View graft_node_to_taxonomy.py
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
>MN908947.3 | |
ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCT | |
GTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACT | |
CACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATC | |
TTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT | |
CGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAAC | |
ACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGG | |
AGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG | |
CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAA | |
ACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACT |
View clades.py
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
[ | |
(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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
>AY179509.1 Mink astrovirus, complete genome | |
CCGAAGTAGGTGTGTGTGTTGCCGTTATGGCTAACAACACTACCAGCGCTCTTCACCCTCGTGGCTCTGGCCAGCGCTGT | |
GTCTATGACACAGTGCTCCGGTTTGGGGACCCCGATGCACGTCGCAGGGGTTTCCAATTGGACGAGGTGTCACATAATAA | |
GTTGTGTGACATTTTTGACAGCGGCCCGCTCCACTTCGCTTTTGGTGATCTTAAAGTGATGAAGGTGGCGGGTGGTGTGG | |
TCACACCGCATAAAACAGTTGTCAAAACAGTCTATGTCTCAGGTGTTCAAGAGGGTAACGATTATGTCACTTTTGCCTTC | |
ACGCCTGGACCTAACGAGTGGCGCGAAGTTGATCCCCGCATCGACAAGCGCACAGCACTCGTCGGTGTCCTTGTGCAAGA | |
ACATAAAAAATTGGACTCAGACCTTAAGGAGTCGCGCCGTGAGTTGTCCCAGCTCAAGTTGGAGCACTCACTGTTGAGAC | |
ATGACTATGAGCGCTTGGTCCGTGAAAAGCCTGGTCCTGCTATGAGAACTTTTAAATTCTCAGCTGTCATCTTTTATGCG | |
TTTTTCCTTGGTTTCCTGCTTATGTCTGCTGTCAAGGGTGAGGTGTATGGTCGCTGTCTTGACAGCGAGCTTAACCTCAA | |
TGGCAACCCTGAAGTGTGTTTGCATTGGGAAGAGGTTAAATCTTTTAGCCTCCAGGTTGCCCTTGCAGACTTCTGGAACA |
View class_cats.rb
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
class BaseKitty | |
def meow | |
nil | |
end | |
end | |
class Nancy < BaseKitty | |
def meow | |
(super || "shshsh") | |
end |
View fetch-refseq-annotations.rb
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/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") |
View exhibits.txt
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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 |
NewerOlder