Mercurial > repos > iuc > hyphy_slac
changeset 40:e46726cd0c9e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy commit cee1ce4bd7d82088b9bf62403bc175c13223e020
| author | iuc |
|---|---|
| date | Wed, 11 Mar 2026 11:14:01 +0000 |
| parents | 307b6a9a520b |
| children | |
| files | macros.xml scripts/hyphy_summary.py scripts/infer_stasis_clusters.py test-data/bstill-in1.json |
| diffstat | 4 files changed, 2053 insertions(+), 681 deletions(-) [+] |
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--- a/macros.xml Wed Feb 25 20:56:08 2026 +0000 +++ b/macros.xml Wed Mar 11 11:14:01 2026 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">2.5.93</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@TOOL_VERSION@">2.5.96</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">24.0</token> <token name="@SHELL_OPTIONS@">export TERM="vt100"; </token>
--- a/scripts/hyphy_summary.py Wed Feb 25 20:56:08 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,679 +0,0 @@ -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 = {} - _ = newick_parser(self.cfel['input']['trees']['0'], False, node_tags, self.cfel, self.arguments, self.labels)['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 = newick_parser(self.slac['input']['trees']['0'], False, node_tags, self.slac, self.arguments, self.labels) - 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: - traverse_tree_in_order(the_tree, self.labels, self.slac['branch attributes']['0'], i, None, root_node) - except Exception: - pass - 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(): - # Skip anything past the end of this section. - if i >= len(info['0']): - continue - 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 _get_incoming_labels(self): - json_data = self._load_json(self.arguments.labels) - self.incoming_labels = json_data - - -def traverse_tree_in_order(node, labels, slac_data, i, parent_tag, root): - node_tag = None - if 'name' not in node: - nn = root - else: - nn = root if node["name"] == 'root' else node["name"] - if nn in slac_data: - node_tag = slac_data[nn]["codon"][0][i] - if (parent_tag != node_tag): - labels[nn] = node_tag - labels[node["name"]] = node_tag - if "children" in node: - for c in node["children"]: - traverse_tree_in_order(c, labels, slac_data, i, node_tag, root) - - -def newick_parser(nwk_str, bootstrap_values, track_tags, json_map, import_settings, tags): - 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 = import_settings.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 tags.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 as e: - pass - print(e) - - 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): - return { - 'json': None, - 'error': - "Unexpected '%s' in '%s[ERROR HERE]%s'" % (nwk_str[location], nwk_str[location - 20:location + 1], nwk_str[location + 1:location + 20]) - } - - 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 as e: - return generate_error(char_index) - print(e) - - 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 as e: - return generate_error(char_index) - print(e) - - 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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/infer_stasis_clusters.py Wed Mar 11 11:14:01 2026 +0000 @@ -0,0 +1,171 @@ +#!/usr/bin/env python3 +""" +B-STILL Stasis Cluster Inference Tool +==================================== +Identifies regional footprints of extreme purifying selection (stasis) in B-STILL +JSON results using a FWER-controlled Hypergeometric Scan Statistic. + +Usage: + python3 infer_stasis_clusters.py input.json --ebf 10 --permutations 10000 --output results.json +""" + +import argparse +import json +import sys +import time + +import numpy as np +from scipy.stats import hypergeom + + +def get_sf_optimized(n, d, L, K, cache): + """Retrieves or computes Hypergeometric Survival Function value.""" + key = (n, d) + if key not in cache: + cache[key] = hypergeom.sf(n - 1, L, K, d) + return cache[key] + + +def scan_intervals(indices, L, K, max_size, sf_cache, threshold=None): + """ + Scans all possible intervals [i, j] anchored by stasis events. + Returns the minimum p-value if threshold is None, else returns all significant segments. + """ + best_p = 1.0 + segments = [] + num_events = len(indices) + + for n in range(3, min(max_size + 1, num_events + 1)): + for i in range(num_events - n + 1): + d = indices[i + n - 1] - indices[i] + 1 + p = get_sf_optimized(n, d, L, K, sf_cache) + + if threshold is None: + if p < best_p: + best_p = p + else: + if p <= threshold: + segments.append({ + "start": int(indices[i] + 1), + "end": int(indices[i + n - 1] + 1), + "p_value": p, + "k": n, + "d": int(d) + }) + + return best_p if threshold is None else segments + + +def merge_segments(segments, merge_dist=15): + """Merges overlapping or nearby significant segments.""" + if not segments: + return [] + segments.sort(key=lambda x: x['start']) + + merged = [] + curr = segments[0] + for next_s in segments[1:]: + if next_s['start'] <= curr['end'] + merge_dist: + curr['end'] = max(curr['end'], next_s['end']) + curr['p_value'] = min(curr['p_value'], next_s['p_value']) + curr['d'] = curr['end'] - curr['start'] + 1 + else: + merged.append(curr) + curr = next_s + merged.append(curr) + return merged + + +def main(): + parser = argparse.ArgumentParser(description="Infer stasis clusters from B-STILL JSON.") + parser.add_argument("input", help="Path to B-STILL JSON result file") + parser.add_argument("--ebf", type=float, default=10.0, help="EBF threshold for defining stasis sites (default: 10.0)") + parser.add_argument("--permutations", type=int, default=10000, help="Number of permutations for FWER control (default: 10000)") + parser.add_argument("--alpha", type=float, default=0.05, help="Family-wise error rate threshold (default: 0.05)") + parser.add_argument("--max-cluster", type=int, default=30, help="Maximum number of stasis sites per interval scan (default: 30)") + parser.add_argument("--merge", type=int, default=15, help="Distance in codons to merge adjacent clusters (default: 15)") + parser.add_argument("--output", help="Path to save results in JSON format") + + args = parser.parse_args() + + try: + with open(args.input, "r") as f: + data = json.load(f) + except Exception as e: + print("Error loading JSON: {0}".format(e)) + sys.exit(1) + + sites = data.get("MLE", {}).get("content", {}).get("0", []) + ebfs = [s[12] if (len(s) > 12 and isinstance(s[12], (int, float))) else 0 for s in sites] + L = len(ebfs) + + if L < 10: + print("Alignment too short for cluster analysis.") + sys.exit(0) + + stasis_indices = np.array([i for i, val in enumerate(ebfs) if val >= args.ebf]) + K = len(stasis_indices) + + print("--- B-STILL Cluster Inference ---") + print("Input: {0}".format(args.input)) + print("Gene Length (L): {0} codons".format(L)) + print("Stasis Sites (K): {0} (EBF >= {1})".format(K, args.ebf)) + + if K < 3: + print("Insufficient stasis sites to form clusters (minimum 3 required).") + sys.exit(0) + + print("Running {0} permutations for FWER control...".format(args.permutations)) + null_min_ps = [] + all_positions = np.arange(L) + sf_cache = {} + + start_time = time.time() + for i in range(args.permutations): + if i > 0 and i % 1000 == 0: + elapsed = time.time() - start_time + print(" Processed {0} permutations... ({1:.1f} per sec)".format(i, i / elapsed)) + shuffled = sorted(np.random.choice(all_positions, K, replace=False)) + min_p = scan_intervals(shuffled, L, K, args.max_cluster, sf_cache) + null_min_ps.append(min_p) + + crit_p = np.percentile(null_min_ps, args.alpha * 100) + print("Gene-specific Critical P-value (FWER {0}): {1:.2e}".format(args.alpha, crit_p)) + + print("Scanning observed sequence for significant clusters...") + raw_segments = scan_intervals(stasis_indices, L, K, args.max_cluster, sf_cache, threshold=crit_p) + + final_clusters = merge_segments(raw_segments, merge_dist=args.merge) + + for c in final_clusters: + c['k'] = sum(1 for idx in stasis_indices if c['start'] <= idx + 1 <= c['end']) + + print("\nFound {0} significant stasis clusters:".format(len(final_clusters))) + if final_clusters: + print("\nLegend:") + print(" k : Number of high-confidence stasis sites within the cluster") + print(" d : Total span of the cluster in codons") + print("\n{:<8} | {:<8} | {:<5} | {:<5} | {:<10}".format("Start", "End", "k", "d", "P-value")) + print("-" * 45) + for c in final_clusters: + print("{:<8} | {:<8} | {:<5} | {:<5} | {:.2e}".format(c['start'], c['end'], c['k'], c['d'], c['p_value'])) + + if args.output: + output_data = { + "input_file": args.input, + "parameters": vars(args), + "summary": { + "gene_length": L, + "total_stasis_sites": K, + "critical_p_value": float(crit_p), + "num_clusters": len(final_clusters) + }, + "clusters": final_clusters + } + with open(args.output, "w") as f: + json.dump(output_data, f, indent=4) + print("\nDetailed results saved to {0}".format(args.output)) + + +if __name__ == "__main__": + main()
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site" + ], + [ + "Prob[alpha=beta=0]", + "Posterior probability of alpha=beta=0" + ], + [ + "Prob[alpha=0]", + "Posterior probability of alpha=0" + ], + [ + "Prob[beta=0]", + "Posterior probability of beta=0" + ], + [ + "Prob[alpha,beta~0]", + "Posterior probability of alpha and beta within a radius of 0.5 of 0" + ], + [ + "Prob[alpha<beta]", + "Posterior probability of positive selection at a site" + ], + [ + "PSRF", + "Potential scale reduction factor - an MCMC mixing measure" + ], + [ + "Neff", + "Estimated effective sample site for Prob [alpha<beta]" + ], + [ + "EBF[alpha=beta=0]", + "Empirical Bayes Factor for alpha=beta=0" + ], + [ + "EBF[alpha=0]", + "Empirical Bayes Factor for alpha=0" + ], + [ + "EBF[beta=0]", + "Empirical Bayes Factor for beta=0" + ], + [ + "EBF[alpha,beta~0]", + "Empirical Bayes Factor for alpha and beta within a radius of 0.5 of 0" + ] + ] + }, + "analysis": { + "authors": "Sergei L Kosakovsky Pond", + "citation": "FUBAR: a fast, unconstrained bayesian approximation for inferring selection (2013), Mol Biol Evol. 30(5):1196-205", + "contact": "spond@temple.edu", + "info": "Perform a B-STILL (Bayesian Significance Test of Invariant Low Likelihoods) \n analysis to detect invariant sites (alpha=beta=0) and quantify their \n posterior probabilities and Empirical Bayes Factors. This is a modified \n version of the standard FUBAR analysis that uses a denser grid around \n zero and reports the probability of a site being effectively invariant.", + "requirements": "in-frame codon alignment (possibly partitioned) and a phylogenetic tree (one per partition)", + "version": "1.0 (B-STILL)" + }, + "input": { + "file name": "/home/danielle/Documents/veg/tools-iuc/tools/hyphy/test-data/fubar-in1.fa.gz", + "number of sequences": 163, + "number of sites": 566, + "partition count": 1, + "trees": { + "0": 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+ } + }, + "_comment": "Trimmed HyPhy B-STILL output (first 120 codon sites, first 13 metrics, removed posterior/grid/etc) to keep infer_stasis_clusters test input under planemo's 1MB lint limit." +}