View ascii-to-dna.py
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#!/usr/bin/env python3 | |
from itertools import product | |
from typing import Dict, Tuple | |
import sys | |
def generate_codon_mapping( | |
dna_alphabet="GATC", |
View download-assemblies-from-ncbi.py
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#!/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: | |
""" |
View graft_node_to_taxonomy.py
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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: |
View nCoV-2019.reference.fasta
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>MN908947.3 | |
ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCT | |
GTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACT | |
CACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATC | |
TTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT | |
CGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAAC | |
ACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGG | |
AGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG | |
CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAA | |
ACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACT |
View clades.py
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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"}), |
View get-barcodes.py
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#!/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) |
View biosamples-omicidx.tab
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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 |
View input.fasta
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>AY179509.1 Mink astrovirus, complete genome | |
CCGAAGTAGGTGTGTGTGTTGCCGTTATGGCTAACAACACTACCAGCGCTCTTCACCCTCGTGGCTCTGGCCAGCGCTGT | |
GTCTATGACACAGTGCTCCGGTTTGGGGACCCCGATGCACGTCGCAGGGGTTTCCAATTGGACGAGGTGTCACATAATAA | |
GTTGTGTGACATTTTTGACAGCGGCCCGCTCCACTTCGCTTTTGGTGATCTTAAAGTGATGAAGGTGGCGGGTGGTGTGG | |
TCACACCGCATAAAACAGTTGTCAAAACAGTCTATGTCTCAGGTGTTCAAGAGGGTAACGATTATGTCACTTTTGCCTTC | |
ACGCCTGGACCTAACGAGTGGCGCGAAGTTGATCCCCGCATCGACAAGCGCACAGCACTCGTCGGTGTCCTTGTGCAAGA | |
ACATAAAAAATTGGACTCAGACCTTAAGGAGTCGCGCCGTGAGTTGTCCCAGCTCAAGTTGGAGCACTCACTGTTGAGAC | |
ATGACTATGAGCGCTTGGTCCGTGAAAAGCCTGGTCCTGCTATGAGAACTTTTAAATTCTCAGCTGTCATCTTTTATGCG | |
TTTTTCCTTGGTTTCCTGCTTATGTCTGCTGTCAAGGGTGAGGTGTATGGTCGCTGTCTTGACAGCGAGCTTAACCTCAA | |
TGGCAACCCTGAAGTGTGTTTGCATTGGGAAGAGGTTAAATCTTTTAGCCTCCAGGTTGCCCTTGCAGACTTCTGGAACA |
View class_cats.rb
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class BaseKitty | |
def meow | |
nil | |
end | |
end | |
class Nancy < BaseKitty | |
def meow | |
(super || "shshsh") | |
end |
View fetch-refseq-annotations.rb
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#!/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") |
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