changeset 1:71bc4fd01351 draft default tip

planemo upload for repository https://github.com/DiDigsDNA/amplicon_sequevars_to_dict commit ca00fa6b41cfb8f6a27901792a4e4d3fc3e1878b
author diane
date Fri, 07 Sep 2018 15:22:34 -0400
parents 8af7fd9b7476
children
files amplicon_sequevars_to_dict.py amplicon_sequevars_to_dict.xml test-data/amplicon_sequevars_to_dict/amplicon_sequevars_with_safelist.fasta test-data/amplicon_sequevars_to_dict/amplicon_sequevars_with_safelist.txt test-data/amplicon_sequevars_to_dict/amplicon_sequevars_without_safelist.fasta test-data/amplicon_sequevars_to_dict/amplicon_sequevars_without_safelist.txt test-data/amplicon_sequevars_to_dict/amplicons.fasta test-data/amplicon_sequevars_to_dict/safelist.fasta test-data/amplicon_sequevars_with_safelist.fasta test-data/amplicon_sequevars_with_safelist.txt test-data/amplicon_sequevars_without_safelist.fasta test-data/amplicon_sequevars_without_safelist.txt test-data/amplicons.fasta test-data/safelist.fasta tools/amplicon_sequevars_to_dict/amplicon_sequevars_to_dict.py tools/amplicon_sequevars_to_dict/amplicon_sequevars_to_dict.xml
diffstat 16 files changed, 753 insertions(+), 753 deletions(-) [+]
line wrap: on
line diff
--- a/amplicon_sequevars_to_dict.py	Fri Sep 07 15:17:08 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,113 +0,0 @@
-#!/usr/bin/env python
-'''Reads in nucleotide sequences from a fasta file as SeqRecords and sorts into a dictionary,
-with unique sequences as keys and lists of SeqRecords sharing these sequevars as values. If the user
-specified a fasta file containing sequences which have been empirically determined to amplify in the 
-PCR (i.e. "safelist"), the sequevars are compared to this safelist prior to being output to fasta. Sequence
-identifiers (usually Genbank accession numbers) of sequences in a sequevar are printed to a text file.
-
-Usage with safelist: python sequevarsToDict.py -s safelist.fasta unmatching_sequences.fasta  Mar20_sequevars
-Usage without safelist: python sequevars_to_dict.py unmatching_sequences.fasta  Mar20_sequevars
-'''
-
-'''Author: Diane Eisler, Molecular Microbiology & Genomics, BCCDC Public Health Laboratory, March 2018'''
-
-import sys,string,os, time, Bio, re, argparse
-from Bio import Seq, SeqIO, SeqUtils, Alphabet, SeqRecord
-from Bio.Alphabet import IUPAC
-from Bio.Seq import Seq
-from Bio.SeqRecord import SeqRecord
-import Bio.Data.IUPACData
-
-#parse command line arguments
-parser = argparse.ArgumentParser()
-parser.add_argument("-s", dest = "safelist", help = "specify filename of previously vetted sequences",
-    action = "store")
-parser.add_argument("fastaToParse")
-parser.add_argument("outFileHandle")
-results = parser.parse_args()
-print("ARGUMENTS:")
-print(results)
-print('safelist = ', results.safelist)
-
-#construct output filenames
-gb_accessionsHandle = results.outFileHandle + ".txt" #user-specified output file name
-gb_accessions= open(gb_accessionsHandle,'w') #output file of GB access #'s and details re: which oligos NOT found
-outputFastaHandle = results.outFileHandle + ".fasta" #create fasta file from  user specified name
-
-def outputInformationFile(sequevars):
-    '''Outputs text file with unique amplicon sequences and id's of sequences in each sequevar.'''
-    localtime = time.asctime(time.localtime(time.time())) #date and time of analysis
-    gb_accessions.write("---------------------------------------------------------------------------\n")
-    gb_accessions.write("RESULTS OF SEARCH FOR EXACT MATCHES TO OLIGONUCLEOTIDES IN QUERY SEQUENCES:\n")
-    gb_accessions.write("---------------------------------------------------------------------------\n\n")
-    gb_accessions.write("Analysis as of: " + localtime + "\n\n")
-    gb_accessions.write("\n---------------------------------------------------------------------------\n")
-    #if there are sequevars for further analysis, output them to the results .txt and fasta files
-    if len(sequevars) > 0: #if there are sequevars to output, write to list with sequence id's in sequevar
-        outputSequevarsToFasta(sequevars) #output fasta file of sequevars i.e.representative record
-        gb_accessions.write("%i Different Amplicon Sequevars Found: %s \n\n" % (len(sequevars),results.fastaToParse))
-        for sequevar in sequevars:
-            print("\nSequevar: %s" % sequevar) #print sequevar to console
-            recordList = sequevars[sequevar]
-            gb_accessions.write("\n\n%i Records in Sequevar: %s" % (len(recordList),sequevar)) #write sequevar to file
-            print("%i Record(s) have this sequence:" % (len(recordList)))
-            for record in recordList:
-                print("\t" + record.id) #print record id to console
-                gb_accessions.write("\n\t" + record.id) #write records with this sequence to file
-    else: #if not sequevars to output, print message to outfile to clarify this
-        gb_accessions.write("No sequevars requiring further investigation.")
-    gb_accessions.write("\n---------------------------------------------------------------------------")
-    gb_accessions.write("\n\nEND OF RESULTS\n")
-    #print output filepaths to console and to search results file
-    gb_accessions.write("\nSearch Results (this file): " + gb_accessionsHandle)
-    print("\nSearch Results: " + gb_accessionsHandle)
-    if len(sequevars) > 0: #if there are sequevars to print to fasta, direct user to fasta file
-        gb_accessions.write("\nFasta sequences for analysis: " + outputFastaHandle)
-        print("Fasta sequences for analysis: " + outputFastaHandle)
-    else:
-        gb_accessions.write("\nFasta sequences for analysis: N/A")
-        print("Fasta sequences for analysis: N/A\n")
-    return
-
-def outputSequevarsToFasta(sequevars):
-    '''Output a fasta file with one representative sequence for each sequevar.'''
-    output_fasta = open(outputFastaHandle, 'w') #create a writeable fasta file
-    sequevars_list = []
-    for sequevar in sequevars:
-        first_record = sequevars[sequevar][0] #grab the first SeqRecord in the list sharing the sequevar
-        sequevars_list.append(first_record)  #add it to the list of SeqRecords
-    SeqIO.write(sequevars_list, output_fasta, "fasta") #write the sequevars to fasta
-    return
-
-with open(results.fastaToParse,'r') as inFile:
-    #read nucleotide sequences from fasta file into SeqRecords, uppercases and adds to a list
-    seqList = [rec.upper() for rec in list(SeqIO.parse(inFile, "fasta", alphabet=IUPAC.ambiguous_dna))]
-    sequevars = {} # empty dictionary of sequevar: list<SeqRecord>
-    safe_seqs = [] # empty list of nucleotide sequences
-
-    if results.safelist: #if safelist specified by user, read these sequences into a list
-        safe_seqs = [record.seq for record in SeqIO.parse(results.safelist, "fasta", alphabet=IUPAC.ambiguous_dna)]
-        print("Safeseqs:")
-        for seq in safe_seqs:
-            print(seq) #print all the vetted unique sequences
-        
-    for record in seqList: #parse SeqRecord for exact match to amplicon or reverse complement
-        sequence = str(record.seq)
-        #check if the sequence has already been tested and vetted (i.e. in safelist)
-        if (sequence in safe_seqs): #only add to dictionary if not previously tested
-            print("Sequence from %s in safe list!" % (record.id) )#print mssg to console
-        else:
-            #if the sequence is a key in the dict, add SeqRecord to list
-            if sequence in sequevars:
-                sequevars[sequence].append(record)
-            else:
-                #add sequence as new key to dict, accessing a list with SeqRecord  as its first item
-                sequevars[sequence] = [record]
-    #get a sorted list of unique sequence keys
-    sorted_unique_seq_keys = sorted(sequevars.keys())
-    #process list of SeqRecords in each sequevar and print to results summary file for end-user        
-    outputInformationFile(sequevars) #output information .txt file
-    #outputSequevarsToFasta(sequevars) #output fasta file of sequevars i.e.representative record      
-
-inFile.close()
-gb_accessions.close()
--- a/amplicon_sequevars_to_dict.xml	Fri Sep 07 15:17:08 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-<tool id="amplicon_sequevars_to_dict" name="Amplicon Sequevars To Dictionary" version="0.0.1">
-  <requirements>
-    <requirement type="package" version="1.70">biopython</requirement>
-  </requirements>
-  <command detect_errors="exit_code"><![CDATA[
-    $__tool_directory__/amplicon_sequevars_to_dict.py
-    '$input_fasta'
-    '$oligo_def_file'
-    '$output_fasta'
-    '$output_txt'
-  ]]></command>
-  <inputs>
-    <param name="input_fasta" format="fasta" type="data" />
-    <param name="oligo_def_file" format="csv" type="data" />
-  </inputs>
-  <outputs>
-      <data format="fasta" name="output_fasta"></data>
-      <data format="txt" name="output_txt"></data>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input_fasta" value="amplicons.fasta" />
-      <param name="oligo_def_file" value="Flu4plex_FluA_oligo_definitions.csv" />
-      <output name="output_fasta" value="output.fasta" />
-      <output name="output_txt" value="output.txt" />
-    </test>
-  </tests>
-  <help><![CDATA[
-    Sorts a fasta file of PCR amplicons into unique sequence groupings (ignoring any present in a trusted sequence'safelist') and outputs sequevars (fasta) and a summary (txt).
-  ]]></help>
-  <citations>
-  </citations>
-</tool>
-
-#NEEDS MODIFICATIONS!!!
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amplicon_sequevars_to_dict/amplicon_sequevars_with_safelist.fasta	Fri Sep 07 15:22:34 2018 -0400
@@ -0,0 +1,36 @@
+>KY925981 A/Bage/LACENRS-294/2011 2011/06/16 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
+CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>KY926040 A/Palmitinho/LACENRS-2595/2009 2009/08/31 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>KY926095 A/Porto Alegre/LACENRS-2380/2013 2013/07/15 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACAGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY926106 A/Santa Cruz do Sul/LACENRS-913/2011 2011/07/11 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>KY950187 A/Linkou/0181/2016 2016/12/21 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF039637 A/Zhejiang/DTID-ZJU01/2013 2013/04/07 7 (MP)
+GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCC
+>MF039638 A/WSN/1933 1933// 7 (MP)
+GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGGGGACTGCAGCGTAGACGCTTTGTCCAAAATGCTC
+>MF441160 A/Korea/KUMC-GR190/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAAAATGCCC
+>MF441174 A/Korea/KUMC-GR689/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTTCAAAATGCCC
+>MF593488 A/Mexico/4104/2016 2016/01/14 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAACGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF599436 A/Kenya/011/2017 2017/03/08 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTCTTCACGCTCACCGTGC
+CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF629795 A/Trivandrum/MCVR261/2009 2009/08/21 7 (MP)
+GACCAATCTTGTCACCCCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amplicon_sequevars_to_dict/amplicon_sequevars_with_safelist.txt	Fri Sep 07 15:22:34 2018 -0400
@@ -0,0 +1,64 @@
+---------------------------------------------------------------------------
+RESULTS OF SEARCH FOR EXACT MATCHES TO OLIGONUCLEOTIDES IN QUERY SEQUENCES:
+---------------------------------------------------------------------------
+
+Analysis as of: Thu Sep  6 18:27:06 2018
+
+
+---------------------------------------------------------------------------
+12 Different Amplicon Sequevars Found: test-data/amplicons.fasta 
+
+
+
+1 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGCCAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+	KY925981
+
+2 Records in Sequevar: GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+	KY926040
+	KY926049
+
+1 Records in Sequevar: GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACAGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+	KY926095
+
+4 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+	KY926106
+	MF441141
+	MF441149
+	MF441161
+
+5 Records in Sequevar: GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+	KY950187
+	KY950217
+	MF599433
+	MF599434
+	MF599438
+
+4 Records in Sequevar: GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCC
+	MF039637
+	MF370249
+	MF370253
+	MF370257
+
+1 Records in Sequevar: GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGGGGACTGCAGCGTAGACGCTTTGTCCAAAATGCTC
+	MF039638
+
+1 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAAAATGCCC
+	MF441160
+
+1 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTTCAAAATGCCC
+	MF441174
+
+1 Records in Sequevar: GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAACGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+	MF593488
+
+1 Records in Sequevar: GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTCTTCACGCTCACCGTGCCAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+	MF599436
+
+1 Records in Sequevar: GACCAATCTTGTCACCCCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+	MF629795
+---------------------------------------------------------------------------
+
+END OF RESULTS
+
+Search Results (this file): test-data/output.txt
+Fasta sequences for analysis: test-data/output.fasta
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amplicon_sequevars_to_dict/amplicon_sequevars_without_safelist.fasta	Fri Sep 07 15:22:34 2018 -0400
@@ -0,0 +1,48 @@
+>KY925925 A/Santo Antonio da Patrulha/LACENRS-2621/2012 2012/08/10 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY925966 A/Porto Alegre/LACENRS-1075/2015 2015/05/29 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>KY925981 A/Bage/LACENRS-294/2011 2011/06/16 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
+CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>KY926040 A/Palmitinho/LACENRS-2595/2009 2009/08/31 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>KY926095 A/Porto Alegre/LACENRS-2380/2013 2013/07/15 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACAGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY926106 A/Santa Cruz do Sul/LACENRS-913/2011 2011/07/11 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>KY950187 A/Linkou/0181/2016 2016/12/21 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF039637 A/Zhejiang/DTID-ZJU01/2013 2013/04/07 7 (MP)
+GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCC
+>MF039638 A/WSN/1933 1933// 7 (MP)
+GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGGGGACTGCAGCGTAGACGCTTTGTCCAAAATGCTC
+>MF441145 A/Korea/KUMC-GR66/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441160 A/Korea/KUMC-GR190/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAAAATGCCC
+>MF441174 A/Korea/KUMC-GR689/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTTCAAAATGCCC
+>MF593488 A/Mexico/4104/2016 2016/01/14 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAACGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF599435 A/Kenya/009/2017 2017/03/06 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF599436 A/Kenya/011/2017 2017/03/08 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTCTTCACGCTCACCGTGC
+CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF629795 A/Trivandrum/MCVR261/2009 2009/08/21 7 (MP)
+GACCAATCTTGTCACCCCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amplicon_sequevars_to_dict/amplicon_sequevars_without_safelist.txt	Fri Sep 07 15:22:34 2018 -0400
@@ -0,0 +1,148 @@
+---------------------------------------------------------------------------
+RESULTS OF SEARCH FOR EXACT MATCHES TO OLIGONUCLEOTIDES IN QUERY SEQUENCES:
+---------------------------------------------------------------------------
+
+Analysis as of: Thu Sep  6 18:19:51 2018
+
+
+---------------------------------------------------------------------------
+16 Different Amplicon Sequevars Found: test-data/amplicons.fasta 
+
+
+
+36 Records in Sequevar: GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+	KY925925
+	KY925930
+	KY925952
+	KY925960
+	KY925968
+	KY926011
+	KY926047
+	KY926053
+	KY926055
+	KY926082
+	KY926097
+	KY926123
+	KY926125
+	KY926132
+	KY950197
+	KY950209
+	KY950219
+	MF593496
+	MF593504
+	MF593512
+	MF593520
+	MF593528
+	MF593533
+	MF593538
+	MF593544
+	MF593549
+	MF593557
+	MF593562
+	MF593570
+	MF593578
+	MF593586
+	MF593594
+	MF593602
+	MF593610
+	MF593615
+	MF593623
+
+23 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+	KY925966
+	KY925996
+	KY926140
+	MF441140
+	MF441142
+	MF441143
+	MF441144
+	MF441146
+	MF441150
+	MF441151
+	MF441153
+	MF441156
+	MF441157
+	MF441163
+	MF441164
+	MF441165
+	MF441166
+	MF441167
+	MF441168
+	MF441169
+	MF441170
+	MF441172
+	MF441173
+
+1 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGCCAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+	KY925981
+
+2 Records in Sequevar: GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+	KY926040
+	KY926049
+
+1 Records in Sequevar: GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACAGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+	KY926095
+
+4 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+	KY926106
+	MF441141
+	MF441149
+	MF441161
+
+5 Records in Sequevar: GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+	KY950187
+	KY950217
+	MF599433
+	MF599434
+	MF599438
+
+4 Records in Sequevar: GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCC
+	MF039637
+	MF370249
+	MF370253
+	MF370257
+
+1 Records in Sequevar: GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGGGGACTGCAGCGTAGACGCTTTGTCCAAAATGCTC
+	MF039638
+
+10 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+	MF441145
+	MF441147
+	MF441148
+	MF441152
+	MF441154
+	MF441155
+	MF441158
+	MF441159
+	MF441162
+	MF441171
+
+1 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAAAATGCCC
+	MF441160
+
+1 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTTCAAAATGCCC
+	MF441174
+
+1 Records in Sequevar: GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAACGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+	MF593488
+
+7 Records in Sequevar: GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGCCAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+	MF599435
+	MF599437
+	MF599439
+	MF599440
+	MF599441
+	MF599442
+	MF599443
+
+1 Records in Sequevar: GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTCTTCACGCTCACCGTGCCAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+	MF599436
+
+1 Records in Sequevar: GACCAATCTTGTCACCCCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+	MF629795
+---------------------------------------------------------------------------
+
+END OF RESULTS
+
+Search Results (this file): amplicon_sequevars_without_safelist.txt
+Fasta sequences for analysis: amplicon_sequevars_without_safelist.fasta
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amplicon_sequevars_to_dict/amplicons.fasta	Fri Sep 07 15:22:34 2018 -0400
@@ -0,0 +1,297 @@
+>KY925925 A/Santo Antonio da Patrulha/LACENRS-2621/2012 2012/08/10 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY925930 A/Novo Hamburgo/LACENRS-385/2016 2016/04/04 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY925952 A/Viamao/LACENRS-1400/2011 2011/08/22 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY925960 A/Gramado/LACENRS-1287/2016 2016/04/29 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY925966 A/Porto Alegre/LACENRS-1075/2015 2015/05/29 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>KY925968 A/Santa Cruz do Sul/LACENRS-2672/2013 2013/07/22 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY925981 A/Bage/LACENRS-294/2011 2011/06/16 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
+CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>KY925996 A/Canoas/LACENRS-1793/2015 2015/07/17 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>KY926011 A/Tres Coroas/LACENRS-1810/2012 2012/07/23 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY926040 A/Palmitinho/LACENRS-2595/2009 2009/08/31 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>KY926047 A/Sao Gabriel/LACENRS-1809/2012 2012/07/23 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY926049 A/Sao Gabriel/LACENRS-1626/2009 2009/08/14 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>KY926053 A/Uruguaiana/LACENRS-296/2016 2016/03/27 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY926055 A/Caibate/LACENRS-903/2012 2012/07/08 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY926082 A/Camaqua/LACENRS-623/2011 2011/07/01 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY926095 A/Porto Alegre/LACENRS-2380/2013 2013/07/15 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACAGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY926097 A/Caxias do Sul/LACENRS-1186/2011 2011/08/31 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY926106 A/Santa Cruz do Sul/LACENRS-913/2011 2011/07/11 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>KY926123 A/Canoas/LACENRS-1320/2016 2016/05/02 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY926125 A/Cruz Alta/LACENRS-499/2012 2012/06/27 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY926132 A/Nova Petropolis/LACENRS-1205/2013 2013/06/07 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY926140 A/Porto Alegre/LACENRS-1887/2015 2015/07/25 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>KY950187 A/Linkou/0181/2016 2016/12/21 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>KY950197 A/Baltimore/0026/2016 2016/01/16 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY950209 A/Baltimore/0077/2016 2016/02/23 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY950217 A/Baltimore/0247/2017 2017/01/25 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>KY950219 A/Linkou/0004/2015 2015/11/06 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF039637 A/Zhejiang/DTID-ZJU01/2013 2013/04/07 7 (MP)
+GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCC
+>MF039638 A/WSN/1933 1933// 7 (MP)
+GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGGGGACTGCAGCGTAGACGCTTTGTCCAAAATGCTC
+>MF370249 A/Changsha/26/2017 2017/02/04 7 (MP)
+GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCC
+>MF370253 A/Changsha/41/2017 2017/03/12 7 (MP)
+GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCC
+>MF370257 A/Changsha/44/2017 2017/03/14 7 (MP)
+GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCC
+>MF441140 A/Korea/KUMC-GR14/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441141 A/Korea/KUMC-GR17/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441142 A/Korea/KUMC-GR18/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441143 A/Korea/KUMC-GR47/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441144 A/Korea/KUMC-GR55/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441145 A/Korea/KUMC-GR66/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441146 A/Korea/KUMC-GR83/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441147 A/Korea/KUMC-GR90/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441148 A/Korea/KUMC-GR92/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441149 A/Korea/KUMC-GR96/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441150 A/Korea/KUMC-GR99/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441151 A/Korea/KUMC-GR115/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441152 A/Korea/KUMC-GR116/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441153 A/Korea/KUMC-GR121/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441154 A/Korea/KUMC-GR124/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441155 A/Korea/KUMC-GR137/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441156 A/Korea/KUMC-GR157/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441157 A/Korea/KUMC-GR159/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441158 A/Korea/KUMC-GR172/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441159 A/Korea/KUMC-GR175/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441160 A/Korea/KUMC-GR190/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAAAATGCCC
+>MF441161 A/Korea/KUMC-GR195/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441162 A/Korea/KUMC-GR202/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441163 A/Korea/KUMC-GR218/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441164 A/Korea/KUMC-GR226/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441165 A/Korea/KUMC-GR227/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441166 A/Korea/KUMC-GR252/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441167 A/Korea/KUMC-GR261/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441168 A/Korea/KUMC-GR281/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441169 A/Korea/KUMC-GR285/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441170 A/Korea/KUMC-GR437/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441171 A/Korea/KUMC-GR567/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441172 A/Korea/KUMC-GR570/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441173 A/Korea/KUMC-GR590/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441174 A/Korea/KUMC-GR689/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTTCAAAATGCCC
+>MF593488 A/Mexico/4104/2016 2016/01/14 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAACGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593496 A/Mexico/4431/2016 2016/03/01 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593504 A/Mexico/4433/2016 2016/02/28 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593512 A/Mexico/4435/2016 2016/03/02 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593520 A/Mexico/4436/2016 2016/02/28 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593528 A/Mexico/4440/2016 2016/03/16 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593533 A/Mexico/4604/2017 2017/02/10 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593538 A/Mexico/4621/2017 2017/02/18 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593544 A/Mexico/4627/2017 2017/02/24 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593549 A/Mexico/4628/2017 2017/03/02 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593557 A/Mexico/4687/2017 2017/03/12 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593562 A/Mexico/4703/2017 2017/03/21 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593570 A/Mexico/7317/2017 2017/01/16 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593578 A/Mexico/8017/2017 2017/01/17 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593586 A/Mexico/8517/2017 2017/01/18 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593594 A/Mexico/11417/2017 2017/01/23 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593602 A/Mexico/12317/2017 2017/01/24 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593610 A/Mexico/15017/2017 2017/01/26 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593615 A/Mexico/15517/2017 2017/01/27 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF593623 A/Mexico/17517/2017 2017/01/30 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>MF599433 A/Kenya/001/2017 2017/01/01 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF599434 A/Kenya/002/2017 2017/01/02 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF599435 A/Kenya/009/2017 2017/03/06 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF599436 A/Kenya/011/2017 2017/03/08 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTCTTCACGCTCACCGTGC
+CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF599437 A/Kenya/014/2017 2017/03/13 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF599438 A/Kenya/015/2017 2017/04/03 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF599439 A/Kenya/008/2017 2017/03/05 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF599440 A/Kenya/010/2017 2017/03/07 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF599441 A/Kenya/012/2017 2017/03/10 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF599442 A/Kenya/013/2017 2017/03/12 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF599443 A/Kenya/003/2017 2017/02/01 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF629795 A/Trivandrum/MCVR261/2009 2009/08/21 7 (MP)
+GACCAATCTTGTCACCCCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amplicon_sequevars_to_dict/safelist.fasta	Fri Sep 07 15:22:34 2018 -0400
@@ -0,0 +1,12 @@
+>KY925925 A/Santo Antonio da Patrulha/LACENRS-2621/2012 2012/08/10 7 (MP)
+GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
+>KY925966 A/Porto Alegre/LACENRS-1075/2015 2015/05/29 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF441145 A/Korea/KUMC-GR66/2011 2011/12/01 7 (MP)
+GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
+CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
+>MF599435 A/Kenya/009/2017 2017/03/06 7 (MP)
+GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
+CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
--- a/test-data/amplicon_sequevars_with_safelist.fasta	Fri Sep 07 15:17:08 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
->KY925981 A/Bage/LACENRS-294/2011 2011/06/16 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
-CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->KY926040 A/Palmitinho/LACENRS-2595/2009 2009/08/31 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->KY926095 A/Porto Alegre/LACENRS-2380/2013 2013/07/15 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACAGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY926106 A/Santa Cruz do Sul/LACENRS-913/2011 2011/07/11 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->KY950187 A/Linkou/0181/2016 2016/12/21 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF039637 A/Zhejiang/DTID-ZJU01/2013 2013/04/07 7 (MP)
-GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCC
->MF039638 A/WSN/1933 1933// 7 (MP)
-GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGGGGACTGCAGCGTAGACGCTTTGTCCAAAATGCTC
->MF441160 A/Korea/KUMC-GR190/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAAAATGCCC
->MF441174 A/Korea/KUMC-GR689/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTTCAAAATGCCC
->MF593488 A/Mexico/4104/2016 2016/01/14 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAACGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF599436 A/Kenya/011/2017 2017/03/08 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTCTTCACGCTCACCGTGC
-CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF629795 A/Trivandrum/MCVR261/2009 2009/08/21 7 (MP)
-GACCAATCTTGTCACCCCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
--- a/test-data/amplicon_sequevars_with_safelist.txt	Fri Sep 07 15:17:08 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,64 +0,0 @@
----------------------------------------------------------------------------
-RESULTS OF SEARCH FOR EXACT MATCHES TO OLIGONUCLEOTIDES IN QUERY SEQUENCES:
----------------------------------------------------------------------------
-
-Analysis as of: Thu Sep  6 18:27:06 2018
-
-
----------------------------------------------------------------------------
-12 Different Amplicon Sequevars Found: test-data/amplicons.fasta 
-
-
-
-1 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGCCAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
-	KY925981
-
-2 Records in Sequevar: GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
-	KY926040
-	KY926049
-
-1 Records in Sequevar: GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACAGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
-	KY926095
-
-4 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
-	KY926106
-	MF441141
-	MF441149
-	MF441161
-
-5 Records in Sequevar: GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
-	KY950187
-	KY950217
-	MF599433
-	MF599434
-	MF599438
-
-4 Records in Sequevar: GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCC
-	MF039637
-	MF370249
-	MF370253
-	MF370257
-
-1 Records in Sequevar: GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGGGGACTGCAGCGTAGACGCTTTGTCCAAAATGCTC
-	MF039638
-
-1 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAAAATGCCC
-	MF441160
-
-1 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTTCAAAATGCCC
-	MF441174
-
-1 Records in Sequevar: GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAACGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
-	MF593488
-
-1 Records in Sequevar: GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTCTTCACGCTCACCGTGCCAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
-	MF599436
-
-1 Records in Sequevar: GACCAATCTTGTCACCCCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
-	MF629795
----------------------------------------------------------------------------
-
-END OF RESULTS
-
-Search Results (this file): test-data/output.txt
-Fasta sequences for analysis: test-data/output.fasta
\ No newline at end of file
--- a/test-data/amplicon_sequevars_without_safelist.fasta	Fri Sep 07 15:17:08 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
->KY925925 A/Santo Antonio da Patrulha/LACENRS-2621/2012 2012/08/10 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY925966 A/Porto Alegre/LACENRS-1075/2015 2015/05/29 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->KY925981 A/Bage/LACENRS-294/2011 2011/06/16 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
-CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->KY926040 A/Palmitinho/LACENRS-2595/2009 2009/08/31 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->KY926095 A/Porto Alegre/LACENRS-2380/2013 2013/07/15 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACAGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY926106 A/Santa Cruz do Sul/LACENRS-913/2011 2011/07/11 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->KY950187 A/Linkou/0181/2016 2016/12/21 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF039637 A/Zhejiang/DTID-ZJU01/2013 2013/04/07 7 (MP)
-GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCC
->MF039638 A/WSN/1933 1933// 7 (MP)
-GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGGGGACTGCAGCGTAGACGCTTTGTCCAAAATGCTC
->MF441145 A/Korea/KUMC-GR66/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441160 A/Korea/KUMC-GR190/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAAAATGCCC
->MF441174 A/Korea/KUMC-GR689/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTTCAAAATGCCC
->MF593488 A/Mexico/4104/2016 2016/01/14 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAACGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF599435 A/Kenya/009/2017 2017/03/06 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF599436 A/Kenya/011/2017 2017/03/08 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTCTTCACGCTCACCGTGC
-CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF629795 A/Trivandrum/MCVR261/2009 2009/08/21 7 (MP)
-GACCAATCTTGTCACCCCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
--- a/test-data/amplicon_sequevars_without_safelist.txt	Fri Sep 07 15:17:08 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,148 +0,0 @@
----------------------------------------------------------------------------
-RESULTS OF SEARCH FOR EXACT MATCHES TO OLIGONUCLEOTIDES IN QUERY SEQUENCES:
----------------------------------------------------------------------------
-
-Analysis as of: Thu Sep  6 18:19:51 2018
-
-
----------------------------------------------------------------------------
-16 Different Amplicon Sequevars Found: test-data/amplicons.fasta 
-
-
-
-36 Records in Sequevar: GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
-	KY925925
-	KY925930
-	KY925952
-	KY925960
-	KY925968
-	KY926011
-	KY926047
-	KY926053
-	KY926055
-	KY926082
-	KY926097
-	KY926123
-	KY926125
-	KY926132
-	KY950197
-	KY950209
-	KY950219
-	MF593496
-	MF593504
-	MF593512
-	MF593520
-	MF593528
-	MF593533
-	MF593538
-	MF593544
-	MF593549
-	MF593557
-	MF593562
-	MF593570
-	MF593578
-	MF593586
-	MF593594
-	MF593602
-	MF593610
-	MF593615
-	MF593623
-
-23 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
-	KY925966
-	KY925996
-	KY926140
-	MF441140
-	MF441142
-	MF441143
-	MF441144
-	MF441146
-	MF441150
-	MF441151
-	MF441153
-	MF441156
-	MF441157
-	MF441163
-	MF441164
-	MF441165
-	MF441166
-	MF441167
-	MF441168
-	MF441169
-	MF441170
-	MF441172
-	MF441173
-
-1 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGCCAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
-	KY925981
-
-2 Records in Sequevar: GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
-	KY926040
-	KY926049
-
-1 Records in Sequevar: GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACAGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
-	KY926095
-
-4 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
-	KY926106
-	MF441141
-	MF441149
-	MF441161
-
-5 Records in Sequevar: GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
-	KY950187
-	KY950217
-	MF599433
-	MF599434
-	MF599438
-
-4 Records in Sequevar: GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCC
-	MF039637
-	MF370249
-	MF370253
-	MF370257
-
-1 Records in Sequevar: GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGGGGACTGCAGCGTAGACGCTTTGTCCAAAATGCTC
-	MF039638
-
-10 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
-	MF441145
-	MF441147
-	MF441148
-	MF441152
-	MF441154
-	MF441155
-	MF441158
-	MF441159
-	MF441162
-	MF441171
-
-1 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAAAATGCCC
-	MF441160
-
-1 Records in Sequevar: GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTTCAAAATGCCC
-	MF441174
-
-1 Records in Sequevar: GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAACGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
-	MF593488
-
-7 Records in Sequevar: GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGCCAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
-	MF599435
-	MF599437
-	MF599439
-	MF599440
-	MF599441
-	MF599442
-	MF599443
-
-1 Records in Sequevar: GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTCTTCACGCTCACCGTGCCAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
-	MF599436
-
-1 Records in Sequevar: GACCAATCTTGTCACCCCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
-	MF629795
----------------------------------------------------------------------------
-
-END OF RESULTS
-
-Search Results (this file): amplicon_sequevars_without_safelist.txt
-Fasta sequences for analysis: amplicon_sequevars_without_safelist.fasta
\ No newline at end of file
--- a/test-data/amplicons.fasta	Fri Sep 07 15:17:08 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,297 +0,0 @@
->KY925925 A/Santo Antonio da Patrulha/LACENRS-2621/2012 2012/08/10 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY925930 A/Novo Hamburgo/LACENRS-385/2016 2016/04/04 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY925952 A/Viamao/LACENRS-1400/2011 2011/08/22 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY925960 A/Gramado/LACENRS-1287/2016 2016/04/29 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY925966 A/Porto Alegre/LACENRS-1075/2015 2015/05/29 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->KY925968 A/Santa Cruz do Sul/LACENRS-2672/2013 2013/07/22 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY925981 A/Bage/LACENRS-294/2011 2011/06/16 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
-CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->KY925996 A/Canoas/LACENRS-1793/2015 2015/07/17 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->KY926011 A/Tres Coroas/LACENRS-1810/2012 2012/07/23 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY926040 A/Palmitinho/LACENRS-2595/2009 2009/08/31 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->KY926047 A/Sao Gabriel/LACENRS-1809/2012 2012/07/23 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY926049 A/Sao Gabriel/LACENRS-1626/2009 2009/08/14 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->KY926053 A/Uruguaiana/LACENRS-296/2016 2016/03/27 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY926055 A/Caibate/LACENRS-903/2012 2012/07/08 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY926082 A/Camaqua/LACENRS-623/2011 2011/07/01 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY926095 A/Porto Alegre/LACENRS-2380/2013 2013/07/15 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACAGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY926097 A/Caxias do Sul/LACENRS-1186/2011 2011/08/31 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY926106 A/Santa Cruz do Sul/LACENRS-913/2011 2011/07/11 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->KY926123 A/Canoas/LACENRS-1320/2016 2016/05/02 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY926125 A/Cruz Alta/LACENRS-499/2012 2012/06/27 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY926132 A/Nova Petropolis/LACENRS-1205/2013 2013/06/07 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY926140 A/Porto Alegre/LACENRS-1887/2015 2015/07/25 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->KY950187 A/Linkou/0181/2016 2016/12/21 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->KY950197 A/Baltimore/0026/2016 2016/01/16 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY950209 A/Baltimore/0077/2016 2016/02/23 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY950217 A/Baltimore/0247/2017 2017/01/25 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->KY950219 A/Linkou/0004/2015 2015/11/06 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF039637 A/Zhejiang/DTID-ZJU01/2013 2013/04/07 7 (MP)
-GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCC
->MF039638 A/WSN/1933 1933// 7 (MP)
-GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGGGGACTGCAGCGTAGACGCTTTGTCCAAAATGCTC
->MF370249 A/Changsha/26/2017 2017/02/04 7 (MP)
-GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCC
->MF370253 A/Changsha/41/2017 2017/03/12 7 (MP)
-GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCC
->MF370257 A/Changsha/44/2017 2017/03/14 7 (MP)
-GACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGGTTTGTCCAAAACGCCC
->MF441140 A/Korea/KUMC-GR14/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441141 A/Korea/KUMC-GR17/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441142 A/Korea/KUMC-GR18/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441143 A/Korea/KUMC-GR47/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441144 A/Korea/KUMC-GR55/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441145 A/Korea/KUMC-GR66/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441146 A/Korea/KUMC-GR83/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441147 A/Korea/KUMC-GR90/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441148 A/Korea/KUMC-GR92/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441149 A/Korea/KUMC-GR96/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441150 A/Korea/KUMC-GR99/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441151 A/Korea/KUMC-GR115/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441152 A/Korea/KUMC-GR116/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441153 A/Korea/KUMC-GR121/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441154 A/Korea/KUMC-GR124/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441155 A/Korea/KUMC-GR137/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441156 A/Korea/KUMC-GR157/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441157 A/Korea/KUMC-GR159/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441158 A/Korea/KUMC-GR172/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441159 A/Korea/KUMC-GR175/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441160 A/Korea/KUMC-GR190/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAAAATGCCC
->MF441161 A/Korea/KUMC-GR195/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441162 A/Korea/KUMC-GR202/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441163 A/Korea/KUMC-GR218/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441164 A/Korea/KUMC-GR226/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441165 A/Korea/KUMC-GR227/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441166 A/Korea/KUMC-GR252/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441167 A/Korea/KUMC-GR261/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441168 A/Korea/KUMC-GR281/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441169 A/Korea/KUMC-GR285/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441170 A/Korea/KUMC-GR437/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441171 A/Korea/KUMC-GR567/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441172 A/Korea/KUMC-GR570/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441173 A/Korea/KUMC-GR590/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441174 A/Korea/KUMC-GR689/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGGTTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTTCAAAATGCCC
->MF593488 A/Mexico/4104/2016 2016/01/14 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAACGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593496 A/Mexico/4431/2016 2016/03/01 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593504 A/Mexico/4433/2016 2016/02/28 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593512 A/Mexico/4435/2016 2016/03/02 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593520 A/Mexico/4436/2016 2016/02/28 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593528 A/Mexico/4440/2016 2016/03/16 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593533 A/Mexico/4604/2017 2017/02/10 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593538 A/Mexico/4621/2017 2017/02/18 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593544 A/Mexico/4627/2017 2017/02/24 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593549 A/Mexico/4628/2017 2017/03/02 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593557 A/Mexico/4687/2017 2017/03/12 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593562 A/Mexico/4703/2017 2017/03/21 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593570 A/Mexico/7317/2017 2017/01/16 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593578 A/Mexico/8017/2017 2017/01/17 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593586 A/Mexico/8517/2017 2017/01/18 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593594 A/Mexico/11417/2017 2017/01/23 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593602 A/Mexico/12317/2017 2017/01/24 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593610 A/Mexico/15017/2017 2017/01/26 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593615 A/Mexico/15517/2017 2017/01/27 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF593623 A/Mexico/17517/2017 2017/01/30 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->MF599433 A/Kenya/001/2017 2017/01/01 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF599434 A/Kenya/002/2017 2017/01/02 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF599435 A/Kenya/009/2017 2017/03/06 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF599436 A/Kenya/011/2017 2017/03/08 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTCTTCACGCTCACCGTGC
-CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF599437 A/Kenya/014/2017 2017/03/13 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF599438 A/Kenya/015/2017 2017/04/03 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF599439 A/Kenya/008/2017 2017/03/05 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF599440 A/Kenya/010/2017 2017/03/07 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF599441 A/Kenya/012/2017 2017/03/10 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF599442 A/Kenya/013/2017 2017/03/12 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF599443 A/Kenya/003/2017 2017/02/01 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF629795 A/Trivandrum/MCVR261/2009 2009/08/21 7 (MP)
-GACCAATCTTGTCACCCCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
--- a/test-data/safelist.fasta	Fri Sep 07 15:17:08 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
->KY925925 A/Santo Antonio da Patrulha/LACENRS-2621/2012 2012/08/10 7 (MP)
-GACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTATCCAAAATGCCC
->KY925966 A/Porto Alegre/LACENRS-1075/2015 2015/05/29 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF441145 A/Korea/KUMC-GR66/2011 2011/12/01 7 (MP)
-GACCAATTCTGTCACCTCTGACTAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGC
-CCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
->MF599435 A/Kenya/009/2017 2017/03/06 7 (MP)
-GACCAATTCTGTCACCTTTGACTAAGGGGATTTTAGGGTTTGTTTTCACGCTCACCGTGC
-CAAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/amplicon_sequevars_to_dict/amplicon_sequevars_to_dict.py	Fri Sep 07 15:22:34 2018 -0400
@@ -0,0 +1,113 @@
+#!/usr/bin/env python
+'''Reads in nucleotide sequences from a fasta file as SeqRecords and sorts into a dictionary,
+with unique sequences as keys and lists of SeqRecords sharing these sequevars as values. If the user
+specified a fasta file containing sequences which have been empirically determined to amplify in the 
+PCR (i.e. "safelist"), the sequevars are compared to this safelist prior to being output to fasta. Sequence
+identifiers (usually Genbank accession numbers) of sequences in a sequevar are printed to a text file.
+
+Usage with safelist: python sequevarsToDict.py -s safelist.fasta unmatching_sequences.fasta  Mar20_sequevars
+Usage without safelist: python sequevars_to_dict.py unmatching_sequences.fasta  Mar20_sequevars
+'''
+
+'''Author: Diane Eisler, Molecular Microbiology & Genomics, BCCDC Public Health Laboratory, March 2018'''
+
+import sys,string,os, time, Bio, re, argparse
+from Bio import Seq, SeqIO, SeqUtils, Alphabet, SeqRecord
+from Bio.Alphabet import IUPAC
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+import Bio.Data.IUPACData
+
+#parse command line arguments
+parser = argparse.ArgumentParser()
+parser.add_argument("-s", dest = "safelist", help = "specify filename of previously vetted sequences",
+    action = "store")
+parser.add_argument("fastaToParse")
+parser.add_argument("outFileHandle")
+results = parser.parse_args()
+print("ARGUMENTS:")
+print(results)
+print('safelist = ', results.safelist)
+
+#construct output filenames
+gb_accessionsHandle = results.outFileHandle + ".txt" #user-specified output file name
+gb_accessions= open(gb_accessionsHandle,'w') #output file of GB access #'s and details re: which oligos NOT found
+outputFastaHandle = results.outFileHandle + ".fasta" #create fasta file from  user specified name
+
+def outputInformationFile(sequevars):
+    '''Outputs text file with unique amplicon sequences and id's of sequences in each sequevar.'''
+    localtime = time.asctime(time.localtime(time.time())) #date and time of analysis
+    gb_accessions.write("---------------------------------------------------------------------------\n")
+    gb_accessions.write("RESULTS OF SEARCH FOR EXACT MATCHES TO OLIGONUCLEOTIDES IN QUERY SEQUENCES:\n")
+    gb_accessions.write("---------------------------------------------------------------------------\n\n")
+    gb_accessions.write("Analysis as of: " + localtime + "\n\n")
+    gb_accessions.write("\n---------------------------------------------------------------------------\n")
+    #if there are sequevars for further analysis, output them to the results .txt and fasta files
+    if len(sequevars) > 0: #if there are sequevars to output, write to list with sequence id's in sequevar
+        outputSequevarsToFasta(sequevars) #output fasta file of sequevars i.e.representative record
+        gb_accessions.write("%i Different Amplicon Sequevars Found: %s \n\n" % (len(sequevars),results.fastaToParse))
+        for sequevar in sequevars:
+            print("\nSequevar: %s" % sequevar) #print sequevar to console
+            recordList = sequevars[sequevar]
+            gb_accessions.write("\n\n%i Records in Sequevar: %s" % (len(recordList),sequevar)) #write sequevar to file
+            print("%i Record(s) have this sequence:" % (len(recordList)))
+            for record in recordList:
+                print("\t" + record.id) #print record id to console
+                gb_accessions.write("\n\t" + record.id) #write records with this sequence to file
+    else: #if not sequevars to output, print message to outfile to clarify this
+        gb_accessions.write("No sequevars requiring further investigation.")
+    gb_accessions.write("\n---------------------------------------------------------------------------")
+    gb_accessions.write("\n\nEND OF RESULTS\n")
+    #print output filepaths to console and to search results file
+    gb_accessions.write("\nSearch Results (this file): " + gb_accessionsHandle)
+    print("\nSearch Results: " + gb_accessionsHandle)
+    if len(sequevars) > 0: #if there are sequevars to print to fasta, direct user to fasta file
+        gb_accessions.write("\nFasta sequences for analysis: " + outputFastaHandle)
+        print("Fasta sequences for analysis: " + outputFastaHandle)
+    else:
+        gb_accessions.write("\nFasta sequences for analysis: N/A")
+        print("Fasta sequences for analysis: N/A\n")
+    return
+
+def outputSequevarsToFasta(sequevars):
+    '''Output a fasta file with one representative sequence for each sequevar.'''
+    output_fasta = open(outputFastaHandle, 'w') #create a writeable fasta file
+    sequevars_list = []
+    for sequevar in sequevars:
+        first_record = sequevars[sequevar][0] #grab the first SeqRecord in the list sharing the sequevar
+        sequevars_list.append(first_record)  #add it to the list of SeqRecords
+    SeqIO.write(sequevars_list, output_fasta, "fasta") #write the sequevars to fasta
+    return
+
+with open(results.fastaToParse,'r') as inFile:
+    #read nucleotide sequences from fasta file into SeqRecords, uppercases and adds to a list
+    seqList = [rec.upper() for rec in list(SeqIO.parse(inFile, "fasta", alphabet=IUPAC.ambiguous_dna))]
+    sequevars = {} # empty dictionary of sequevar: list<SeqRecord>
+    safe_seqs = [] # empty list of nucleotide sequences
+
+    if results.safelist: #if safelist specified by user, read these sequences into a list
+        safe_seqs = [record.seq for record in SeqIO.parse(results.safelist, "fasta", alphabet=IUPAC.ambiguous_dna)]
+        print("Safeseqs:")
+        for seq in safe_seqs:
+            print(seq) #print all the vetted unique sequences
+        
+    for record in seqList: #parse SeqRecord for exact match to amplicon or reverse complement
+        sequence = str(record.seq)
+        #check if the sequence has already been tested and vetted (i.e. in safelist)
+        if (sequence in safe_seqs): #only add to dictionary if not previously tested
+            print("Sequence from %s in safe list!" % (record.id) )#print mssg to console
+        else:
+            #if the sequence is a key in the dict, add SeqRecord to list
+            if sequence in sequevars:
+                sequevars[sequence].append(record)
+            else:
+                #add sequence as new key to dict, accessing a list with SeqRecord  as its first item
+                sequevars[sequence] = [record]
+    #get a sorted list of unique sequence keys
+    sorted_unique_seq_keys = sorted(sequevars.keys())
+    #process list of SeqRecords in each sequevar and print to results summary file for end-user        
+    outputInformationFile(sequevars) #output information .txt file
+    #outputSequevarsToFasta(sequevars) #output fasta file of sequevars i.e.representative record      
+
+inFile.close()
+gb_accessions.close()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/amplicon_sequevars_to_dict/amplicon_sequevars_to_dict.xml	Fri Sep 07 15:22:34 2018 -0400
@@ -0,0 +1,35 @@
+<tool id="amplicon_sequevars_to_dict" name="Amplicon Sequevars To Dictionary" version="0.0.1">
+  <requirements>
+    <requirement type="package" version="1.70">biopython</requirement>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+    $__tool_directory__/amplicon_sequevars_to_dict.py
+    '$input_fasta'
+    '$oligo_def_file'
+    '$output_fasta'
+    '$output_txt'
+  ]]></command>
+  <inputs>
+    <param name="input_fasta" format="fasta" type="data" />
+    <param name="oligo_def_file" format="csv" type="data" />
+  </inputs>
+  <outputs>
+      <data format="fasta" name="output_fasta"></data>
+      <data format="txt" name="output_txt"></data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_fasta" value="amplicons.fasta" />
+      <param name="oligo_def_file" value="Flu4plex_FluA_oligo_definitions.csv" />
+      <output name="output_fasta" value="output.fasta" />
+      <output name="output_txt" value="output.txt" />
+    </test>
+  </tests>
+  <help><![CDATA[
+    Sorts a fasta file of PCR amplicons into unique sequence groupings (ignoring any present in a trusted sequence'safelist') and outputs sequevars (fasta) and a summary (txt).
+  ]]></help>
+  <citations>
+  </citations>
+</tool>
+
+#NEEDS MODIFICATIONS!!!
\ No newline at end of file