fredyr

/// K-mer counting
/// Basic Zig port of kc-c1.c from https://github.com/lh3/kmer-cnt/blob/master/kc-c1.c
///
/// zig build -Doptimize=ReleaseFast
/// wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR174/003/ERR1741363/ERR1741363_1.fastq.gz
///
/// time ./kc-c1 ERR1741363_1.fastq.gz                       => real  0m20,494s
/// time pigz -dc ERR1741363_1.fastq.gz | zig-out/bin/kc-z1  => real  0m20,336s
///
const std = @import("std");

fredyr

#!/usr/bin/env bash
set -e
# run script with sudo

# cleanup
apt -y autoremove

# update all security patches
apt-get -y -s dist-upgrade | grep "^Inst" | \
    grep -i securi | awk -F " " {'print $2'} | \

fredyr

#/usr/bin/env bash
set -e
ENV=snp_tree
source miniconda3/etc/profile.d/conda.sh
if !(conda info --envs | grep $ENV); then
    echo "Installing dependencies..."
    # conda config --add channels defaults
    # conda config --add channels bioconda
    # conda config --add channels conda-forge
    conda create --name $ENV python=3.9 mafft snp-sites snp-dists quicktree -q -y

fredyr

import sys
from io import StringIO

import pandas
from Bio.Phylo.TreeConstruction import DistanceMatrix


def distance_matrix(snp_tab):
    df = pandas.read_csv(snp_tab, sep='\t', header=0)
    cols = list(df.columns)[1:]

fredyr

"""Takes a CSV distance matrix and renders it as a MST."""

import sys

import matplotlib.pyplot as plt
import networkx as nx
import pandas
from scipy.sparse.csgraph import minimum_spanning_tree

fredyr

import inspect
from urllib.parse import urlparse


class ParameterSet:
    pass


class Field:
    def __init__(self, description, **kwargs):

fredyr

type bitnum = (int, list bool);

let elem_of_list ls => ReactRe.arrayToElement (Array.of_list ls);

let text s => ReactRe.stringToElement s;

let cell_col bit => {
  let color = if bit {"light"} else {"dark"};
  <div className=("cell " ^ color) />
};

fredyr

0 info it worked if it ends with ok
1 verbose cli [ '/usr/local/bin/node',
1 verbose cli   '/usr/local/bin/npm',
1 verbose cli   '--verbose',
1 verbose cli   'install' ]
2 info using [email protected]
3 info using [email protected]
4 silly loadCurrentTree Starting
5 silly install loadCurrentTree
6 silly install readLocalPackageData

fredyr

(defmacro lwt (&rest args)
  (destructuring-bind (b1 wh b2 &rest body) args
    `(let* (,@b2 ,@b1) ,@body)))

(macroexpand-all
 '(lwt ((w (* x y)))
       :where
       ((x 2)
        (y 3))
       (+ 1 w)))

fredyr

(defmacro lwt (&rest args)
  (destructuring-bind (b1 wh b2 &rest body) args
    `(let* (,@b2 ,@b1) ,@body)))

(macroexpand-all
 '(lwt ((w (* x y)))
       :where
       ((x 2)
        (y 3))
       (+ 1 w)))