eharkins

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

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
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

{
  "$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

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-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": [