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#!/usr/bin/env python3

import xml.etree.ElementTree as ET
from pprint import pprint
import code

tree = ET.parse('biosample_result.xml')

def expand_blob(blob, attributes={}):
    '''

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pretty-blastn () {
    column_names=(qaccver saccver pident length mismatch gapopen qstart qend sstart send slen evalue bitscore)
    column_names_string=$(IFS=' ' ; echo "${column_names[*]}")
    header=$(IFS=',' ; echo "${column_names[*]}")
    echo "${header}"
    blastn \
      -outfmt "10 delim=, ${column_names_string}" \
      "${@}"
}

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# Rule to count the number of lines in input.interleaved.fastq
rule count_lines:
    input:
        "input.interleaved.fastq"
    output:
        "line_count.txt"
    shell:
        "wc -l < {input} > {output}"

# Rule to convert paired-end FASTQ files to interleaved format

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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",

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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:
    """

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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:

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dokku postgresql rsync nightly backup

This is a rough guide to automating a nightly 7-day rolling remote backup of your PostgreSQL database(s) for your dokku app(s). There is a slight difference if you are using an older version of Dokku.

This will save the comprssed output of pg_dump as well as the contents of the /home directory on your dokku machine (just in case).

You will need to create a shell script in /root and edit the cron file.

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#!/usr/bin/env python

# Shannon Diversity Index
# http://en.wikipedia.org/wiki/Shannon_index

import sys

def sdi(data):
    """ Given a hash { 'species': count } , returns the SDI
    

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cellvibr.io
pelobact.er
shewane.la
myxococc.us
stigmate.la
cystobact.er
nannocyst.is
vitreosci.la
lysobact.er
simonsie.la