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@karthikraman
karthikraman / parseBLAST_eval.py
Created Jun 8, 2015
Parse BLAST XML output, with an e-value cutoff
View parseBLAST_eval.py
#!/usr/bin/python
import sys
from optparse import OptionParser
usage="Usage: %prog -f <filename> -p <positives> -l <length>"
parser = OptionParser(usage)
parser.add_option("-f", "--file", dest="filename", help="write report to FILE")
parser.add_option("-p", "--positives", type="float", dest="pos", help="% positives")
parser.add_option("-l", "--length", type="float", dest="len", help="% length")
import re
View pdfjoin.sh
#!/bin/bash
if [[ $# -eq 0 ]]
then
echo "Usage: `basename $0` <output file> <input files>"
exit 1
fi
ofile=$1
if [[ -f $ofile ]]
then
@karthikraman
karthikraman / bubbleplot.m
Created Jun 8, 2015
BubblePlot for MATLAB
View bubbleplot.m
function h=bubbleplot(varargin)
%BUBBLEPLOT Bubble plot, using MATLAB's scatter
%
% x, y -- data
%
x=varargin{1}(:);
y=varargin{2}(:);
data=sortrows([x y]);
@karthikraman
karthikraman / pdfpextr.sh
Last active Aug 29, 2015
Bash: PDF page extractor
View pdfpextr.sh
#Courtesy: http://www.linuxjournal.com/content/tech-tip-extract-pages-pdf
#Add this to your .bashrc
function pdfpextr()
{
# this function uses 3 arguments:
# $1 is the first page of the range to extract
# $2 is the last page of the range to extract
# $3 is the input file
# output file will be named "inputfile_pXX-pYY.pdf"
View Beamer-block.sublime-snippet
<snippet>
<content><![CDATA[
\begin{block}{${1:title}}
\begin{itemize}
\item ${2:items}.
\end{itemize}
\end{block}
]]></content>
<!-- Optional: Set a tabTrigger to define how to trigger the snippet -->
<tabTrigger>block</tabTrigger>
View beamer-columns.sublime-snippet
<snippet>
<content><![CDATA[
\begin{columns}
\begin{column}{${1:2.5in}}
$3
\end{column}
\begin{column}{${2:2.5in}}
\end{column}
\end{columns}
@karthikraman
karthikraman / starred_item.tex
Created Oct 17, 2015
starred items in enumerate
View starred_item.tex
% From http://tex.stackexchange.com/questions/52715/modifying-labels-on-some-enumerated-items
\def\asteriskitem{*}
\makeatletter
\def\sitem{%
\expandafter\let\expandafter\originallabel\csname labelenum\romannumeral\@enumdepth\endcsname
\expandafter\def\csname labelenum\romannumeral\@enumdepth\expandafter\endcsname\expandafter{%
\expandafter\asteriskitem\originallabel}%
\item
\expandafter\let\csname labelenum\romannumeral\@enumdepth\endcsname\originallabel
}
View Beamer-fragile-frame.sublime-snippet
<snippet>
<content><![CDATA[\\begin{frame}[fragile]{${1:title}}
$2
\\end{frame}]]></content>
<tabTrigger>fframe</tabTrigger>
<scope>text.tex.latex</scope>
<description>Beamer frame</description>
</snippet>
@karthikraman
karthikraman / Beamer-python.sublime-snippet
Last active Oct 19, 2015
Snippet TeX python code block
View Beamer-python.sublime-snippet
<snippet>
<content><![CDATA[
\begin{python}
${1}
\end{python}
]]></content>
<!-- Optional: Set a tabTrigger to define how to trigger the snippet -->
<tabTrigger>py</tabTrigger>
<!-- Optional: Set a scope to limit where the snippet will trigger -->
<scope>text.tex.latex</scope>
View hypercube_graph.py
import networkx as nx
import matplotlib.pyplot as plt
from math import log
def hypercube_graph(n):
"""Create a hypercube graph of size n
(int) -> Graph
"""
H = nx.Graph()
for i in range(2**n):
for j in range(n):
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