audy

#!/usr/bin/env python3

from itertools import product

from typing import Dict, Tuple
import sys


def generate_codon_mapping(
    dna_alphabet="GATC",

audy

#!/usr/bin/env python3

import os
import downloads
from joblib import Parallel, delayed
from itertools import islice
from tqdm import tqdm

def get_gbk_path(assembly) -> str:
    """

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:

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

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[
    (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)

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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 	

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>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")