eharkins

{
  "$schema": "https://vega.github.io/schema/vega-lite/v2.json",
  "description": "Shows the relationship between horsepower and the numbver of cylinders using tick marks.",
  "data": {

    "values":
      [{"seq_id": ["5258-4"], "position": 7, "mut_from": "T", "mut_to": "I"}, {"seq_id": ["5258-4"], "position": 26, "mut_from": "S", "mut_to": "N"}, {"seq_id": ["5258-4"], "position": 39, "mut_from": "Y", "mut_to": "S"}, {"seq_id": ["5258-4"], "position": 57, "mut_from": "S", "mut_to": "Y"}, {"seq_id": ["5258-4"], "position": 107, "mut_from": "K", "mut_to": "R"}, {"seq_id": ["145307-1"], "position": 7, "mut_from": "T", "mut_to": "I"}, {"seq_id": ["145307-1"], "position": 22, "mut_from": "S", "mut_to": "A"}, {"seq_id": ["145307-1"], "position": 26, "mut_from": "S", "mut_to": "N"}, {"seq_id": ["145307-1"], "position": 39, "mut_from": "Y", "mut_to": "S"}, {"seq_id": ["145307-1"], "position": 45, "mut_from": "P", "mut_to": "Q"}, {"seq_id": ["145307-1"], "position": 57, "mut_from": "S", "mut_to": "Y"}, {"seq_id": [

eharkins

def parse_fasta_string(fasta_string):
  return dict([tuple(s.replace('\n', ':', 1).replace('\n','').split(':')) for s in fasta_string.split('>')[1:]])

eharkins

{
  "$schema": "https://vega.github.io/schema/vega/v4.json",
  "width": 1000,
  "height": 1000,
  "padding": 5,

  "signals": [
     { "name": "sortby", "value": "none",
      "bind": {"input": "select", "options": ["none", "data.lbi", "data.lbr"]} },
    { "name": "method", "value": "cluster",

eharkins

#!/usr/bin/env python
import os
import argparse
import subprocess
import csv
import sys

def parse_args():
    parser = argparse.ArgumentParser(description='run cft bin/blast.py for seed clusters from partis yaml files specified in an input csv. write results to specified outdir.')
    parser.add_argument(

eharkins

import re
import sys
from Bio.SeqRecord import SeqRecord
from Bio import SeqIO
from Bio.Seq import Seq

"""
to calculate avg rate of inferred ambiguous nucleotides for many "ancestralStates" raxml-ng output files, do:

1. fd ancestralStates -x python amb_rate.py > amb_rates.txt

eharkins

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import yaml
import argparse
import os

parser = argparse.ArgumentParser(description='Process some info.yaml.')
parser.add_argument('infile', type=str,
                    help='input info.yaml')

eharkins