first commit - script parses a multiFASTA and output a separate fasta file for each sequence header

cross_species_comparison/scripts/parse_FASTA.py

+#!usr/bin/env python3
+
+import string
+import random
+import sys
+import os
+from Bio import SeqIO
+
+## usage python3 parse_FASTA.py [input.fasta] > [output.fasta]
+
+file = sys.argv[1]
+
+# Loop through all the files in the variable
+with open(file, 'r') as all_TWARs:
+
+    # for each record (TWAR header) in the file parse it as a FASTA
+    for record in SeqIO.parse(all_TWARs, "fasta"):
+        # set the record ID to a variable
+        id = record.id
+        # set the TWAR sequence to a variable
+        seq = record.seq
+
+        print(">" + str(id) + "\n" + str(seq) + "*")
+all_TWARs.close()