Andrew Perry pansapiens

## gist:204861
<!--
 Django template snippet that gives the current time,
 as an "RFC-822 compliant" date-time suitable for RSS feeds.

 Of course, you will probably never need to use this, since
 generating RSS feeds via Django templates isn't the best way ...
 you should use the Django feed syndication framework instead
 ( https://docs.djangoproject.com/en/dev/ref/contrib/syndication/ )
-->

## ec2unifiedshell.py
#!/usr/bin/python

WhatThisIS="""

This is a hacked together script to connect to all of your running EC2 instances, and to provide a single SSH prompt amongst all of them, and to assist in uploading, splitting, and downloading files. email me at winniningham at and email server called gmail.com :P

"""

import paramiko
from numpy import *

## gae_json_rest.py
from google.appengine.ext import webapp
from google.appengine.ext.webapp import util
from django.utils import simplejson as json
from google.appengine.ext import db
import re

import pdb, sys
debugger = pdb.Pdb(stdin=sys.__stdin__, stdout=sys.__stdout__)


## gist:3127897
javascript:(function(){var%20url_regex=/(https?:\/\/(?:[-\w\.]+)+(?::\d+)?)((?:\/([\w/_\-\.]*(\?\S+)?)?)?)/,url_results=url_regex.exec(document.location),new_url%20=%20url_results[1]+".proxy.com"+url_results[2];window.location=new_url;})()

## gist:6016434
while true; do if host www.example.com | grep "192.168.0.1"; then sleep 3600; else printf "\a"; xmessage -center "Domain propagated"; fi done

## standalone_html.py
#!/usr/bin/env python
# A simple script to suck up HTML, convert any images to inline Base64
# encoded format and write out the converted file.
#
# Usage: python standalone_html.py <input_file.html> <output_file.html>
#
# TODO: Consider MHTML format: https://en.wikipedia.org/wiki/MHTML

import os
from bs4 import BeautifulSoup

## gist:a40a847f37a7aa5d0dc9
# Tools:
# sf-convert: http://sw-tools.pdb.org/apps/SF-CONVERT/doc/V1-0-00/documentation.html
# Coot
# CCP4
# Pymol

# Get mmCIF format structure factors, and PDB coordinates
wget http://www.rcsb.org/pdb/files/r4J1Ysf.ent.gz
wget http://www.rcsb.org/pdb/files/4J1Y.pdb.gz
gunzip r4J1Ysf.ent.gz 4J1Y.pdb.gz

## inmembrane_signalp_trim.ipynb

      
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                pansapiens
                / inmembrane_signalp_trim.ipynb
            
            
              Created
              September 3, 2015 00:56
            
              
                Example of trimming SignalP predicted signal sequences using inmembrane
              
          
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## cloudstor_link_convert.py
#!/usr/bin/env python
"""
Takes a list of CloudStor download page links and turns them
into direct download links, suitable for use with wget -i or
aria2 -i.

$ convert_cloudstor_links.py page_links.txt >direct_links.txt
$ wget --content-disposition -c -i direct_links.txt
"""
import sys

## merge_dicts.py
# This version accepts any number of dictionaries
# http://stackoverflow.com/a/26853961
def merge_dicts(*dict_args):
    """
    Given any number of dicts, shallow copy and merge into a new dict,
    precedence goes to key value pairs in latter dicts.
    """
    result = {}
    for dictionary in dict_args:
        result.update(dictionary)
	<!--
	Django template snippet that gives the current time,
	as an "RFC-822 compliant" date-time suitable for RSS feeds.

	Of course, you will probably never need to use this, since
	generating RSS feeds via Django templates isn't the best way ...
	you should use the Django feed syndication framework instead
	( https://docs.djangoproject.com/en/dev/ref/contrib/syndication/ )
	-->
	#!/usr/bin/python

	WhatThisIS="""

	This is a hacked together script to connect to all of your running EC2 instances, and to provide a single SSH prompt amongst all of them, and to assist in uploading, splitting, and downloading files. email me at winniningham at and email server called gmail.com :P

	"""

	import paramiko
	from numpy import *
	from google.appengine.ext import webapp
	from google.appengine.ext.webapp import util
	from django.utils import simplejson as json
	from google.appengine.ext import db
	import re

	import pdb, sys
	debugger = pdb.Pdb(stdin=sys.__stdin__, stdout=sys.__stdout__)
	#!/usr/bin/env python
	# A simple script to suck up HTML, convert any images to inline Base64
	# encoded format and write out the converted file.
	#
	# Usage: python standalone_html.py <input_file.html> <output_file.html>
	#
	# TODO: Consider MHTML format: https://en.wikipedia.org/wiki/MHTML

	import os
	from bs4 import BeautifulSoup
	# Tools:
	# sf-convert: http://sw-tools.pdb.org/apps/SF-CONVERT/doc/V1-0-00/documentation.html
	# Coot
	# CCP4
	# Pymol

	# Get mmCIF format structure factors, and PDB coordinates
	wget http://www.rcsb.org/pdb/files/r4J1Ysf.ent.gz
	wget http://www.rcsb.org/pdb/files/4J1Y.pdb.gz
	gunzip r4J1Ysf.ent.gz 4J1Y.pdb.gz
	#!/usr/bin/env python
	"""
	Takes a list of CloudStor download page links and turns them
	into direct download links, suitable for use with wget -i or
	aria2 -i.

	$ convert_cloudstor_links.py page_links.txt >direct_links.txt
	$ wget --content-disposition -c -i direct_links.txt
	"""
	import sys
	# This version accepts any number of dictionaries
	# http://stackoverflow.com/a/26853961
	def merge_dicts(*dict_args):
	"""
	Given any number of dicts, shallow copy and merge into a new dict,
	precedence goes to key value pairs in latter dicts.
	"""
	result = {}
	for dictionary in dict_args:
	result.update(dictionary)