Cathal Garvey cathalgarvey

## jlgz_dump.go
package main

import (
  "compress/gzip"
  "os"
  "bufio"
  "fmt"
  "log"
)

## chacha20
# Pure Python ChaCha20
# Based on Numpy implementation: https://gist.github.com/chiiph/6855750
# Based on http://cr.yp.to/chacha.html
#
# I wanted an implementation of ChaCha in clean, understandable Python
# as a way to get a handle on the algorithm for porting to another language.
# There are plenty of bindings but few pure implementations, because
# Pure Python is too slow for normal practical use in Cryptography.
#
# The preceding implementation used NumPy, which avoided a lot of the

## setupbiopython.sh
#!/bin/bash
# This script installs Python3, ipython, pip, and uses pip to install biopython.
# You'll be asked for your password.
sudo apt-get install python3-dev ipython3 python3-pip build-essential
sudo pip install biopython
# That's it, two lines!

## VersionedDict
class VersionedDict(dict):
    '''A dictionary sublcass that remembers all or a defined number of prior entries for a key.
    Allows reversion by number from "head" or by absolute reference in revision list.
    Allows retrieval of currently retained revision history for a key.
    Deletion deletes all revisions, not merely the most recent.
    If instantiated with the "revisions" keyword and an integer argument, only retains that many revisions per entry.'''

    def __init__(self, *args, **kwargs):
        revisions = kwargs.pop('revisions', None)
        self._allowed_revisions = abs(int(revisions))

## grep_tweets
#!/usr/bin/env python3
import time
import datetime
import json
import re

timestamp_format = '%a %b %d %H:%M:%S %z %Y'
def twitter_timestamp_to_obj(time_string):
    'Returns a timezone-aware datetime object.'
    return datetime.datetime.strptime(time_string, timestamp_format)

## cat_tweets
#!/usr/bin/env python3
import time
import datetime
import os
import json

timestamp_format = '%a %b %d %H:%M:%S %z %Y'
def twitter_timestamp_to_obj(time_string):
    'Returns a timezone-aware datetime object.'
    return datetime.datetime.strptime(time_string, timestamp_format)

## wordsoupfixer.py
#!/usr/bin/env python3

import sys
fixfile = sys.argv[1]

with open(fixfile) as InputFile:
    word_soup = InputFile.read()

# Strip off excess whitespace and any trailing ellipsis.
word_soup = word_soup.strip().strip(".!?")

## countfiles
#!/usr/bin/env python3
import os
from sys import argv

# Walk through folders recursively, list the full path and number of (extension) files found in each.

basefolder = os.path.expanduser(argv[1])
filetype = str(argv[2]).lower()
output = []

## EcoliK12_OptimalCodons
{
 "End": {
  "TAG": {
   "frequency": 0.0,
   "relfreq": 0.0
  },
  "localfrequency": 2.74,
  "TGA": {
   "frequency": 0.98,
   "relfreq": 0.3576642335766423

## RestrictionEnzymes.json
{
  "binsi": {
    "target_site": "CCWGG",
    "name": "BinSI",
    "suppliers": [],
    "source": "ATCC 15702",
    "references": [
      "Khosaka, T., Kiwaki, M., Rak, B., (1983) FEBS Lett., vol. 163, pp. 170-174."
    ],
    "prototype": "EcoRII",
	# Pure Python ChaCha20
	# Based on Numpy implementation: https://gist.github.com/chiiph/6855750
	# Based on http://cr.yp.to/chacha.html
	#
	# I wanted an implementation of ChaCha in clean, understandable Python
	# as a way to get a handle on the algorithm for porting to another language.
	# There are plenty of bindings but few pure implementations, because
	# Pure Python is too slow for normal practical use in Cryptography.
	#
	# The preceding implementation used NumPy, which avoided a lot of the
	#!/bin/bash
	# This script installs Python3, ipython, pip, and uses pip to install biopython.
	# You'll be asked for your password.
	sudo apt-get install python3-dev ipython3 python3-pip build-essential
	sudo pip install biopython
	# That's it, two lines!
	class VersionedDict(dict):
	'''A dictionary sublcass that remembers all or a defined number of prior entries for a key.
	Allows reversion by number from "head" or by absolute reference in revision list.
	Allows retrieval of currently retained revision history for a key.
	Deletion deletes all revisions, not merely the most recent.
	If instantiated with the "revisions" keyword and an integer argument, only retains that many revisions per entry.'''

	def __init__(self, args, *kwargs):
	revisions = kwargs.pop('revisions', None)
	self._allowed_revisions = abs(int(revisions))
	#!/usr/bin/env python3
	import time
	import datetime
	import json
	import re

	timestamp_format = '%a %b %d %H:%M:%S %z %Y'
	def twitter_timestamp_to_obj(time_string):
	'Returns a timezone-aware datetime object.'
	return datetime.datetime.strptime(time_string, timestamp_format)
	#!/usr/bin/env python3

	import sys
	fixfile = sys.argv[1]

	with open(fixfile) as InputFile:
	word_soup = InputFile.read()

	# Strip off excess whitespace and any trailing ellipsis.
	word_soup = word_soup.strip().strip(".!?")
	#!/usr/bin/env python3
	import os
	from sys import argv

	# Walk through folders recursively, list the full path and number of (extension) files found in each.

	basefolder = os.path.expanduser(argv[1])
	filetype = str(argv[2]).lower()
	output = []
	{
	"End": {
	"TAG": {
	"frequency": 0.0,
	"relfreq": 0.0
	},
	"localfrequency": 2.74,
	"TGA": {
	"frequency": 0.98,
	"relfreq": 0.3576642335766423
	{
	"binsi": {
	"target_site": "CCWGG",
	"name": "BinSI",
	"suppliers": [],
	"source": "ATCC 15702",
	"references": [
	"Khosaka, T., Kiwaki, M., Rak, B., (1983) FEBS Lett., vol. 163, pp. 170-174."
	],
	"prototype": "EcoRII",