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benjeffery / gist:3834641
Created October 4, 2012 16:08
Iterate over a fasta with a single sequence in
@contextlib.contextmanager
def fasta_sequence(file):
with open(file, 'r') as f:
f.next() #loose the header row
def generator():
for line in f:
for char in line.strip():
yield char
yield generator()
@benjeffery
benjeffery / gist:3834877
Created October 4, 2012 16:48
Hetrozygosity
from collections import Counter
def hetrozygosity(reads):
base_count = Counter(reads)
return 1.0-(float(base_count.most_common(1)[0][1])/sum(base_count.values()))
We couldn’t find that file to show.
@benjeffery
benjeffery / mat2png.py
Last active August 29, 2015 14:15
mat2png
#USAGE: python mat2png FILENAME.mat MATRIXNAME
import h5py
import sys
import png
import numpy as np
mat = h5py.File(sys.argv[1], 'r')
print mat['OutputStructure'].keys()
print mat['OutputStructure']['PreProcess'].keys()
<Draggable handle='.header'
start={initPosition.toObject()}
moveOnStartChange={true}
onStop={this.handleMoveStop}>
<Resizable width={initSize.get('width')} height={initSize.get('height')}
minConstraints={[150, 150]}
maxConstraints={[500, 300]}
onResize={this.handleResize}
onResizeStop={this.handleResizeStop}>
<div className="popup"
sql>explain select * from "variants" order by "QD" limit 1000;
+------------------------------------------------------------------------------------------------------+
| mal |
+======================================================================================================+
| function user.s3_1{autoCommit=true}():void; |
| X_1124:void := querylog.define("explain select * from \"variants\" order by \"QD\" limit 1000;", |
: "default_pipe",6416); :
| barrier X_10651 := language.dataflow(); |
| X_455 := bat.new(nil:oid,nil:str); |
| X_463 := bat.append(X_455,"Ag1000G.variants"); |
import requests
def dl(path, filename):
try:
r = requests.get(path, stream=True)
if r.status_code == 200:
with open(filename, 'wb') as f:
for chunk in r:
f.write(chunk)
print "done", path

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function chooseMode(jsProps, cssProps) {
if (cssProps.length == 0 && jsProps.length == 0) // IE <10, other early browser, no method works there. In Opera CSS works though
return bowser.opera ? 'css' : 'warning';
if (cssProps.length == 0 && jsProps.length > 0) // IE >10 even EDGE... sigh
return 'js';
if (cssProps.length == 1 && cssProps[0] == 'optimiseSpeed' && jsProps.length == 0) //A few earlier browsers report this prop, but it only works for images
return 'warning';
if (_.includes(cssProps, '-webkit-optimize-contrast') || _.includes(cssProps, '-moz-crisp-edges') || _.includes(cssProps, 'crisp-edges') || _.includes(cssProps, 'pixelated')) {
if (!bowser.check({chrome: "41"})) //Earlier chromes only support css on IMG
return 'js';
accountsservice/xenial-updates,now 0.6.40-2ubuntu11.3 amd64 [installed]
acl/xenial,now 2.2.52-3 amd64 [installed]
acpi-support/xenial,now 0.142 amd64 [installed]
acpid/xenial,now 1:2.0.26-1ubuntu2 amd64 [installed]
add-apt-key/xenial,xenial,now 1.0-0.5 all [installed]
adduser/xenial,xenial,now 3.113+nmu3ubuntu4 all [installed]
adobe-flashplugin/now 1:20170214.1-0ubuntu0.16.04.1 amd64 [installed,upgradable to: 1:20170616.1-0ubuntu0.16.04.1]
adwaita-icon-theme/sarah,sarah,now 3.18.0-2ubuntu3mint2 all [installed]
adwaita-icon-theme-full/sarah,sarah,now 3.18.0-2ubuntu3mint2 all [installed]
alsa-base/xenial,xenial,now 1.0.25+dfsg-0ubuntu5 all [installed]