benjeffery

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");                                                   |

benjeffery

<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"

benjeffery

#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()

benjeffery

We couldn’t find that file to show.

benjeffery

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()))

benjeffery

@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()