Create read_fasta_file_v2.py

read_fasta_file_v2.py

@@ -0,0 +1,31 @@
+from itertools import groupby
+
+
+class readfasta(object):
+
+    def __init__(self, infile):
+        self.infile = infile
+
+    def read(self):
+        file_format = {'fasta':1, 'faa':2, 'fna':3}
+        if self.infile.split('.')[-1].lower() in file_format:
+            read_file = open(self.infile)
+            faiter = (x[1] for x in groupby(read_file, lambda line: line[0] == ">"))
+            for header in faiter:
+                header = next(header)[1:].strip()
+                seq = "".join(s.strip() for s in next(faiter))
+                yield header, seq
+
+        else:
+            filetype = self.infile.split('.')[-1]
+            raise Exception(f'Can only read FASTA file format with file extensions fasta, faa or fna')
+
+
+class decoy_pro(object):
+    def __init__(self, protein):
+        self.protein = protein
+
+    def Reverse(self):
+        pro = [self.protein[p] for p in range(len(self.protein)) if p+1 == len(self.protein)] + [self.protein[p] for p in range(len(self.protein)) if p+1 != len(self.protein)]
+        pro.reverse()
+        return ''.join(pro)