audy

import taxonomy

tax = taxonomy.Taxonomy.from_ncbi("ncbi_taxdump/")

FULL_RANKS = [ 'superkingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species']

def get_scalar(d: dict, key: str):
    if key in d:
        vals = d[key]
        if len(vals) == 1:

audy

>MN908947.3
ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCT
GTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACT
CACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATC
TTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT
CGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAAC
ACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGG
AGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG
CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAA
ACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACT

audy

[
    (None, {"id": "447834", "parent": "447833", "rank": "subspecies"}),
    (None, {"id": "447833", "parent": "111897", "rank": "species"}),
    (None, {"id": "111897", "parent": "1664845", "rank": "genus"}),
    (None, {"id": "1664845", "parent": "42282", "rank": "tribe"}),
    (None, {"id": "42282", "parent": "33415", "rank": "subfamily"}),
    (None, {"id": "33415", "parent": "37572", "rank": "family"}),
    (None, {"id": "37572", "parent": "104431", "rank": "superfamily"}),
    (None, {"id": "104431", "parent": "37567", "rank": "clade"}),
    (None, {"id": "37567", "parent": "41197", "rank": "clade"}),

audy

#!/usr/bin/env python3

# usage: cat reads.fastq | ./get-barcodes.py

from Bio import SeqIO
from collections import defaultdict

BARCODE_SIZE = 14

counts = defaultdict(lambda: 0)

audy

model 	STRING 	NULLABLE 	
taxonomy_name 	STRING 	NULLABLE 	
description 	STRING 	NULLABLE 	
title 	STRING 	NULLABLE 	
gsm 	STRING 	NULLABLE 	
attributes 	STRING 	REPEATED 	
dbgap 	STRING 	NULLABLE 	
attribute_recs 	RECORD 	REPEATED 	
attribute_recs. unit 	STRING 	NULLABLE 	
attribute_recs. display_name 	STRING 	NULLABLE 	

audy

>AY179509.1 Mink astrovirus, complete genome
CCGAAGTAGGTGTGTGTGTTGCCGTTATGGCTAACAACACTACCAGCGCTCTTCACCCTCGTGGCTCTGGCCAGCGCTGT
GTCTATGACACAGTGCTCCGGTTTGGGGACCCCGATGCACGTCGCAGGGGTTTCCAATTGGACGAGGTGTCACATAATAA
GTTGTGTGACATTTTTGACAGCGGCCCGCTCCACTTCGCTTTTGGTGATCTTAAAGTGATGAAGGTGGCGGGTGGTGTGG
TCACACCGCATAAAACAGTTGTCAAAACAGTCTATGTCTCAGGTGTTCAAGAGGGTAACGATTATGTCACTTTTGCCTTC
ACGCCTGGACCTAACGAGTGGCGCGAAGTTGATCCCCGCATCGACAAGCGCACAGCACTCGTCGGTGTCCTTGTGCAAGA
ACATAAAAAATTGGACTCAGACCTTAAGGAGTCGCGCCGTGAGTTGTCCCAGCTCAAGTTGGAGCACTCACTGTTGAGAC
ATGACTATGAGCGCTTGGTCCGTGAAAAGCCTGGTCCTGCTATGAGAACTTTTAAATTCTCAGCTGTCATCTTTTATGCG
TTTTTCCTTGGTTTCCTGCTTATGTCTGCTGTCAAGGGTGAGGTGTATGGTCGCTGTCTTGACAGCGAGCTTAACCTCAA
TGGCAACCCTGAAGTGTGTTTGCATTGGGAAGAGGTTAAATCTTTTAGCCTCCAGGTTGCCCTTGCAGACTTCTGGAACA

audy

class BaseKitty
  def meow
    nil
  end
end

class Nancy < BaseKitty
  def meow
    (super || "shshsh")
  end

audy

#!/usr/bin/env ruby

require "open-uri"
require "parallel"

open("https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt") do |handle|
  handle.gets # skip header
  handle.gets
  Parallel.each(handle, :in_processes => 6, :progress => 'downloading') do |line|
    row = line.split("\t")

audy

audy

2017-04-01	2017-10-01	The Bear & Peacock Brewery	 Orlando, FL
2017-02-01		Nude Nite	 Orlando, FL
2016-09-01		Small Works Show City Arts Factory	 Orlando, FL
2016-08-01		Declaration of the Mind 1st Thursdays	 Orlando Museum of Art, FL
2016-07-01		Rock (People's Choice Award Winner)	 1st Thursdays, Orlando Museum of Art, FL
2016-03-01		Viva La Diva	 1st Thursdays, Orlando Museum of Art, FL
2016-03-01		Nude Nite	 Tampa, FL
2016-02-01		Peace and Harmony	 1st Thursdays, Orlando Museum of Art, FL
2016-10-01			 Winter Park, FL
2012-08-01			 Vegas Gallery, Las Vegas, AZ