def clean_outliers(self): from seq_util import hamming_distance as distance """Remove outlier viruses""" remove_viruses = [] outlier_seqs = [ "-----------ATGAAGGCCATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGCGTGATACCACTGACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGTCCGGACTGTCTCAACTGTACAGATCTGGATGTGGCCTTGGGCAGGCCAATGTGTGTGGGGACCACACCTTCTGCTAAAGCTTCAATACTCCACGAAGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGGCAACTACCCAATCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAAGCACCAGGAGGACCTTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAAATCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAAGGACAACTACAAAAATGCAACGAACCCACTAACAGTAGAAGTACCATACATTTGTGCAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATAACAAAACCCAAATGAAGAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGACTTTCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTTGTTGATTACATGGTGCAAAGACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGCGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCATTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAGGCCATAGGAAATTGCCCAATATGGGTGAAGACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACGTCCCATGGGGCACATGGAGTAGCGGTGGCAGCAGACCTTAAGAGCACTCAAGAGGCCATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTGGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGGATGAACTCCACAACGAAATACTAGAACTAGACGAGAAAGTGGATGATCTCAGAGCTGATACAATAAGCTCACAAATAGAACTCGCAGTCCTGCTTTCCAATGAAGGAATAATAAACAGTGAAGATGAACATCTCTTGGCTCTTGAAAGAAAGCTGAAGAAAATGCTGGGCCCCTCTGCTGTAGAGATAGGGAATGGATGCTTTGAAACCAAACACAAGTGCAACCAGACCTGTCTCGACAGAATAGCTGCTGGTACCTTTGATGCAGGAGAATTTTCTCTCCCCACCTTTGATTCACTGAATATTACTGCTGCATCTTTAAATGACGATGGATTGGATAATCATACTATACTGCTTTACTACTCAACTGCTGCCTCCAGTTTGGCTGTAACACTGATGATAGCTATCTTTGTTGTTTATATGGTCTCCAGAGACAATGTTTCTTGCTCCATCTGTCTATAA--------------------------------------------------------------------------", "-----------------------------------------------------------------------------ACATCGTCAAACTCACCTCAAGTGGTCAAAACAGCTCCTCAAGGGGAGGACAACGTCACTGGCGTGATACCACTGACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGCCCAGACTGTCTCAACTGTACAGATCTGGATGTGGCCTTGGGCAGACCAATGTGCACGGGGAAAATACCCTCGGCAAGAGTTTCAATACTCCATGAAGTCAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAACTACCCAACCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCACAACGTTATCAATGCAGAAAATGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAGAAACGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAAGGACAACAACAAAAATGCAACGAATCCACTAACAGTAGAAGTACCATACATTTGTACAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATAACAAAACCCAAATGAAGAGCCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGACTTCCCAGATCAAACAGAAGACGGAGGATTACCACAAAGCGGCAGAATTGTTGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCATTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAGAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAAAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTAAAAACACCTTTAAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTGAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTGGCGGCAGACCTTAAAAGTACACAAGAAGCTATAAATAAGATAACAAAAAATCTCAATTCTTTGAGTGAGCTAGAAGTAAAGAACCTTCAAAGACTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAGAAAGTGGATGATCTCAGAGCTGACACTATAAGCTCACAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGACGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGACATAGGAAACGGATGCTTCGAAACCAAACACAAATGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCCCTCCCCACTTTTGATTCATTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTAATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAG-------------------------------------------------------------------------------------------------------" ] for outlier_seq in outlier_seqs: for v in self.viruses: dist = distance(Seq(outlier_seq), v) if (dist < 0.02): remove_viruses.append(v) if self.verbose>1: print "\tremoving", v.strain self.viruses = MultipleSeqAlignment([v for v in self.viruses if v not in remove_viruses])
def clean_outliers_by_sequence(self):
from seq_util import hamming_distance as distance
"""Remove outlier viruses"""
remove_viruses = []
outlier_seqs = [
"-----------ATGAAGGCCATAATTGTACTACTCATGGTAGTAACATCCAATGCAGATCGAATCTGCACTGGGATAACATCTTCAAACTCACCTCATGTGGTCAAAACAGCTACTCAAGGGGAGGTCAATGTGACTGGCGTGATACCACTGACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGTCCGGACTGTCTCAACTGTACAGATCTGGATGTGGCCTTGGGCAGGCCAATGTGTGTGGGGACCACACCTTCTGCTAAAGCTTCAATACTCCACGAAGTCAGACCTGTTACATCCGGGTGCTTTCCTATAATGCACGACAGAACAAAAATCAGGCAACTACCCAATCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCAAAACGTTATCGATGCAGAAAAAGCACCAGGAGGACCTTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAAAATCGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAAGGACAACTACAAAAATGCAACGAACCCACTAACAGTAGAAGTACCATACATTTGTGCAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATAACAAAACCCAAATGAAGAACCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGACTTTCCAGATCAAACAGAAGACGGAGGACTACCACAAAGCGGCAGAATTGTTGTTGATTACATGGTGCAAAGACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGCGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCATTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAAAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAGAACATGCAAAGGCCATAGGAAATTGCCCAATATGGGTGAAGACACCCTTGAAGCTGGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTAAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCTTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACGTCCCATGGGGCACATGGAGTAGCGGTGGCAGCAGACCTTAAGAGCACTCAAGAGGCCATAAACAAGATAACAAAAAATCTCAACTCTTTGAGTGAGCTGGAAGTAAAGAATCTTCAAAGACTAAGCGGTGCCATGGATGAACTCCACAACGAAATACTAGAACTAGACGAGAAAGTGGATGATCTCAGAGCTGATACAATAAGCTCACAAATAGAACTCGCAGTCCTGCTTTCCAATGAAGGAATAATAAACAGTGAAGATGAACATCTCTTGGCTCTTGAAAGAAAGCTGAAGAAAATGCTGGGCCCCTCTGCTGTAGAGATAGGGAATGGATGCTTTGAAACCAAACACAAGTGCAACCAGACCTGTCTCGACAGAATAGCTGCTGGTACCTTTGATGCAGGAGAATTTTCTCTCCCCACCTTTGATTCACTGAATATTACTGCTGCATCTTTAAATGACGATGGATTGGATAATCATACTATACTGCTTTACTACTCAACTGCTGCCTCCAGTTTGGCTGTAACACTGATGATAGCTATCTTTGTTGTTTATATGGTCTCCAGAGACAATGTTTCTTGCTCCATCTGTCTATAA--------------------------------------------------------------------------",
"-----------------------------------------------------------------------------ACATCGTCAAACTCACCTCAAGTGGTCAAAACAGCTCCTCAAGGGGAGGACAACGTCACTGGCGTGATACCACTGACAACAACACCAACAAAATCTTATTTTGCAAATCTCAAAGGAACAAGGACCAGAGGGAAACTATGCCCAGACTGTCTCAACTGTACAGATCTGGATGTGGCCTTGGGCAGACCAATGTGCACGGGGAAAATACCCTCGGCAAGAGTTTCAATACTCCATGAAGTCAGACCTGTTACATCTGGGTGCTTTCCTATAATGCACGACAGAACAAAAATTAGACAACTACCCAACCTTCTCAGAGGATATGAAAATATCAGGTTATCAACCCACAACGTTATCAATGCAGAAAATGCACCAGGAGGACCCTACAGACTTGGAACCTCAGGATCTTGCCCTAACGCTACCAGTAGAAACGGATTTTTCGCAACAATGGCTTGGGCTGTCCCAAAGGACAACAACAAAAATGCAACGAATCCACTAACAGTAGAAGTACCATACATTTGTACAGAAGGGGAAGACCAAATTACTGTTTGGGGGTTCCATTCAGATAACAAAACCCAAATGAAGAGCCTCTATGGAGACTCAAATCCTCAAAAGTTCACCTCATCTGCTAATGGAGTAACCACACATTATGTTTCTCAGATTGGCGACTTCCCAGATCAAACAGAAGACGGAGGATTACCACAAAGCGGCAGAATTGTTGTTGATTACATGATGCAAAAACCTGGGAAAACAGGAACAATTGTCTATCAAAGAGGTGTTTTGTTGCCTCAAAAGGTGTGGTGCGCGAGTGGCAGGAGCAAAGTAATAAAAGGGTCATTGCCTTTAATTGGTGAAGCAGATTGCCTTCATGAAGAATACGGTGGATTAAACAAAAGCAAGCCTTACTACACAGGAAAACATGCAAAAGCCATAGGAAATTGCCCAATATGGGTAAAAACACCTTTAAAGCTTGCCAATGGAACCAAATATAGACCTCCTGCAAAACTATTGAAGGAAAGGGGTTTCTTCGGAGCTATTGCTGGTTTCCTAGAAGGAGGATGGGAAGGAATGATTGCAGGTTGGCACGGATACACATCTCACGGAGCACATGGAGTGGCAGTGGCGGCAGACCTTAAAAGTACACAAGAAGCTATAAATAAGATAACAAAAAATCTCAATTCTTTGAGTGAGCTAGAAGTAAAGAACCTTCAAAGACTAAGTGGTGCCATGGATGAACTCCACAACGAAATACTCGAGCTGGATGAGAAAGTGGATGATCTCAGAGCTGACACTATAAGCTCACAAATAGAACTTGCAGTCTTGCTTTCCAACGAAGGAATAATAAACAGTGAAGACGAGCATCTATTGGCACTTGAGAGAAAACTAAAGAAAATGCTGGGTCCCTCTGCTGTAGACATAGGAAACGGATGCTTCGAAACCAAACACAAATGCAACCAGACCTGCTTAGACAGGATAGCTGCTGGCACCTTTAATGCAGGAGAATTTTCCCTCCCCACTTTTGATTCATTGAACATTACTGCTGCATCTTTAAATGATGATGGATTGGATAACCATACTATACTGCTCTATTACTCAACTGCTGCTTCTAGTTTGGCTGTAACATTAATGCTAGCTATTTTTATTGTTTATATGGTCTCCAGAG-------------------------------------------------------------------------------------------------------"
]
for outlier_seq in outlier_seqs:
for v in self.viruses:
dist = distance(Seq(outlier_seq), v)
if (dist < 0.02):
remove_viruses.append(v.strain)
if self.verbose > 1:
print "\tremoving", v.strain
self.viruses = MultipleSeqAlignment(
[v for v in self.viruses if v.strain not in remove_viruses])
def clean_reassortants(self): from seq_util import hamming_distance as distance """Remove viruses from the outbreak of triple reassortant pH1N1""" remove_viruses = [] reassortant_seqs = [ "ATGAAGACTATCATTGCTTTTAGCTGCATTTTATGTCTGATTTTCGCTCAAAAACTTCCCGGAAGTGACAACAGCATGGCAACGCTGTGCCTGGGACACCATGCAGTGCCAAACGGAACATTAGTGAAAACAATCACGGATGACCAAATTGAAGTGACTAATGCTACTGAGCTGGTCCAGAGTTCCTCAACAGGTGGAATATGCAACAGTCCTCACCAAATCCTTGATGGGAAAAATTGCACACTGATAGATGCTCTATTGGGGGACCCTCATTGTGATGACTTCCAAAACAAGGAATGGGACCTTTTTGTTGAACGAAGCACAGCCTACAGCAACTGTTACCCTTATTACGTGCCGGATTATGCCACCCTTAGATCATTAGTTGCCTCATCCGGCAACCTGGAATTTACCCAAGAAAGCTTCAATTGGACTGGAGTTGCTCAAGGCGGATCAAGCTATGCCTGCAGAAGGGGATCTGTTAACAGTTTCTTTAGTAGATTGAATTGGTTGTATAACTTGAATTACAAGTATCCAGAGCAGAACGTAACTATGCCAAACAATGACAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAACCAACCTATATGTCCAAGCATCAGGGAGAGTTATAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGGTCTAGACCCTGGGTAAGGGGTGTCTCCAGCATAATAAGCATCTATTGGACGATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCCCCTCGGGGTTACTTCAAAATACAAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACACATTGATGAATGCAATTCTGAATGCATTACTCCAAATGGAAGCATTCCCAATGACAAACCTTTTCAAAATGTAAACAAGATCACATATGGAGCCTGTCCCAGATATGTTAAGCAAAACACCCTGAAATTGGCAACAGGAATGCGGAATGTACCAGAGAAACAAACTAGAGGCATATTCGGCGCAATTGCAGGTTTCATAGAAAATGGTTGGGAGGGAATGGTAGACGGTTGGTACGGTTTCAGGCATCAGAATTCTGAAGGCACAGGACAAGCAGCAGATCTTAAAAGCACTCAAGCAGCAATCAACCAAATCACCGGGAAACTAAATAGAGTAATCAAGAAAACAAACGAGAAATTCCATCAAATCGAAAAAGAATTCTCAGAAGTAGAAGGAAGAATTCAGGACCTAGAGAAATACGTTGAAGACACTAAAATAGATCTCTGGTCTTACAACGCTGAGATTCTTGTTGCCCTGGAGAACCAACATACAATTGATTTAACCGACTCAGAGATGAGCAAACTGTTCGAAAGAACAAGAAGGCAACTGCGGGAAAATGCTGAGGACATGGGCAATGGTTGCTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCATGATATATACAGAAACGAGGCATTAAACAATCGGTTCCAGATCAAAGGTGTTCAGCTAAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGCTTTTTGCTTTGTGTTGTTCTGCTGGGGTTCATTATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA", "ATGAAGACTATCATTGCTTTTAGCTGCATCTTATGTCAGATCTCCGCTCAAAAACTCCCCGGAAGTGACAACAGCATGGCAACGCTGTGCCTGGGGCATCACGCAGTACCAAACGGAACGTTAGTGAAAACAATAACAGATGACCAAATTGAAGTGACTAATGCTACTGAGCTGGTCCAGAGTACCTCAAAAGGTGAAATATGCAGTAGTCCTCACCAAATCCTTGATGGAAAAAATTGTACACTGATAGATGCTCTATTGGGAGACCCTCATTGTGATGACTTCCAAAACAAGAAATGGGACCTTTTTGTTGAACGAAGCACAGCTTACAGCAACTGTTACCCTTATTATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACCCTGGAATTTACTCAAGAAAGCTTCAATTGGACTGGGGTTGCTCAAGACGGAGCAAGCTATTCTTGCAGAAGGGAATCTGAAAACAGTTTCTTTAGTAGATTGAATTGGTTATATAGTTTGAATTACAAATATCCAGCGCTGAACGTAACTATGCCAAACAATGACAAATTTGACAAATTGTACATTTGGGGGGTACACCACCCGGGTACGGACAAGGACCAAACCAGTCTATATATTCAAGCATCAGGGAGAGTTACAGTCTCCACCAAATGGAGCCAACAAACTGTAATCCCGAATATCGGGTCTAGACCCTGGATAAGGGGTGTCTCCAGCATAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCCCCTCGGGGTTACTTCAAAATACAAAGTGGGAAAAGCTCAATAATGAGGTCAGATGCACACATTGGCAACTGCAACTCTGAATGCATTACCCCAAATGGAAGCATTCCCAACGACAAACCTTTTCAAAATGTAAACAGAATAACATATGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTAGCAACAGGAATGCGGAATGTACCAGAGAAACAAACTAGAGGCATATTCGGCGCAATCGCAGGTTTCATAGAAAATGGTTGGGAAGGGATGGTGGACGGTTGGTATGGTTTCAGGCATCAAAACTCTGAAGGCACAGGGCAAGCAGCAGATCTTAAAAGCACTCAAGCGGCAATCAACCAAATCACCGGGAAACTAAATAGAGTAATCAAGAAGACGAATGAAAAATTCCATCAGATCGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTAGAGAGATACGTTGAAGACACTAAAATAGACCTCTGGTCTTACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATTTAACTGACTCAGAAATGAACAAACTGTTCGAAAGGACAAGGAAGCAACTGCGGGAAAATGCTGAGGACATGGGCAATGGATGCTTTAAAATATATCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGACGAAGCAGTAAACAATCGGTTCCAGATCAAAGGTGTTCAGCTGAAGTTAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGCTTTTTGCTTTGTGCTGTTCTGCTAGGATTCATTATGTGGGCATGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA", "ATGAAGACTAGTAGTTCTGCTATATACATTGCAA------------------------CCGCAAATG---------CAGACACATTATGTATAGGTTATCATGCAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCAAACTGAGAGGGGTAGCCCCATTGCATTTG--------------------GGTAAATGTAACATTGCTGGCTGGATCC------------------------------------TGGGAAATCCAGAGTGTGACACTCTCCACAGCAAGCTCATGGTCCTACATCGTGGAAACATCTAAGACAATGGAACGTGCTACCCAGGAGATTTCATCAATTATGAGGAGCTAAGGTCATCATTTGAAAGGTTTGAGATATTACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTTCCTCAAGCTGGAGCAA---------------------------AAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAA------------------------------AGCTCAGCAAATCCTACATTTGGGGCATTCACCATCCATCTACTAGTGCTGACCAA-------CAAAGTCTCTATCAGAGTGCAGATGCATATGTTTTATCAAAATACAGCAAGAAGTTCAAG--CCGGAAATAGCAGTAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTATTGGTACCGAGATATGCATTCGCAATGGAAA----GAAATGCTGGATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCCAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGCGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACAAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAAAACTTATATGAAAAGGTAAGAAGCCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCATCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA", "ATGAAGACTATCATTGCTTTGAGCTACATTTTATGTCTGGTTTTCGCTCAAAAACTTCCCGGAAATGACAACAGCACGGCAACGCTGTGCCTGGGGCACCATGCAGTGCCAAACGGAACGCTAGTGAAAACAATCACGAATGACCAAATTGAAGTAACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTAGAATATGCGACAGTCCTCACCAAATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCATTGTGATGGCTTCCAAAACAAGGAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGTCTCCCTTAGGTCACTAGTTGCCTCATCAGGCACGCTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCGCTCAGAATGGAACAAGCTCTGCTTGCAAAAGGAGATCCGATAAAAGTTTCTTTAGTAGATTGAATTGGTTGCACCAATTAAAATACAAATATCCAGCACTGAACGTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACAGACAGTGACCAAATCAGCCTATATGCTCAAGCATCAGGGAGAGTCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTGGACCCTGGGTAAGGGGTGTCTCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTCGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGGTCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGGCAAACCATTTCAAAATGTAAACAGGATCACATATGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGGAATGTGCCAGAGAAACAAACTAGAGGCATATTCGGTGCAATCGCGGGCTTCATAGAAAATGGTTGGGAGGGAATGATGGACGGTTGGTACGGTTTCAGGCATCAGAATTCTGAGGGCACAGGGCAAGCAGCAGATCTTAAAAGCACTCAAGCAGCAATCAACCAAATCAACGGGAAACTGAATAGGTTAATCGAGAAAACGAACGAGAAATTCCATCAAATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTCGAGGACACTAAAATAGATCTCTGGTCGTACAATGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAGAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGGTCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGACGAAGCATTGAACAACCGGTTCCAGATCAAAGGTGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTATTGTTTTACTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA" ] for reassortant_seq in reassortant_seqs: for v in self.viruses: dist = distance(Seq(reassortant_seq), v) if (dist < 0.02): remove_viruses.append(v) if self.verbose>1: print "\tremoving", v.strain self.viruses = MultipleSeqAlignment([v for v in self.viruses if v not in remove_viruses])
def clean_reassortants(self):
from seq_util import hamming_distance as distance
"""Remove viruses from the outbreak of triple reassortant pH1N1"""
remove_viruses = []
reassortant_seqs = [
"ATGAAGACTATCATTGCTTTTAGCTGCATTTTATGTCTGATTTTCGCTCAAAAACTTCCCGGAAGTGACAACAGCATGGCAACGCTGTGCCTGGGACACCATGCAGTGCCAAACGGAACATTAGTGAAAACAATCACGGATGACCAAATTGAAGTGACTAATGCTACTGAGCTGGTCCAGAGTTCCTCAACAGGTGGAATATGCAACAGTCCTCACCAAATCCTTGATGGGAAAAATTGCACACTGATAGATGCTCTATTGGGGGACCCTCATTGTGATGACTTCCAAAACAAGGAATGGGACCTTTTTGTTGAACGAAGCACAGCCTACAGCAACTGTTACCCTTATTACGTGCCGGATTATGCCACCCTTAGATCATTAGTTGCCTCATCCGGCAACCTGGAATTTACCCAAGAAAGCTTCAATTGGACTGGAGTTGCTCAAGGCGGATCAAGCTATGCCTGCAGAAGGGGATCTGTTAACAGTTTCTTTAGTAGATTGAATTGGTTGTATAACTTGAATTACAAGTATCCAGAGCAGAACGTAACTATGCCAAACAATGACAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAACCAACCTATATGTCCAAGCATCAGGGAGAGTTATAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGGTCTAGACCCTGGGTAAGGGGTGTCTCCAGCATAATAAGCATCTATTGGACGATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCCCCTCGGGGTTACTTCAAAATACAAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACACATTGATGAATGCAATTCTGAATGCATTACTCCAAATGGAAGCATTCCCAATGACAAACCTTTTCAAAATGTAAACAAGATCACATATGGAGCCTGTCCCAGATATGTTAAGCAAAACACCCTGAAATTGGCAACAGGAATGCGGAATGTACCAGAGAAACAAACTAGAGGCATATTCGGCGCAATTGCAGGTTTCATAGAAAATGGTTGGGAGGGAATGGTAGACGGTTGGTACGGTTTCAGGCATCAGAATTCTGAAGGCACAGGACAAGCAGCAGATCTTAAAAGCACTCAAGCAGCAATCAACCAAATCACCGGGAAACTAAATAGAGTAATCAAGAAAACAAACGAGAAATTCCATCAAATCGAAAAAGAATTCTCAGAAGTAGAAGGAAGAATTCAGGACCTAGAGAAATACGTTGAAGACACTAAAATAGATCTCTGGTCTTACAACGCTGAGATTCTTGTTGCCCTGGAGAACCAACATACAATTGATTTAACCGACTCAGAGATGAGCAAACTGTTCGAAAGAACAAGAAGGCAACTGCGGGAAAATGCTGAGGACATGGGCAATGGTTGCTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCATGATATATACAGAAACGAGGCATTAAACAATCGGTTCCAGATCAAAGGTGTTCAGCTAAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGCTTTTTGCTTTGTGTTGTTCTGCTGGGGTTCATTATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA",
"ATGAAGACTATCATTGCTTTTAGCTGCATCTTATGTCAGATCTCCGCTCAAAAACTCCCCGGAAGTGACAACAGCATGGCAACGCTGTGCCTGGGGCATCACGCAGTACCAAACGGAACGTTAGTGAAAACAATAACAGATGACCAAATTGAAGTGACTAATGCTACTGAGCTGGTCCAGAGTACCTCAAAAGGTGAAATATGCAGTAGTCCTCACCAAATCCTTGATGGAAAAAATTGTACACTGATAGATGCTCTATTGGGAGACCCTCATTGTGATGACTTCCAAAACAAGAAATGGGACCTTTTTGTTGAACGAAGCACAGCTTACAGCAACTGTTACCCTTATTATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACCCTGGAATTTACTCAAGAAAGCTTCAATTGGACTGGGGTTGCTCAAGACGGAGCAAGCTATTCTTGCAGAAGGGAATCTGAAAACAGTTTCTTTAGTAGATTGAATTGGTTATATAGTTTGAATTACAAATATCCAGCGCTGAACGTAACTATGCCAAACAATGACAAATTTGACAAATTGTACATTTGGGGGGTACACCACCCGGGTACGGACAAGGACCAAACCAGTCTATATATTCAAGCATCAGGGAGAGTTACAGTCTCCACCAAATGGAGCCAACAAACTGTAATCCCGAATATCGGGTCTAGACCCTGGATAAGGGGTGTCTCCAGCATAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCCCCTCGGGGTTACTTCAAAATACAAAGTGGGAAAAGCTCAATAATGAGGTCAGATGCACACATTGGCAACTGCAACTCTGAATGCATTACCCCAAATGGAAGCATTCCCAACGACAAACCTTTTCAAAATGTAAACAGAATAACATATGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTAGCAACAGGAATGCGGAATGTACCAGAGAAACAAACTAGAGGCATATTCGGCGCAATCGCAGGTTTCATAGAAAATGGTTGGGAAGGGATGGTGGACGGTTGGTATGGTTTCAGGCATCAAAACTCTGAAGGCACAGGGCAAGCAGCAGATCTTAAAAGCACTCAAGCGGCAATCAACCAAATCACCGGGAAACTAAATAGAGTAATCAAGAAGACGAATGAAAAATTCCATCAGATCGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTAGAGAGATACGTTGAAGACACTAAAATAGACCTCTGGTCTTACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATTTAACTGACTCAGAAATGAACAAACTGTTCGAAAGGACAAGGAAGCAACTGCGGGAAAATGCTGAGGACATGGGCAATGGATGCTTTAAAATATATCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGACGAAGCAGTAAACAATCGGTTCCAGATCAAAGGTGTTCAGCTGAAGTTAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGCTTTTTGCTTTGTGCTGTTCTGCTAGGATTCATTATGTGGGCATGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA",
"ATGAAGACTAGTAGTTCTGCTATATACATTGCAA------------------------CCGCAAATG---------CAGACACATTATGTATAGGTTATCATGCAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCAAACTGAGAGGGGTAGCCCCATTGCATTTG--------------------GGTAAATGTAACATTGCTGGCTGGATCC------------------------------------TGGGAAATCCAGAGTGTGACACTCTCCACAGCAAGCTCATGGTCCTACATCGTGGAAACATCTAAGACAATGGAACGTGCTACCCAGGAGATTTCATCAATTATGAGGAGCTAAGGTCATCATTTGAAAGGTTTGAGATATTACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTTCCTCAAGCTGGAGCAA---------------------------AAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAA------------------------------AGCTCAGCAAATCCTACATTTGGGGCATTCACCATCCATCTACTAGTGCTGACCAA-------CAAAGTCTCTATCAGAGTGCAGATGCATATGTTTTATCAAAATACAGCAAGAAGTTCAAG--CCGGAAATAGCAGTAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTATTGGTACCGAGATATGCATTCGCAATGGAAA----GAAATGCTGGATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCCAAATATGTAAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGCGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACAAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAAAACTTATATGAAAAGGTAAGAAGCCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCATCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATTTAA",
"ATGAAGACTATCATTGCTTTGAGCTACATTTTATGTCTGGTTTTCGCTCAAAAACTTCCCGGAAATGACAACAGCACGGCAACGCTGTGCCTGGGGCACCATGCAGTGCCAAACGGAACGCTAGTGAAAACAATCACGAATGACCAAATTGAAGTAACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTAGAATATGCGACAGTCCTCACCAAATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCATTGTGATGGCTTCCAAAACAAGGAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGTCTCCCTTAGGTCACTAGTTGCCTCATCAGGCACGCTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCGCTCAGAATGGAACAAGCTCTGCTTGCAAAAGGAGATCCGATAAAAGTTTCTTTAGTAGATTGAATTGGTTGCACCAATTAAAATACAAATATCCAGCACTGAACGTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACAGACAGTGACCAAATCAGCCTATATGCTCAAGCATCAGGGAGAGTCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTGGACCCTGGGTAAGGGGTGTCTCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTCGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGGTCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGGCAAACCATTTCAAAATGTAAACAGGATCACATATGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGGAATGTGCCAGAGAAACAAACTAGAGGCATATTCGGTGCAATCGCGGGCTTCATAGAAAATGGTTGGGAGGGAATGATGGACGGTTGGTACGGTTTCAGGCATCAGAATTCTGAGGGCACAGGGCAAGCAGCAGATCTTAAAAGCACTCAAGCAGCAATCAACCAAATCAACGGGAAACTGAATAGGTTAATCGAGAAAACGAACGAGAAATTCCATCAAATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTCGAGGACACTAAAATAGATCTCTGGTCGTACAATGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAGAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGGTCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGACGAAGCATTGAACAACCGGTTCCAGATCAAAGGTGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTATTGTTTTACTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATTTGA",
"--------------------------------------------------------------------------------AACGCTATGCCTGGGACACCATGCAGTACCAAATGGAACGTTAGTGAAAACAATCACGGATGACCAAATTGAAGTGACTAATGCTACTGAGCTGGTTCAAAGTTCCTCAACAGGTAGAATATGTAACAGTCCTCACCACATCCTTGATGGGAAAAATTGCACACTGATAGATGCTCTATTGGGAGACCCTCATTGTGATGACTTCCAAAACAAGGAATGGGACCTTTTTGTTGAACGAAGCACAGCCTACAGCAACTGCTACCCTTATTATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACCCTGGAATTCACCCAAGAAAGCTTCAATTGGACCGGAGTTACTCAAGATGGATCAAGCTATACTTGCAGAAGGAAATCTGTTAACAGTTTCTTTAGTAGATTAAATTGGTTGCATAATTTGGACTACAAATATCCAGCGCTGAACGTAACTATGCCAAACAATGACAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAGGGACCAAACCAACCTATATGTTCAAGCATCAGGGAGAGTTACAGTCTCCACAAAAAGAAGCCAACAAACTGTAATCCCGAACATCGGATCTAGACCCTGGGTAAGGGGTGTCTCCAGCATAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGAAATCTAATTGCCCCTCGGGGTTACTTCAAAATACAAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAACTGCAATTCTGAATGCATTACTCCAAATGGAAGCATTCCCAATGACAAACCTTTTCAAAATGTAAACAGGATCACATATGGGGCCTGTCCAAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGGAATGTACCAGAGAAACAAACTAGAGGCATATTCGGCGCAATCGCAGGCTTCATAGAAAATGGTTGGGAGGGGATGGTGGACGGTTGGTACGGTTTCAGGCATCAAAATTCTGAAGGCACAGGACAAGCAGCAGATCTTAAAAGTACTCAAGCAGCAATCAACCAAATCACCGGGAAACTGAATAGAGTAATCAAGAAAACGAACGAGAAATTCCATCAAATCGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTAGAGAAATACGTTGAAGACACTAAAATAGATCTCTGGTCTTACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATTTAACTGACTCAGAAATGAACAAACTGTTCGAAAGAACAAGGAAGCAACTGCGGGAAAATGCTGAGGACATGGGCAATGGTTGCTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGACGAGGCATTAAACAATCGGTTCCAGATCAAAAGTGTTCAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATGTCATGCTTTTTGCTTTGTGTTGTTCTGCTGGGGTTCATTATGTGGACCTGCCAAAAAGGCAACATTAAGTGCAACATTTGCATTTGA"
]
for reassortant_seq in reassortant_seqs:
for v in self.viruses:
dist = distance(Seq(reassortant_seq), v)
if (dist < 0.02):
remove_viruses.append(v)
if self.verbose > 1:
print "\tremoving", v.strain
self.viruses = MultipleSeqAlignment(
[v for v in self.viruses if v not in remove_viruses])
