--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/antigenic_site_extraction.py	Thu Jul 04 19:36:38 2019 -0400
@@ -0,0 +1,95 @@
+#!/usr/bin/env python
+
+'''Accepts fasta files of amino acid sequence, extracts specific amino acids (defined in a csv index array),
+and outputs extracted sequences - representing flu antigenic sites - to fasta (default) or csv.'''
+
+'''Author: Diane Eisler, Molecular Microbiology & Genomics, BCCDC Public Health Laboratory,Sept 2017'''
+
+import sys,string,os, time, Bio, argparse
+from Bio import Seq, SeqIO, SeqUtils, Alphabet, SeqRecord
+from Bio.SeqRecord import SeqRecord
+from Bio.Alphabet import IUPAC
+from Bio.Seq import Seq
+
+#parse command line arguments
+parser = argparse.ArgumentParser()
+parser.add_argument("-c","--csv",help="export extracted antigenic sites to csv file",action="store_true")
+parser.add_argument("inFileHandle1") #batch fasta file with sequences to be parsed
+parser.add_argument("inFileHandle2") # .csv file containing positions of aa's to extract
+parser.add_argument("outFileHandle") #user-specified name for output file of extracted aa seq's
+args = parser.parse_args()
+
+#inFileHandle1 = sys.argv[1] #batch fasta file with sequences to be parsed
+#inFileHandle2 = sys.argv[2] # .csv file containing positions of aa's to extract
+#outFileHandle = sys.argv[3] #user-specified name for output file of extracted aa seq's
+
+outFile= open(args.outFileHandle,'w') #open a writable, appendable output file
+localtime = time.asctime(time.localtime(time.time())) #date and time of analysis
+seqList = [] #list of aa sequence objects to parse for oligo sequences
+indexArray = [] # .csv list of aa's corresponding to antigenic site positions
+extractedSeqList = [] #list of extracted antigenic sites extracted from seqList
+
+def extract_aa_from_sequence(record):
+    """Extract specific amino acids from SeqRecord, create new SeqRecord and append to list."""
+    original_sequence = str(record.seq) #pull out the SeqRecord's Seq object and ToString it
+    new_sequence = "" #set variable to empty
+    new_id = record.id #store the same sequence id as the original sequence
+    #iterate over each position in index array, extract corresponding aa and add to string
+    for pos in indexArray:
+        char = original_sequence[pos-1] #aa positions must be zero indexed
+        new_sequence = new_sequence + char
+    rec = SeqRecord(Seq(new_sequence,IUPAC.protein), id = record.id, name = "", description = "")
+    extractedSeqList.append(rec) #add new SeqRecord object to the list
+
+with open (args.inFileHandle2,'r') as inFile2:
+    '''Open csv file containing amino acid positions to extract and add to list.'''
+    #read items separated by comma's to position list
+    positionList = ""   
+    for line in inFile2:
+        #remove whitespace from the end of each line
+        strippedLine = line.rstrip()
+        #split the line at commas and assigned the returned list as indexArray
+        positionList = strippedLine.split(',')
+    #Convert string items in positionList from strings to int and add to indexArray
+    for item in positionList:
+        indexArray.append(int(item))
+    #print number of amino acids to extract and array to console as user check
+    print("Amino Acid positions to extract: %i " %(len(indexArray)))
+    print(indexArray)
+
+with open(args.inFileHandle1,'r') as inFile:
+    '''Open fasta of amino acid sequences to parse, uppercase and add to protein Sequence list.'''
+    #read in Sequences from fasta file, uppercase and add to seqList
+    for record in SeqIO.parse(inFile, "fasta", alphabet=IUPAC.protein):
+        record = record.upper()
+        seqList.append(record) #add Seq to list of Sequences
+    #print number of sequences to be process as user check
+    print("\n%i flu sequences will be extracted for antigenic sites..." % len(seqList))
+    #parse each target sequence object
+    for record in seqList:
+        extract_aa_from_sequence(record)
+
+#print original and extracted sequence
+for x in range(0, len(seqList)):
+    print("Original %s: %i amino acids,\tExtracted: %i" % (seqList[x].id,len(seqList[x]),len(extractedSeqList[x])))
+
+#determine if output format is fasta (default) or csv
+if args.csv:
+    #write csv file of extracted antigenic sits
+    for record in extractedSeqList:
+        #outFile.write(record.id),","
+        name_part = (record.id).rstrip() + ','
+        sequence = str(record.seq).strip()
+        csv_seq = ",".join(sequence)
+        comma_separated_sequence = name_part + csv_seq + "\n"
+        print(comma_separated_sequence)
+        outFile.write(comma_separated_sequence)
+else:
+    #write fasta file of extracted antigenic sites
+    SeqIO.write(extractedSeqList,outFile,"fasta")
+
+print("\n%i Sequences Extracted to Output file: %s"  % ((len(extractedSeqList),args.outFileHandle)))
+inFile.close()
+inFile2.close()
+outFile.close()
+