warning about seq type and suppress warnings for mpl sizing

snipit/scripts/snp_functions.py

@@ -11,6 +11,8 @@
 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
@@ -20,6 +22,7 @@
 import matplotlib.patches as patches
 from matplotlib.patches import Polygon
 
+
 colour_list = ["lightgrey","white"]
 colour_cycle = cycle(colour_list)
 END_FORMATTING = '\033[0m'
@@ -64,7 +67,7 @@ def check_ref(recombi_mode):
         sys.exit(-1)
 
 
-def qc_alignment(alignment,reference,sequence_type,cds_mode,cwd):
+def qc_alignment(alignment,reference,cds_mode,sequence_type,cwd):
     lengths = []
     lengths_info = []
     num_seqs = 0
@@ -108,6 +111,8 @@ def qc_alignment(alignment,reference,sequence_type,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):