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karthikraman /
Created Jun 8, 2015
Parse BLAST XML output, with an e-value cutoff
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
if [[ $# -eq 0 ]]
echo "Usage: `basename $0` <output file> <input files>"
exit 1
if [[ -f $ofile ]]
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
data=sortrows([x y]);
karthikraman /
Last active Aug 29, 2015
Bash: PDF page extractor
#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
\item ${2:items}.
<!-- Optional: Set a tabTrigger to define how to trigger the snippet -->
View beamer-columns.sublime-snippet
karthikraman / starred_item.tex
Created Oct 17, 2015
starred items in enumerate
View starred_item.tex
% From
\expandafter\let\expandafter\originallabel\csname labelenum\romannumeral\@enumdepth\endcsname
\expandafter\def\csname labelenum\romannumeral\@enumdepth\expandafter\endcsname\expandafter{%
\expandafter\let\csname labelenum\romannumeral\@enumdepth\endcsname\originallabel
View Beamer-fragile-frame.sublime-snippet
<description>Beamer frame</description>
karthikraman / Beamer-python.sublime-snippet
Last active Oct 19, 2015
Snippet TeX python code block
View Beamer-python.sublime-snippet
<!-- Optional: Set a tabTrigger to define how to trigger the snippet -->
<!-- Optional: Set a scope to limit where the snippet will trigger -->
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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