new files

Author: Rahi13

get_amino_acid_pos.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Jun  3 18:20:54 2021
+
+@author: rahinavelkar
+"""
+
+#The script take single or multiple fasta sequences and prints the desired amino acid and the respective position in the fasta sequence
+# To match a single position add aa = 'S', for multiple amino acid residues use aa = 'S|T|K'
+#generates a space seperated file with accession, matched amino acid, position of the matched amino acid
+
+import re
+
+infile = "/Users/rahinavelkar/Desktop/scripts/input.fasta"
+outfile = "/Users/rahinavelkar/Desktop/scripts/get_aa_pos_biopython.txt"
+amino_acid = []
+pos = []
+fasta = {}
+aa = 'K|T|S'  
+
+
+from Bio import SeqIO
+for seq_record in SeqIO.parse(infile, "fasta"):
+    fasta[seq_record.id] = seq_record.seq
+
+for name,seq in fasta.items():
+    pattern = re.finditer(aa, str(seq))
+    for i in pattern:
+        match_location = i.start() + 1
+        pos.append(str(match_location))
+        match_amino_acid = i.group()
+        amino_acid.append(match_amino_acid)
+    sourceFile = open(outfile,'a')    
+    print(name, ("|").join(amino_acid), ("|").join(pos), file=sourceFile)
+    sourceFile.close()
+    
+print('Done')