--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/hyphy_summary.py	Wed Jun 09 06:59:09 2021 +0000
@@ -0,0 +1,668 @@
+import argparse
+import json
+import re
+from collections import defaultdict
+
+import BioExt
+from Bio import SeqIO
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+from BioExt.uds import _align_par
+
+
+class HyPhySummary(object):
+
+    def __init__(self, arguments, summary_json=None, annotation_json=None):
+        self.arguments = arguments
+        self.ref_map = ''
+        self.summary_json = {}
+        self.annotation_json = {}
+        self.include_in_annotation = {}
+        self.test_map = {}
+        self.site_reports = {}
+        self.labels = {}
+        self.ref_seq_map = []
+        self.cfel = {}
+        self.relax = {}
+        self.busted = {}
+        self.slac = {}
+        self.fel = {}
+        self.meme = {}
+        self.meme_full = {}
+        self.prime = {}
+        self.fade = {}
+        self.bgm = {}
+        self.ref_genes = [
+            ['genome', 'ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTGTCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCAGACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGAGATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTGATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTGGCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTAGGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCCTACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTTAACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAAGCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGTACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAAGGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAATTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAGAAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATTTGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAACAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTCAACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTTAAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACAGTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTACTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAGTTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGTGAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTATTATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAATGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGTGAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTAAACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAAGCTTGTGTTGAAGAAGTTACAACAACTCTGGAAGAAACTAAGTTCCTCACAGAAAACTTGTTACTTTATATTGACATTAATGGCAATCTTCATCCAGATTCTGCCACTCTTGTTAGTGACATTGACATCACTTTCTTAAAGAAAGATGCTCCATATATAGTGGGTGATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAATGCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAATGGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTATTATCTCTAATGAGAAGCAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGCAGAAGAAACACGCAAATTAATGCCTGTCTGTGTGGAAACTAAAGCCATAGTTTCAACTATACAGCGTAAATATAAGGGTATTAAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAACAACTGTAGCGTCACTTATCAACACACTTAACGATCTAAATGAAACTCTTGTTACAATGCCACTTGGCTATGTAACACATGGCTTAAATTTGGAAGAAGCTGCTCGGTATATGAGATCTCTCAAAGTGCCAGCTACAGTTTCTGTTTCTTCACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAGAACATTTTATTGAAACCATCTCACTTGCTGGTTCCTATAAAGATTGGTCCTATTCTGGACAATCTACACAACTAGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCACCTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTAAGGTGTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACAACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGTAAAACATTTTATGTTTTACCTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTGATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAATGGTTTAACTTCTATTAAATGGGCAGATAACAACTGTTATCTTGCCACTGCATTGTTAACACTCCAACAAATAGAGTTGAAGTTTAATCCACCTGCTCTACAAGATGCTTATTACAGAGCAAGGGCTGGTGAAGCTGCTAACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAATGAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGTGGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTACATGGGCACACTTTCTTATGAACAATTTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTCACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGTGAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATAACTTCTAAAGAAACTTTGTATTGCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGTTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAATTGACCCTAAGTTGGACAATTATTATAAGAAAGACAATTCTTATTTCACAGAGCAACCAATTGATCTTGTACCAAACCAACCATATCCAAACGCAAGCTTCGATAATTTTAAGTTTGTATGTGATAATATCAAATTTGCTGATGATTTAAACCAGTTAACTGGTTATAAGAAACCTGCTTCAAGAGAGCTTAAAGTTACATTTTTCCCTGACTTAAATGGTGATGTGGTGGCTATTGATTATAAACACTACACACCCTCTTTTAAGAAAGGAGCTAAATTGTTACATAAACCTATTGTTTGGCATGTTAACAATGCAACTAATAAAGCCACGTATAAACCAAATACCTGGTGTATACGTTGTCTTTGGAGCACAAAACCAGTTGAAACATCAAATTCGTTTGATGTACTGAAGTCAGAGGACGCGCAGGGAATGGATAATCTTGCCTGCGAAGATCTAAAACCAGTCTCTGAAGAAGTAGTGGAAAATCCTACCATACAGAAAGACGTTCTTGAGTGTAATGTGAAAACTACCGAAGTTGTAGGAGACATTATACTTAAACCAGCAAATAATAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTTACTATTAAGAAACCTAATGAATTATCTAGAGTATTAGGTTTGAAAACCCTTGCTACTCATGGTTTAGCTGCTGTTAATAGTGTCCCTTGGGATACTATAGCTAATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTACAACTACTAACATAGTTACACGGTGTTTAAACCGTGTTTGTACTAATTATATGCCTTATTTCTTTACTTTATTGCTACAATTGTGTACTTTTACTAGAAGTACAAATTCTAGAATTAAAGCATCTATGCCGACTACTATAGCAAAGAATACTGTTAAGAGTGTCGGTAAATTTTGTCTAGAGGCTTCATTTAATTATTTGAAGTCACCTAATTTTTCTAAACTGATAAATATTATAATTTGGTTTTTACTATTAAGTGTTTGCCTAGGTTCTTTAATCTACTCAACCGCTGCTTTAGGTGTTTTAATGTCTAATTTAGGCATGCCTTCTTACTGTACTGGTTACAGAGAAGGCTATTTGAACTCTACTAATGTCACTATTGCAACCTACTGTACTGGTTCTATACCTTGTAGTGTTTGTCTTAGTGGTTTAGATTCTTTAGACACCTATCCTTCTTTAGAAACTATACAAATTACCATTTCATCTTTTAAATGGGATTTAACTGCTTTTGGCTTAGTTGCAGAGTGGTTTTTGGCATATATTCTTTTCACTAGGTTTTTCTATGTACTTGGATTGGCTGCAATCATGCAATTGTTTTTCAGCTATTTTGCAGTACATTTTATTAGTAATTCTTGGCTTATGTGGTTAATAATTAATCTTGTACAAATGGCCCCGATTTCAGCTATGGTTAGAATGTACATCTTCTTTGCATCATTTTATTATGTATGGAAAAGTTATGTGCATGTTGTAGACGGTTGTAATTCATCAACTTGTATGATGTGTTACAAACGTAATAGAGCAACAAGAGTCGAATGTACAACTATTGTTAATGGTGTTAGAAGGTCCTTTTATGTCTATGCTAATGGAGGTAAAGGCTTTTGCAAACTACACAATTGGAATTGTGTTAATTGTGATACATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGTTGCGAGAGACTTGTCACTACAGTTTAAAAGACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCATCTTTACTTTGATAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGACAACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAGTTTTTGATGGTAAATCAAAATGTGAAGAATCATCTGCAAAATCAGCGTCTGTTTACTACAGTCAGCTTATGTGTCAACCTATACTGTTACTAGATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTTAATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTGAACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGTTGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATCAATCTGACATAGAAGTTACTGGCGATAGTTGTAATAACTATATGCTCACCTATAACAAAGTTGAAAACATGACACCCCGTGACCTTGGTGCTTGTATTGACTGTAGTGCGCGTCATATTAATGCGCAGGTAGCAAAAAGTCACAACATTGCTTTGATATGGAACGTTAAAGATTTCATGTCATTGTCTGAACAACTACGAAAACAAATACGTAGTGCTGCTAAAAAGAATAACTTACCTTTTAAGTTGACATGTGCAACTACTAGACAAGTTGTTAATGTTGTAACAACAAAGATAGCACTTAAGGGTGGTAAAATTGTTAATAATTGGTTGAAGCAGTTAATTAAAGTTACACTTGTGTTCCTTTTTGTTGCTGCTATTTTCTATTTAATAACACCTGTTCATGTCATGTCTAAACATACTGACTTTTCAAGTGAAATCATAGGATACAAGGCTATTGATGGTGGTGTCACTCGTGACATAGCATCTACAGATACTTGTTTTGCTAACAAACATGCTGATTTTGACACATGGTTTAGCCAGCGTGGTGGTAGTTATACTAATGACAAAGCTTGCCCATTGATTGCTGCAGTCATAACAAGAGAAGTGGGTTTTGTCGTGCCTGGTTTGCCTGGCACGATATTACGCACAACTAATGGTGACTTTTTGCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACACCATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTTTAAAGATGCTTCTGGTAAGCCAGTACCATATTGTTATGATACCAATGTACTAGAAGGTTCTGTTGCTTATGAAAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACCTTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATCAGAAGCTGGTGTTTGTGTATCTACTAGTGGTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCAGGAGTTTTCTGTGGTGTAGATGCTGTAAATTTACTTACTAATATGTTTACACCACTAATTCAACCTATTGGTGCTTTGGACATATCAGCATCTATAGTAGCTGGTGGTATTGTAGCTATCGTAGTAACATGCCTTGCCTACTATTTTATGAGGTTTAGAAGAGCTTTTGGTGAATACAGTCATGTAGTTGCCTTTAATACTTTACTATTCCTTATGTCATTCACTGTACTCTGTTTAACACCAGTTTACTCATTCTTACCTGGTGTTTATTCTGTTATTTACTTGTACTTGACATTTTATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATGTTCACACCTTTAGTACCTTTCTGGATAACAATTGCTTATATCATTTGTATTTCCACAAAGCATTTCTATTGGTTCTTTAGTAATTACCTAAAGAGACGTGTAGTCTTTAATGGTGTTTCCTTTAGTACTTTTGAAGAAGCTGCGCTGTGCACCTTTTTGTTAAATAAAGAAATGTATCTAAAGTTGCGTAGTGATGTGCTATTACCTCTTACGCAATATAATAGATACTTAGCTCTTTATAATAAGTACAAGTATTTTAGTGGAGCAATGGATACAACTAGCTACAGAGAAGCTGCTTGTTGTCATCTCGCAAAGGCTCTCAATGACTTCAGTAACTCAGGTTCTGATGTTCTTTACCAACCACCACAAACCTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCCATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTTGATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAGATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGGACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAGTTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTTACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGGTTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCATGCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTACGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTTTCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGGCTATGAAGTACAATTATGAACCTCTAACACAAGACCATGTTGACATACTAGGACCTCTTTCTGCTCAAACTGGAATTGCCGTTTTAGATATGTGTGCTTCATTAAAAGAATTACTGCAAAATGGTATGAATGGACGTACCATATTGGGTAGTGCTTTATTAGAAGATGAATTTACACCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACAATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAGTTTTAGTCCAGAGTACTCAATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTCTGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCCACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATATGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTGTGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTCTTAGGCTATTTTTGTACTTGTTACTTTGGCCTCTTTTGTTTACTCAACCGCTACTTTAGACTGACTCTTGGTGTTTATGATTACTTAGTTTCTACACAGGAGTTTAGATATATGAATTCACAGGGACTACTCCCACCCAAGAATAGCATAGATGCCTTCAAACTCAACATTAAATTGTTGGGTGTTGGTGGCAAACCTTGTATCAAAGTAGCCACTGTACAGTCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTACACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACTTGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATCTATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTATACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGTGTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGGTGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTAAAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATGACCCTGTGGGTTTTACACTTAAAAACACAGTCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCAGTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCACAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAAATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTTGTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTCCAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCAACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGACACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATGATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTTAAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAAGATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTGTAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGTTGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTAAAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATGACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACCTACAAGTTTTGGACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAGCTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGTATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTCAGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTATGACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTCAGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAGACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCTAACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGACTTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCCTACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTCTCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAGGAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAGTGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTTAGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATAGATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACCAGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTCACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTACAACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGCATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTATGCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTATGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATACAATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCCGGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTATAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATACATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGATAACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAGGCTGTTGGGGCTTGTGTTCTTTGCAATTCACAGACTTCATTAAGATGTGGTGCTTGCATACGTAGACCATTCTTATGTTGTAAATGCTGTTACGACCATGTCATATCAACATCACATAAATTAGTCTTGTCTGTTAATCCGTATGTTTGCAATGCTCCAGGTTGTGATGTCACAGATGTGACTCAACTTTACTTAGGAGGTATGAGCTATTATTGTAAATCACATAAACCACCCATTAGTTTTCCATTGTGTGCTAATGGACAAGTTTTTGGTTTATATAAAAATACATGTGTTGGTAGCGATAATGTTACTGACTTTAATGCAATTGCAACATGTGACTGGACAAATGCTGGTGATTACATTTTAGCTAACACCTGTACTGAAAGACTCAAGCTTTTTGCAGCAGAAACGCTCAAAGCTACTGAGGAGACATTTAAACTGTCTTATGGTATTGCTACTGTACGTGAAGTGCTGTCTGACAGAGAATTACATCTTTCATGGGAAGTTGGTAAACCTAGACCACCACTTAACCGAAATTATGTCTTTACTGGTTATCGTGTAACTAAAAACAGTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACCGAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATTAAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATATCTCAGATGAGTTTTCTAGCAATGTTGCAAATTATCAAAAGGTTGGTATGCAAAAGTATTCTACACTCCAGGGACCACCTGGTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGTGTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGATAAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACATTAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGAAATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCAGCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCACAAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTATAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGCTCAGAATATGACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTAATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTTGCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTCTTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACACTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACTCATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTATCACCCGCGAAGAAGCTATAAGACATGTACGTGCATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTGTTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTATGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAACACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAAGTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATCTATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTTTCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTATGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCATGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTTAAGCGTGTTGACTGGACTATTGAATATCCTATAATTGGTGATGAACTGAAGATTAATGCGGCTTGTAGAAAGGTTCAACACATGGTTGTTAAAGCTGCATTATTAGCAGACAAATTCCCAGTTCTTCACGACATTGGTAACCCTAAAGCTATTAAGTGTGTACCTCAAGCTGATGTAGAATGGAAGTTCTATGATGCACAGCCTTGTAGTGACAAAGCTTATAAAATAGAAGAATTATTCTATTCTTATGCCACACATTCTGACAAATTCACAGATGGTGTATGCCTATTTTGGAATTGCAATGTCGATAGATATCCTGCTAATTCCATTGTTTGTAGATTTGACACTAGAGTGCTATCTAACCTTAACTTGCCTGGTTGTGATGGTGGCAGTTTGTATGTAAATAAACATGCATTCCACACACCAGCTTTTGATAAAAGTGCTTTTGTTAATTTAAAACAATTACCATTTTTCTATTACTCTGACAGTCCATGTGAGTCTCATGGAAAACAAGTAGTGTCAGATATAGATTATGTACCACTAAAGTCTGCTACGTGTATAACACGTTGCAATTTAGGTGGTGCTGTCTGTAGACATCATGCTAATGAGTACAGATTGTATCTCGATGCTTATAACATGATGATCTCAGCTGGCTTTAGCTTGTGGGTTTACAAACAATTTGATACTTATAACCTCTGGAACACTTTTACAAGACTTCAGAGTTTAGAAAATGTGGCTTTTAATGTTGTAAATAAGGGACACTTTGATGGACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACACTGTTTACACAAAAGTTGATGGTGTTGATGTAGAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCATTTGAGCTTTGGGCTAAGCGCAACATTAAACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGACATTGCTGCTAATACTGTGATCTGGGACTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAACCAACTGAAACGATTTGTGCACCACTCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTATTTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCCCAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAGAAAGTTGATGGTGTTGTCCAACAATTACCTGAAACTTACTTTACTCAGAGTAGAAATTTACAAGAATTTAAACCCAGGAGTCAAATGGAAATTGATTTCTTAGAATTAGCTATGGATGAATTCATTGAACGGTATAAATTAGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTAGTCATAGTCAGTTAGGTGGTTTACATCTACTGATTGGACTAGCTAAACGTTTTAAGGAATCACCTTTTGAATTAGAAGATTTTATTCCTATGGACAGTACAGTTAAAAACTATTTCATAACAGATGCGCAAACAGGTTCATCTAAGTGTGTGTGTTCTGTTATTGATTTATTACTTGATGATTTTGTTGAAATAATAAAATCCCAAGATTTATCTGTAGTTTCTAAGGTTGTCAAAGTGACTATTGACTATACAGAAATTTCATTTATGCTTTGGTGTAAAGATGGCCATGTAGAAACATTTTACCCAAAATTACAATCTAGTCAAGCGTGGCAACCGGGTGTTGCTATGCCTAATCTTTACAAAATGCAAAGAATGCTATTAGAAAAGTGTGACCTTCAAAATTATGGTGATAGTGCAACATTACCTAAAGGCATAATGATGAATGTCGCAAAATATACTCAACTGTGTCAATATTTAAACACATTAACATTAGCTGTACCCTATAATATGAGAGTTATACATTTTGGTGCTGGTTCTGATAAAGGAGTTGCACCAGGTACAGCTGTTTTAAGACAGTGGTTGCCTACGGGTACGCTGCTTGTCGATTCAGATCTTAATGACTTTGTCTCTGATGCAGATTCAACTTTGATTGGTGATTGTGCAACTGTACATACAGCTAATAAATGGGATCTCATTATTAGTGATATGTACGACCCTAAGACTAAAAATGTTACAAAAGAAAATGACTCTAAAGAGGGTTTTTTCACTTACATTTGTGGGTTTATACAACAAAAGCTAGCTCTTGGAGGTTCCGTGGCTATAAAGATAACAGAACATTCTTGGAATGCTGATCTTTATAAGCTCATGGGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCATCATCTGAAGCATTTTTAATTGGATGTAATTATCTTGGCAAACCACGCGAACAAATAGATGGTTATGTCATGCATGCAAATTACATATTTTGGAGGAATACAAATCCAATTCAGTTGTCTTCCTATTCTTTATTTGACATGAGTAAATTTCCCCTTAAATTAAGGGGTACTGCTGTTATGTCTTTAAAAGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAGGTAGACTTATAATTAGAGAAAACAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAAACGAACAATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGAATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTCGCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCTTGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGTGTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACTCACACCTTTTGCTCGTTGCTGCTGGCCTTGAAGCCCCTTTTCTCTATCTTTATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAATAATAATGAGGCTTTGGCTTTGCTGGAAATGCCGTTCCAAAAACCCATTACTTTATGATGCCAACTATTTTCTTTGCTGGCATACTAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTACTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATGGGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCAACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGCCTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAATTTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGATCTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGATTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTCCTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAATAAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTCTCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGTGATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAGCAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACATACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACTGTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTGCTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAAGATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTGTAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCCGTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAATTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCTGTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGAAGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTGATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAGTAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACTGCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTCCAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAAAAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAACATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGTAGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCAATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGGTAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGGCAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCCAAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACAATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACGTGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGCTGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGCTGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCTTTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTACGATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAATTTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA']
+        ]
+        # 0-based gene coordinates
+        # from, to, name, within gene codon offset (to deal with ORF1a/b overlap)
+        self.gene_coordinates = [[265, 13482, 'ORF1a', 0],
+                                 [13467, 21554, 'ORF1b', -1],
+                                 [21562, 25383, 'S', 0],
+                                 [25392, 26219, 'ORF3a', 0],
+                                 [26244, 26471, 'E', 0],
+                                 [26522, 27190, 'M', 0],
+                                 [27201, 27386, 'ORF6', 0],
+                                 [27393, 27758, 'ORF7a', 0],
+                                 [27893, 28258, 'ORF8', 0],
+                                 [28273, 29532, 'N', 0],
+                                 [29557, 29673, 'ORF10', 0]]
+        self.score_matrix_ = BioExt.scorematrices.DNA95.load()
+        if summary_json is not None:
+            self.summary_json = summary_json
+        if annotation_json is not None:
+            self.annotation_json = annotation_json
+        try:
+            if arguments.summary_input:
+                with open(arguments.summary_input) as fh:
+                    self.summary_json = json.load(fh)
+        except Exception:
+            pass
+        try:
+            if arguments.annotation_input:
+                with open(arguments.annotation_input) as fh:
+                    self.annotation_json = json.load(fh)
+        except Exception:
+            pass
+        self.gene = self.arguments.gene
+        self._get_incoming_labels()
+        self._get_map()
+
+    def summary(self):
+        try:
+            if self.summary_json is not None:
+                if self.gene not in self.summary_json:
+                    self.summary_json[self.gene] = {}
+            if self.cfel is not None:
+                self.cfel_summary()
+            if self.relax is not None:
+                self.relax_summary()
+            if self.busted is not None:
+                self.busted_summary()
+            if self.slac is not None:
+                self.slac_summary()
+            if self.fel is not None:
+                self.fel_summary()
+            if self.meme is not None:
+                self.meme_summary()
+            if self.meme_full is not None:
+                self.meme_full_summary()
+            if self.prime is not None:
+                self.prime_summary()
+            if self.fade is not None:
+                self.fade_summary()
+            if self.bgm is not None:
+                self.bgm_summary()
+        except Exception:
+            if self.gene:
+                del self.summary_json[self.gene]
+                if self.gene in self.annotation_json:
+                    del self.annotation_json[self.gene]
+            raise
+        return self.annotation_json, self.summary_json
+
+    def cfel_summary(self):
+        self.cfel = self._load_json(self.arguments.cfel)
+        if self.cfel is None:
+            return
+        node_tags = {}
+        _ = self._newick_parser(self.cfel['input']['trees']['0'], False, node_tags, self.cfel)['json']
+        if self.summary_json is not None:
+            omegas = {}
+            T = {}
+            for k in [[k.split('*')[1], v[0][0]] for k, v in self.cfel['fits']['Global MG94xREV']['Rate Distributions'].items()]:
+                if k[0] != 'background':
+                    self.test_map[k[0]] = 'Test'
+                else:
+                    self.test_map[k[0]] = 'Reference'
+                omegas[k[0]] = k[1]
+                T[k[0]] = 0.
+            for branch, nt in (self.cfel['tested']['0']).items():
+                if branch not in node_tags:
+                    node_tags[branch] = []
+                info = self.cfel['branch attributes']['0'][branch]
+                if nt != '':
+                    T[nt] += info['Global MG94xREV']
+                node_tags[branch].append(info['Global MG94xREV'])
+            self.summary_json[self.gene]['rates'] = {'mean-omega': omegas, 'T': T}
+        beta_indices = []
+        p_indices = []
+        subs = []
+        for i, tag in enumerate(self.cfel['MLE']['headers']):
+            if tag[0].find('beta') == 0:
+                beta_indices.append([i, re.split(r'\(|\)', tag[0])[1]])
+            elif tag[0].find('P-value') == 0:
+                p_indices.append([i, re.split(r'\(|\)|for ', tag[0])[1]])
+            elif tag[0].find('subs') == 0:
+                subs.append([i, re.split(r'\(|\)', tag[0])[1]])
+        for i, row in enumerate(self.cfel['MLE']['content']['0']):
+            if self.annotation_json is not None and len(self.ref_map):  # if this is specified, write everything out
+                gs = self._get_genomic_annotation(i)
+                if gs[0] >= 0:
+                    self.include_in_annotation[i] = gs[0]
+                    self.annotation_json[gs[0]] = {
+                        'G': gs[1],
+                        'S': gs[2],
+                        'index': i,
+                        'bCFEL': {
+                            'p': row[4],
+                            'a': row[0],
+                            'b': self._make_report_dict(row, beta_indices),
+                            'pi': self._make_report_dict(row, p_indices),
+                            'pp': row[-2],
+                            's': self._make_report_dict(row, subs),
+                            'q': row[-3]
+                        }
+                    }
+            if row[-4] <= self.arguments.pvalue:
+                self.site_reports[i] = {'cfel': row}
+
+    def relax_summary(self):
+        self.relax = self._load_json(self.arguments.relax)
+        if self.relax is None:
+            return
+        if self.summary_json is not None:
+            relax_d = {}
+        for r, rr in self.summary_json[self.gene]['rates']['mean-omega'].items():
+            relax_d[r] = []
+            for ignored, rd in self.relax['fits']['RELAX alternative']['Rate Distributions'][self.test_map[r]].items():
+                relax_d[r].append(rd)
+        self.summary_json[self.gene]['rates']['relax'] = relax_d
+        self.summary_json[self.gene]['relax'] = {
+            'p': self.relax['test results']['p-value'],
+            'K': self.relax['test results']['relaxation or intensification parameter']
+        }
+
+    def busted_summary(self):
+        self.busted = self._load_json(self.arguments.busted)
+        if self.busted is None:
+            return
+        if self.summary_json is not None:
+            self.summary_json[self.gene]['rates']['busted'] = self.busted['fits']['Unconstrained model']['Rate Distributions']
+            self.summary_json[self.gene]['busted'] = {'p': self.busted['test results']['p-value'], }
+
+    def slac_summary(self):
+        self.slac = self._load_json(self.arguments.slac)
+        if self.slac is None:
+            return
+
+        def def_value():
+            return defaultdict(int)
+        compressed_subs = {}
+        node_tags = {}
+        the_tree = self._newick_parser(self.slac['input']['trees']['0'], False, node_tags, self.slac)['json']
+        root_node = None
+        if self.summary_json is not None:
+            for branch, info in self.slac['branch attributes']['0'].items():
+                if branch in node_tags:
+                    node_tags[branch].append(info['Global MG94xREV'])
+                else:
+                    root_node = branch
+            self.summary_json[self.gene]['tree'] = self.slac['input']['trees']['0']
+            self.summary_json[self.gene]['tree_tags'] = node_tags
+        if len(self.include_in_annotation):
+            for i in self.include_in_annotation:
+                report = self.annotation_json[self.include_in_annotation[i]]
+                counts_codon_site = {}
+                counts_aa_site = {}
+                gs = self._get_genomic_annotation(i)
+                if gs[0] >= 0:
+                    self.labels[root_node] = self.slac['branch attributes']['0'][root_node]['codon'][0][i]
+                    try:
+                        self._traverse_tree_in_order(the_tree, self.slac['branch attributes']['0'], i, None, root_node)
+                    except Exception:
+                        raise
+                    compressed_subs[gs[0]] = self.labels
+                for k in set([k[0] for k in node_tags.values()]):
+                    if len(k):
+                        counts_codon_site[k] = defaultdict(int)
+                        counts_aa_site[k] = defaultdict(int)
+                for branch, tag in node_tags.items():
+                    if len(tag[0]) > 0 and tag[1] is False:
+                        codon = self.slac['branch attributes']['0'][branch]['codon'][0][i]
+                        aa = self.slac['branch attributes']['0'][branch]['amino-acid'][0][i]
+                        counts_codon_site[tag[0]][codon] += 1
+                        counts_aa_site[tag[0]][aa] += 1
+                report['cdn'] = counts_codon_site
+                report['aa'] = counts_aa_site
+            self.summary_json[self.gene]['subs'] = compressed_subs
+
+    def fel_summary(self):
+        self.fel = self._load_json(self.arguments.fel)
+        if None in [self.fel, self.cfel]:
+            return
+        for i, row in enumerate(self.fel['MLE']['content']['0']):
+            if i in self.include_in_annotation:
+                self.annotation_json[self.include_in_annotation[i]]['bFEL'] = {'a': row[0], 'b': row[1], 'p': row[4]}
+            if i in self.site_reports or row[4] <= self.arguments.pvalue and row[1] > row[0]:
+                if i in self.site_reports:
+                    self.site_reports[i]['fel'] = row
+                else:
+                    self.site_reports[i] = {'fel': row,
+                                            'cfel': self.cfel['MLE']['content']['0'][i]}
+
+    def meme_summary(self):
+        self.meme = self._load_json(self.arguments.meme)
+        if None in [self.fel, self.cfel, self.meme]:
+            return
+        for i, row in enumerate(self.meme['MLE']['content']['0']):
+            if i in self.include_in_annotation:
+                self.annotation_json[self.include_in_annotation[i]]['bMEME'] = {
+                    'p': row[6],
+                    'a': row[0],
+                    'b+': row[3],
+                    'w+': row[4],
+                    'b-': row[1],
+                    'w-': row[2],
+                    'br': row[7]
+                }
+            if i in self.site_reports or row[6] <= self.arguments.pvalue:
+                if i in self.site_reports:
+                    self.site_reports[i]['meme'] = row
+                else:
+                    self.site_reports[i] = {'meme': row,
+                                            'fel': self.fel['MLE']['content']['0'][i],
+                                            'cfel': self.cfel['MLE']['content']['0'][i]}
+        # annotate branches with EBF support
+        for n, info in self.meme['branch attributes']['0'].items():
+
+            if n in self.summary_json[self.gene]['tree_tags']:
+                sig_sites = []
+                for tag, ebf in info.items():
+                    bits = tag.split(' ')
+                    if len(bits) >= 4 and ebf >= 100:
+                        sig_sites.append(self.include_in_annotation[int(bits[2]) - 1])
+                self.summary_json[self.gene]['tree_tags'][n].append(sig_sites)
+
+    def meme_full_summary(self):
+        self.meme_full = self._load_json(self.arguments.meme_full)
+        if None in [self.fel, self.cfel, self.meme, self.meme_full]:
+            return
+        for i, row in enumerate(self.meme_full['MLE']['content']['0']):
+            if i in self.include_in_annotation:
+                self.annotation_json[self.include_in_annotation[i]]['lMEME'] = {
+                    'p': row[6],
+                    'a': row[0],
+                    'b+': row[3],
+                    'w+': row[4],
+                    'b-': row[1],
+                    'w-': row[2],
+                    'br': row[7]
+                }
+            if i in self.site_reports or row[6] <= self.arguments.pvalue:
+                if i in self.site_reports:
+                    self.site_reports[i]['full-meme'] = row
+                else:
+                    self.site_reports[i] = {'full-meme': row,
+                                            'meme': self.meme['MLE']['content']['0'][i],
+                                            'fel': self.fel['MLE']['content']['0'][i],
+                                            'cfel': self.cfel['MLE']['content']['0'][i]}
+        # annotate branches with EBF support
+        for n, info in self.meme_full['branch attributes']['0'].items():
+            if n in self.summary_json[self.gene]['tree_tags']:
+                sig_sites = []
+                for tag, ebf in info.items():
+                    bits = tag.split(' ')
+                    if len(bits) >= 4 and ebf >= 100:
+                        sig_sites.append(self.include_in_annotation[int(bits[2]) - 1])
+                self.summary_json[self.gene]['tree_tags'][n].append(sig_sites)
+
+    def prime_summary(self):
+        self.prime = self._load_json(self.arguments.prime)
+        if self.prime is None:
+            return
+        if self.summary_json is not None:
+            h = self.prime['MLE']['headers']
+            self.summary_json[self.gene]['prime-properties'] = [h[k][1].replace('Importance for ', '') for k in range(6, len(h), 3)]
+        if len(self.include_in_annotation):
+            for i in self.include_in_annotation:
+                report = self.annotation_json[self.include_in_annotation[i]]
+                prime_info = self.prime['MLE']['content']['0'][i]
+                if prime_info:
+                    report['prime'] = {
+                        'p': [prime_info[k] for k in ([5, ] + list(range(7, len(prime_info), 3)))],
+                        'lambda': [prime_info[k] for k in range(6, len(prime_info), 3)]
+                    }
+                else:
+                    report['prime'] = None  # invariable
+
+    def fade_summary(self):
+        self.fade = self._load_json(self.arguments.fade)
+        if self.fade is None:
+            return
+        if len(self.include_in_annotation):
+            for i in self.include_in_annotation:
+                report = self.annotation_json[self.include_in_annotation[i]]
+                report['fade'] = {}
+                for residue, info in self.fade['MLE']['content'].items():
+                    if len(residue) == 1:
+                        report['fade'][residue] = {'rate': info['0'][i][1], 'BF': info['0'][i][-1]}
+
+    def bgm_summary(self):
+        self.bgm = self._load_json(self.arguments.bgm)
+        if self.bgm is None:
+            return
+        if self.summary_json is not None:
+            try:
+                self.summary_json[self.gene]['bgm'] = self.bgm['MLE']['content']
+            except KeyError:
+                self.summary_json[self.gene]['bgm'] = []
+
+    def _load_json(self, filename):
+        if filename is None:
+            return None
+        try:
+            with open(filename, 'r') as fh:
+                return json.load(fh)
+        except Exception:
+            raise
+
+    def _get_map(self):
+        for seq_record in SeqIO.parse(self.arguments.combined, 'fasta'):
+            seq_id = seq_record.description
+            ref_seq_re = re.compile(self.arguments.name)
+            if ref_seq_re.search(seq_id):
+                ref_seq = str(seq_record.seq).upper()
+                self.aligned_str = None
+
+                def output_record(x):
+                    listified_input = list(x)
+                    if len(listified_input) == 1:
+                        self.aligned_str = listified_input[0]
+
+                def ignore_record(x):
+                    pass
+                for s in self.ref_genes:
+                    _align_par(SeqRecord(Seq(s[1]), id=s[0]), [SeqRecord(Seq(ref_seq), id='ref')],
+                               self.score_matrix_, False, False, 0.8, ignore_record, output_record)
+                    if (self.aligned_str is not None):
+                        break
+                self.ref_map = self.aligned_str.seq.strip('-')
+                c = 0
+                i = 0
+                map_to_genome = []
+                while i < len(self.ref_map):
+                    if self.ref_map[i:i + 3] != '---':
+                        map_to_genome.append(i)
+                    i += 3
+                i = 0
+                c = 0
+                while i < len(ref_seq):
+                    if ref_seq[i:i + 3] != '---':
+                        self.ref_seq_map.append(map_to_genome[c // 3] + self.aligned_str.annotations['position'])
+                        c += 3
+                    else:
+                        self.ref_seq_map.append(-1)
+                    i += 3
+        if self.summary_json is not None:
+            if self.gene not in self.summary_json:
+                self.summary_json[self.gene] = dict()
+            self.summary_json[self.gene]['map'] = self.ref_seq_map
+
+    def _make_report_dict(self, row, indices):
+        result = {}
+        for i, t in indices:
+            result[t] = row[i]
+        return result
+
+    def _get_genomic_annotation(self, site):
+        genomic_site_coord = -1
+        gene_name = ''
+        gene_site = -1
+        if len(self.ref_seq_map):
+            genomic_site_coord = self.ref_seq_map[site]
+            if genomic_site_coord < 0:
+                gene_site = 'Not in SC2 (deletion)'
+            else:
+                gene_name = None
+                for k in self.gene_coordinates:
+                    if k[0] <= genomic_site_coord and k[1] > genomic_site_coord:
+                        genomic_site = ((genomic_site_coord + k[3]) - k[0]) // 3
+                        gene_name = k[2]
+                        gene_site = genomic_site + 1
+                        break
+                if gene_name is None:
+                    gene_name = 'Not mapped'
+        else:
+            gene_name = 'N/A'
+        return (genomic_site_coord, gene_name, gene_site)
+
+    def _traverse_tree_in_order(self, node, slac_data, i, parent_tag, root):
+        node_tag = None
+        if node is None:
+            return
+        try:
+            nn = root if node['name'] == 'root' else node['name']
+        except Exception:
+            raise
+        if nn in slac_data:
+            node_tag = slac_data[nn]['codon'][0][i]
+            if (parent_tag != node_tag):
+                self.labels[nn] = node_tag
+                self.labels[node['name']] = node_tag
+        if 'children' in node:
+            for c in node['children']:
+                if c is not None:
+                    if 'name' in c:
+                        self._traverse_tree_in_order(c, slac_data, i, node_tag, root)
+
+    def _match_node_names(self, qry_node, ref_node, mapping):
+        if 'children' in qry_node and 'children' in ref_node:
+            mapping[ref_node['name']] = qry_node['name']
+            if len(qry_node['children']) != len(ref_node['children']):
+                raise Exception('Internal topology mismatch')
+            for i, n in enumerate(ref_node['children']):
+                self._match_node_names(qry_node['children'][i], n, mapping)
+        elif 'children' in qry_node:
+            raise Exception('Topology mismatch')
+        elif 'children' in ref_node:
+            raise Exception('Topology mismatch')
+        else:
+            if qry_node['name'] != ref_node['name']:
+                raise Exception('Leaf name mismatch')
+
+    def _get_incoming_labels(self):
+        json_data = self._load_json(self.arguments.labels)
+        self.incoming_labels = json_data
+
+    def _newick_parser(self, nwk_str, bootstrap_values, track_tags, json_map):
+        clade_stack = []
+        automaton_state = 0
+        current_node_name = ''
+        current_node_attribute = ''
+        current_node_annotation = ''
+        quote_delimiter = None
+        name_quotes = {"'": 1, '"': 1}
+
+        def add_new_tree_level():
+            new_level = {'name': None}
+            the_parent = clade_stack[len(clade_stack) - 1]
+            if ('children' not in the_parent):
+                the_parent['children'] = []
+            clade_stack.append(new_level)
+            the_parent['children'].append(clade_stack[len(clade_stack) - 1])
+            clade_stack[len(clade_stack) - 1]['original_child_order'] = len(the_parent['children'])
+
+        def finish_node_definition():
+            nonlocal current_node_name
+            nonlocal current_node_annotation
+            nonlocal current_node_attribute
+            this_node = clade_stack.pop()
+            if (bootstrap_values and 'children' in this_node):
+                this_node['bootstrap_values'] = current_node_name
+            else:
+                this_node['name'] = current_node_name
+            this_node['attribute'] = current_node_attribute
+            this_node['annotation'] = current_node_annotation
+            try:
+                if 'children' not in this_node:
+                    node_tag = self.arguments.default_tag
+                    if json_map:
+                        tn = json_map['branch attributes']['0'][this_node['name']]
+                    else:
+                        tn = this_node
+                    nn = tn['original name'] if 'original name' in tn else tn['name']
+                    for k, v in self.incoming_labels.items():
+                        if nn.find(k) >= 0:
+                            node_tag = v
+                            break
+                else:
+                    counts = {}
+                    node_tag = ''
+                    for n in this_node['children']:
+                        counts[n['tag']] = 1 + (counts[n['tag']] if n['tag'] in counts else 0)
+                    if len(counts) == 1:
+                        node_tag = list(counts.keys())[0]
+                    this_node['tag'] = node_tag
+            except Exception:
+                raise
+            if track_tags is not None:
+                track_tags[this_node['name']] = [this_node['tag'], 'children' in this_node]
+            current_node_name = ''
+            current_node_attribute = ''
+            current_node_annotation = ''
+
+        def generate_error(location):
+            unexpected = nwk_str[location]
+            before = nwk_str[location - 20:location + 1]
+            after = nwk_str[location + 1:location + 20]
+            return {
+                'json': None,
+                'error': 'Unexpected %s in %s [ERROR HERE] %s' % (unexpected, before, after)
+            }
+        tree_json = {'name': 'root'}
+        clade_stack.append(tree_json)
+        space = re.compile(r'\s')
+        for char_index in range(len(nwk_str)):
+            try:
+                current_char = nwk_str[char_index]
+                if automaton_state == 0:
+                    # look for the first opening parenthesis
+                    if (current_char == '('):
+                        add_new_tree_level()
+                        automaton_state = 1
+                elif automaton_state == 1 or automaton_state == 3:
+                    # case 1: // name
+                    # case 3: { // branch length
+                    # reading name
+                    if (current_char == ':'):
+                        automaton_state = 3
+                    elif current_char == ',' or current_char == ')':
+                        try:
+                            finish_node_definition()
+                            automaton_state = 1
+                            if (current_char == ','):
+                                add_new_tree_level()
+                        except Exception:
+                            return generate_error(char_index)
+                    elif (current_char == '('):
+                        if len(current_node_name) > 0:
+                            return generate_error(char_index)
+                        else:
+                            add_new_tree_level()
+                    elif (current_char in name_quotes):
+                        if automaton_state == 1 and len(current_node_name) == 0 and len(current_node_attribute) == 0 and len(current_node_annotation) == 0:
+                            automaton_state = 2
+                            quote_delimiter = current_char
+                            continue
+                        return generate_error(char_index)
+                    else:
+                        if (current_char == '['):
+                            if len(current_node_annotation):
+                                return generate_error(char_index)
+                            else:
+                                automaton_state = 4
+                        else:
+                            if (automaton_state == 3):
+                                current_node_attribute += current_char
+                            else:
+                                if (space.search(current_char)):
+                                    continue
+                                if (current_char == ';'):
+                                    char_index = len(nwk_str)
+                                    break
+                                current_node_name += current_char
+                elif automaton_state == 2:
+                    # inside a quoted expression
+                    if (current_char == quote_delimiter):
+                        if (char_index < len(nwk_str - 1)):
+                            if (nwk_str[char_index + 1] == quote_delimiter):
+                                char_index += 1
+                                current_node_name += quote_delimiter
+                                continue
+                            quote_delimiter = 0
+                            automaton_state = 1
+                            continue
+                    else:
+                        current_node_name += current_char
+                elif automaton_state == 4:
+                    # inside a comment / attribute
+                    if (current_char == ']'):
+                        automaton_state = 3
+                    else:
+                        if (current_char == '['):
+                            return generate_error(char_index)
+                        current_node_annotation += current_char
+            except Exception:
+                return generate_error(char_index)
+
+        if (len(clade_stack) != 1):
+            return generate_error(len(nwk_str) - 1)
+
+        if (len(current_node_name)):
+            tree_json['name'] = current_node_name
+
+        return {
+            'json': tree_json,
+            'error': None
+        }
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Summarize selection analysis results.')
+    parser.add_argument('--combined', help='Combined reference and query alignment from TN-93', required=False, type=str)
+    parser.add_argument('--pvalue', help='p-value to use', required=False, type=float, default=0.05)
+    parser.add_argument('--gene', help='Name of the gene or sequence being analyzed', required=False, type=str)
+    parser.add_argument('--labels', help='JSON file with labels', required=False, type=str)
+    parser.add_argument('--annotation-output', help='Write a JSON file with site annotations', required=True, type=str)
+    parser.add_argument('--summary-output', help='Write a JSON file here segment annotations', required=True, type=str)
+    parser.add_argument('--annotation-inputs', help='Comma-separated list of site annotation files to merge', required=False, type=str)
+    parser.add_argument('--summary-inputs', help='Comma-separated list of segment annotation files to merge', required=False, type=str)
+    parser.add_argument('--default-tag', help='Default name for sequences that have no explicit label', required=False, type=str, default='Reference')
+    parser.add_argument('--name', help='The sequence ID to highlight', required=False, default='MN908947')
+    parser.add_argument('--mode', help='Operation mode, generate a summary or merge multiple summaries', type=str, choices=['summary', 'merge'], default='summary')
+    parser.add_argument('--relax', help='Path to RELAX.json file', required=False, type=str)
+    parser.add_argument('--busted', help='Path to BUSTED.json file', required=False, type=str)
+    parser.add_argument('--slac', help='Path to SLAC.json file', required=False, type=str)
+    parser.add_argument('--fel', help='Path to FEL.json file', required=False, type=str)
+    parser.add_argument('--cfel', help='Path to CFEL.json file', required=False, type=str)
+    parser.add_argument('--meme', help='Path to MEME.json file', required=False, type=str)
+    parser.add_argument('--meme-full', help='Path to MEME-full.json file', dest='meme_full', required=False, type=str)
+    parser.add_argument('--prime', help='Path to PRIME.json file', required=False, type=str)
+    parser.add_argument('--fade', help='Path to FADE.json file', required=False, type=str)
+    parser.add_argument('--bgm', help='Path to BGM.json file', required=False, type=str)
+    arguments = parser.parse_args()
+    if arguments.mode == 'summary':
+        analyzer = HyPhySummary(arguments)
+        annotation_json, summary_json = analyzer.summary()
+        if annotation_json is not None:
+            with open(arguments.annotation_output, 'w') as fh:
+                json.dump(annotation_json, fh, indent=1)
+        if summary_json is not None:
+            with open(arguments.summary_output, 'w') as fh:
+                json.dump(summary_json, fh, indent=1)
+    else:
+        summary = {}
+        annotation = {}
+        for filename in arguments.annotation_inputs.split(','):
+            with open(filename, 'r') as fh:
+                annotation.update(json.load(fh))
+        for filename in arguments.summary_inputs.split(','):
+            with open(filename, 'r') as fh:
+                summary.update(json.load(fh))
+        with open(arguments.annotation_output, 'w') as fh:
+            json.dump(annotation, fh, indent=1)
+        with open(arguments.summary_output, 'w') as fh:
+            json.dump(summary, fh, indent=1)
+    exit(0)