Merge pull request #38 from aineniamh/prior-to-reversion

aa merge in

snipit/command.py

@@ -73,7 +73,7 @@ def main(sysargs = sys.argv[1:]):
     else:
         args = parser.parse_args(sysargs)
 
-    num_seqs,ref_input,record_ids,length = sfunks.qc_alignment(args.alignment,args.reference,args.cds_mode,cwd)
+    num_seqs,ref_input,record_ids,length = sfunks.qc_alignment(args.alignment,args.reference,args.cds_mode,args.sequence_type,cwd)
 
 
     if args.reference:

snipit/scripts/snp_functions.py

@@ -10,6 +10,10 @@
 import math
 from itertools import groupby, count
 from collections import OrderedDict
+from enum import Enum
+import warnings
+warnings.filterwarnings('ignore')
+
 
 # imports from other modules
 from Bio import SeqIO
@@ -19,6 +23,7 @@
 import matplotlib.patches as patches
 from matplotlib.patches import Polygon
 
+
 colour_list = ["lightgrey","white"]
 colour_cycle = cycle(colour_list)
 END_FORMATTING = '\033[0m'
@@ -58,7 +63,7 @@ def check_ref(recombi_mode):
         sys.exit(-1)
 
 
-def qc_alignment(alignment,reference,cds_mode,cwd):
+def qc_alignment(alignment,reference,cds_mode,sequence_type,cwd):
     lengths = []
     lengths_info = []
     num_seqs = 0
@@ -102,6 +107,8 @@ def qc_alignment(alignment,reference,cds_mode,cwd):
         sys.stderr.write(red("Error: CDS mode flag used but alignment length not a multiple of 3.\n"))
         sys.exit(-1)
 
+    print(green(f"Note:") + f" assuming the alignment provided is of type {sequence_type}. If this is not the case, change input --sequence-type")
+
     return num_seqs,ref_input,record_ids,lengths[0]
 
 def reference_qc(reference, record_ids,cwd):
@@ -261,10 +268,13 @@ def find_snps(reference_seq,input_seqs,show_indels):
 
     return snp_dict,record_snps,len(var_counter)
 
-def find_ambiguities(alignment,snp_dict):
-
 
+def find_ambiguities(alignment, snp_dict,sequence_type):
 
+    if sequence_type == "nt":
+        amb = NT_AMBIG
+    if sequence_type == "aa":
+        amb = AA_AMBIG
 
 
     snp_sites = collections.defaultdict(list)