % (record.id)
+    print("---------------------------------------------------------------------")
+    print("Parsing %s for matching flu clade definitions..." % (record.id))
     matchList = [] #empty list to hold clades that match 100%
     #iterate over each tuple in the clade list
     for clade in cladeList:
@@ -38,7 +38,7 @@
         shouldFind = len(sites) #number of sites that should match
         found = 0 #a counter to hold matches to antigenic sites
         #iterate over each position in sites dictionary
-        for pos, aa in sites.iteritems():
+        for pos, aa in sites.items():
             #translate pos to corresponding index in target sequence
             index = int(pos) - 1
             #if record at index has same amino acid as 'aa', increment 'found'
@@ -87,11 +87,11 @@
         #add the clade info as a tuple to the cladeList[]
         oneClade =(name, depth, sites)
         cladeList.append(oneClade)
-    print "The List of Clades:"
+    print("The List of Clades:")
     for clade in cladeList:
-        print "Clade Name: %s Depth: %i Antigenic Sites: %i" % (clade[0], clade[1], len(clade[2]))
-        for pos, aa in clade[2].iteritems():
-            print "Pos: %s\tAA: %s" % (pos,aa)
+        print("Clade Name: %s Depth: %i Antigenic Sites: %i" % (clade[0], clade[1], len(clade[2])))
+        for pos, aa in clade[2].items():
+            print("Pos: %s\tAA: %s" % (pos,aa))
 
 '''opens readable input file of sequences to parse using filename from cmd line,
     instantiates as AA Sequence objects, with ppercase sequences'''
@@ -100,7 +100,7 @@
     for record in SeqIO.parse(inFile, "fasta", alphabet=IUPAC.protein):
         record = record.upper()
         seqList.append(record) #add Seq to list of Sequences
-    print "\n%i flu HA sequences will be compared to current clade definitions..." % len(seqList)
+    print("\n%i flu HA sequences will be compared to current clade definitions..." % len(seqList))
     #parse each target sequence object
     for record in seqList:
         clade_call = '' #empty variale for final clade call on sequence
@@ -116,10 +116,10 @@
         #empty list return, no matches
         else:
             clade_call = "No_Match"
-        print clade_call
+        print(clade_call)
         seq_name = record.id
         mod_name = seq_name + "_" + clade_call
-        print "New Sequence Name: " + mod_name
+        print("New Sequence Name: " + mod_name)
         record.id = mod_name
 
 
diff -r 0d3dad155413 -r bb1cdfafee59 test-data/input_fasta.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_fasta.fasta	Mon Feb 04 18:34:14 2019 -0500
@@ -0,0 +1,2 @@
+>test
+QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERNKAYSSCYPYDVPDYASLRSLVASSGTLEFNNESFNWAGVTQNGTSSSCIRGSKSSFFSRLNWLTHLNSKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQISLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPERQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDW
diff -r 0d3dad155413 -r bb1cdfafee59 test-data/output.fa
--- a/test-data/output.fa	Thu Jan 17 19:09:30 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
->test_3C.3a test
-QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILD
-GENCTLIDALLGDPQCDGFQNKKWDLFVERNKAYSSCYPYDVPDYASLRSLVASSGTLEF
-NNESFNWAGVTQNGTSSSCIRGSKSSFFSRLNWLTHLNSKYPALNVTMPNNEQFDKLYIW
-GVHHPGTDKDQISLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPG
-DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRI
-TYGACPRYVKQSTLKLATGMRNVPERQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEG
-RGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDL
-WSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGS
-IRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDW
diff -r 0d3dad155413 -r bb1cdfafee59 test-data/output.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.fasta	Mon Feb 04 18:34:14 2019 -0500
@@ -0,0 +1,10 @@
+>test_3C.3a test
+QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILD
+GENCTLIDALLGDPQCDGFQNKKWDLFVERNKAYSSCYPYDVPDYASLRSLVASSGTLEF
+NNESFNWAGVTQNGTSSSCIRGSKSSFFSRLNWLTHLNSKYPALNVTMPNNEQFDKLYIW
+GVHHPGTDKDQISLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPG
+DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRI
+TYGACPRYVKQSTLKLATGMRNVPERQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEG
+RGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDL
+WSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGS
+IRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDW
diff -r 0d3dad155413 -r bb1cdfafee59 test-data/test_input.fasta
--- a/test-data/test_input.fasta	Thu Jan 17 19:09:30 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
->test
-QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERNKAYSSCYPYDVPDYASLRSLVASSGTLEFNNESFNWAGVTQNGTSSSCIRGSKSSFFSRLNWLTHLNSKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQISLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPERQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHNVYRDEALNNRFQIKGVELKSGYKDW