added option to override file extension requirement for reading fasta

src/sequence_analysis/seq_set.py

@@ -7,7 +7,7 @@
 
 class SeqSet(SeqSet_cpp):
     """This class holds a list of sequence objects of a given type."""
-    def __init__(self, file_name=None, list_of_seqs=None):
+    def __init__(self, file_name=None, list_of_seqs=None, force_suffix=True):
         """
         Overload the constructor so that you can set file name in one go.
 
@@ -23,6 +23,8 @@ def __init__(self, file_name=None, list_of_seqs=None):
                 raise ValueError
             if Path(file_name).suffix in [".fasta", ".fna", ".fa", ".ffn", ".frn", ".fst"]:
                 self.read_fasta(file_name)
+            elif not force_suffix:
+                self.read_fasta(file_name)
             else:
                 print(f"ERROR: file with suffix {Path(file_name).suffix} not supported.")
                 raise ValueError
@@ -62,4 +64,4 @@ def get_sequence_with_name(self, name):
         sset = self.find_subset_with_names([name])
         if len(sset) == 0:
             return None
-        return sset.records[0]
+        return sset.records[0]