peterk87

# assuming that the file is tab-delimited ('\t')
delim = '\t'

# binary file path:
binary_patterns_filename = "binary_patterns.txt"

# get all of the lines in the binary patterns file
lines = [line.rstrip() for line in open(binary_patterns_filename, "r")]

# 1st line should contain the headers

peterk87

import os
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio import SeqIO

# get all sequence records for the specified genbank file
recs = [rec for rec in SeqIO.parse("genbank_file.gbk", "genbank")]

# print the number of sequence records that were extracted

peterk87

import sys
import math


def getContTable(ar1, ar2):
    cont = {}
    for i in xrange(0, len(ar1)):
        keyAr1 = ar1[i]
        keyAr2 = ar2[i]
        if keyAr1 in cont:

peterk87

Windows Registry Editor Version 5.00

[HKEY_CLASSES_ROOT\*\shell\Open in Sublime Text 2]
"Icon"="C:\\Program Files\\Sublime Text 2\\sublime_text.exe"

[HKEY_CLASSES_ROOT\*\shell\Open in Sublime Text 2\command]
@="\"C:\\\\Program Files\\\\Sublime Text 2\\\\sublime_text.exe\" \"%1\""

[HKEY_CLASSES_ROOT\Directory\Background\shell\Open in Sublime Text 2\command]
@="\"C:\\\\Program Files\\\\Sublime Text 2\\\\sublime_text.exe\" \"%v\""

peterk87

import os

# get a list of files containing a certain string/extension
l = [f for f in os.listdir('.')	if '.markers' in f]

lFNA = [f for f in os.listdir('.')	if '.fna' in f]

# print the matching files to stdout
# get commandline command for running MIST
print 'MIST.exe -j mist.json -T tmp -t ' + ' -t '.join(l) + ' ' + ' '.join(lFNA)

peterk87

 .nH, .Bk, .gstt, .gbqfif, .mG, .mD, font, div.im, .amn, .hP, .Ap, .Ar.Au, .editable, .ej, .Bu, .M9, .fN, div#loading, div.nr.tMHS5d, div.ip.adB, .ef, .eh, .dW.E, .cf {
	background-color: #161612!important;
	color: #D7D8D1!important;
}
.gD, .gK, .gH, .ii a , iw, amt{
	color: #97FFFF;
}
a {
  color: #D7D8D1!important;
}

peterk87

{
	"bold_folder_labels": true,
	"fade_fold_buttons": false,
	"font_size": 9,
	"highlight_line": true,
	"highlight_modified_tabs": true,
	"ignored_packages":
	[
		"Vintage"
	],

peterk87

/*Dark CSS theme for regex match of .*mightytext.net.* */
textarea, div, span, body, .nav-tabs, div#pinnedContent, .thread-tab {
	background-color: rgb(30,30,30) !important;
	color: rgb(170,170,170) !important;
}
span {
	background-color: transparent !important;
}
a#share-button-main, a#follow-button-main, span#alert-bottom-right-corner {
	visibility: hidden !important;

peterk87

/*IPython Notebook Dark CSS style*/
/*URLs matching the regexp: .*127.0.0.1:8\d\d\d.* */
body {
	background-color: #111 !important; 
	color: #ccc !important;
}


.dropdown-menu>li>a, li, ul {
  color: #ccc !important;

peterk87

Sublime Text 2 – Useful Shortcuts (PC)

Loosely ordered with the commands I use most towards the top. Sublime also offer full documentation.

Editing

Ctrl+C	copy current line (if no selection)
Ctrl+X	cut current line (if no selection)
Ctrl+⇧+K	delete line
Ctrl+↩	insert line after