ebelter

import os
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord

with open("asm.fasta", "w") as out_f:
    for i in (1000000, 250000, 100000, 10000, 5000, 2000, 0):
        record = SeqRecord(Seq(("ATGC" * int(i/4)) + "A"), id="SEQ_{}".format(i+1), description="")
        SeqIO.write(record, out_f, "fasta")

ebelter

#!/bin/bash
set -e

USAGE="USAGE: ${0} AWS_CONFIG_FILE

PURPOSE
The script will save AWS secret credentials to a given network readable file name, and export the AWS_CONFIG_FILE environment variable. This will allow the running of the AWS CLI to manipulate files in buckets. The reason for the script is the default location of AWS credentials/config is in the user's HOME directory, and these are not mounted when using the lims-i1-datatransfer LSF queue.

PROCESS
Writes the given AWS credentials to the given network aws config file. Also sets teh file permissions to user rw only.

ebelter

###
# Reader with Sniffer
###
import csv, sys
if len(sys.argv) != 2: raise Exception("Gimme input file")
with open(sys.argv[1], "r") as f:
    dialect = csv.Sniffer().sniff(f.read(1024))
    f.seek(0)
    rdr = csv.reader(f, dialect)
    wtr = csv.writer(sys.stdout, delimiter="\t", quoting=csv.QUOTE_ALL)

ebelter

# Python classes become iterator with a __iter__ and __next__ function.
#  * the __iter__ function does not need to return self, just something that can __next__
#  * raise StopIteration to indicate the itrerator is complete

class TheCount():
    def __init__(self, start, stop):
        self.current = start - 1
        self.stop = stop

    def __iter__(self):

ebelter

A tutorial on running graph_tool in docker on MacOS

Below are are 2 examples:

• Run a basic docker to create, save as PNG, and view a simple graph with two vertices
• Run a docker connecting to a Mac display. Then create, view with GTK windows, save as PDF, and view a Barabási–Albert model graph

The benefit of using the GTK windows is being able to skip the save/view steps hile developing a graph.

Install Docker

Skip if docker is already installed on your Mac. Instructions are here:

ebelter

## STRUCTURE ##
|- myproject/
|--     __init__.py
|--     mymodule.py
|- tests/
|--      __init__.py
|--     test_mymodule.py

## RUNNING ##

ebelter

import sys

def tryit(msg=None):
    sys.stderr.write("***\nBEFORE\n")
    try:
        sys.stderr.write("TRY\n")
        if msg is not None:
            raise Exception(msg)
    except BaseException as ex: # Can be specific exceptions, add as tuple or separate blocks
    sys.stderr.write("EXCEPT\n")

ebelter

#!/bin/bash

# General Linux: The Localtime File
mv /etc/localtime /etc/localtime.bak
ln -s /usr/share/zoneinfo/America/Chicago /etc/localtime

# General Linux: ENV
export TZ='America/Chicago'

# Cent OS 7+: timedatectl (other subcommands available)

ebelter

######
# remote user: edbelter 
# remote host: bastion1

######
# Create a Key. If the key is for a different user, specify a different RSA file name.
$ ssh-keygen -t rsa
Generating public/private rsa key pair.
Enter file in which to save the key (/Users/ebelter/.ssh/id_rsa): bastion_rsa
Enter passphrase (empty for no passphrase): 

ebelter

# GCE INIT
$ gcloud init

# Set Sample - fill in __HERE__
SAMPLE=__HERE__; export SAMPLE

# DL FASTAS from object store
$ cd /mnt/disks/data/reads
$ mkdir -p ${SAMPLE}