View compare.py
from __future__ import print_function
import sys
from collections import defaultdict
def parse(fn):
loci = set()
with open(fn) as F:
for L in F:
L = L.strip()
View lol
http://prune.da-shiz.net/uploads/jeff/sbf-battlefield-vietnam-world-tournament-recordings/20IDvs.sbf_-_Jun.10.mp3
http://prune.da-shiz.net/uploads/jeff/sbf-battlefield-vietnam-world-tournament-recordings/Pinc.vs.pfg_-_Apr.27.mp3
View gist:9881bb6c789686eeaa1c26f92c7a0456
Do proportion of SVs plots
See what BAF and logR are of my BP clusters that don't have SVs -- are they subclonal? Do they have smaller deviations?
We should report these nulls back to PCAWG-6 -- now?
Can we use our results to help PCAWG-6 -- ask them to look for non-consensus SVs that one or two methods called around our wll-supported BPs
Send list of BPs to PCAWG6, along with CN states upstream and downstream
Send this list to group, which can check BAF and logR
Include TRAs, but throw out small SVs
Geoff: Anything < 500 kb is often missed by CN methods for duplications or deletions
View gist:900e41d72423f1b162cdb3d337924f2c
function fetch_packages(db, on_done) {
// Your code goes here. You must return an array of objects that looks like
// this (which you can infer from looking at what fields we reference in
// index.html):
//
// [ { sent_on: '2016-06-27 14:31:03',
// due_on: '2016-06-28 08:00:00',
// received_on: null,
// shipper_name: 'Nils Olav',
// receiver_name: 'William Windsor',
View gist:bf808bc887f6b54b5d6d13b58d8a3ca3
CnvParser
Caller: main()
Then: grouper.add_cnvs(cn_regions)
CnvFormatter
MultisampleCnvCombiner
Called by grouper.add_cnvs()
Segmenter
View README
These are the proportions of variants possessing features used in each question for the various questions comprising ECE1508 assignment 1.
View output.txt
Initial:
[[0 1 1 0 1]
[0 0 1 0 1]
[0 0 0 0 0]
[0 1 1 0 1]
[0 0 0 0 0]]
Top:
[[0 1 1 0 1]
[0 0 1 0 1]
View gist:e636b2fd3bfafb947d5b
Olympic Weightlifting Level I (eight one-hour classes)
This 8 week class is designed for true beginners with little to no previous weight training experience. Participants will learn the basics of weightlifting starting with the Olympic squat and deadlift and moving to the power snatch and power clean in a progressive manner. By the end of the session, participants will gain hip and shoulder flexibility along with leg and core strength.
Fundamentals of Weight Training (six one-hour classes)
Learn to train effectively and safely following appropriate exercise progressions under the supervision of a certified trainer. Participants will be introduced to a series of fundamental exercises commonly used in training programs such as squats, lunges and rows. Participants will learn how to create a personalized program using a variety of training methods and be familiarized with most of the equipment in the weight room.
View find-best-hit.py
#!/usr/bin/env python3
'''
For each query listed in a BLAST XML results file, determine how much of the
query sequence is covered by the "best" hit. The best hit is deemed to be the
one in which the summed bitscores of its compatible HSPs is highest. Mutually
compatible HSPs are deemed to be ones that neither overlap nor "cross" each
other.
Usage:
cat blast_results.xml | find-best-hit.py