Skip to content

Instantly share code, notes, and snippets.

Jeff Wintersinger jwintersinger

View GitHub Profile
jwintersinger / bt.txt
Created Nov 17, 2019
projectppm backtrace
View bt.txt
# Segfault when running with `example2.txt`
# Compiled with `gcc -g -O0 project_onto_PPM.c' on GCC 7.3.0
# Kernel version: Linux nia-login01.scinet.local 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
jawinter@nia-login01 ~/work/projectppm-problem $ ls
example1.npz example2.txt projectppm
jawinter@nia-login01 ~/work/projectppm-problem $ ~/tmp/Efficient-Projection-onto-the-Perfect-Phylogeny-Model/a.out exam
ple2.txt out.txt 1
Segmentation fault
# Backtrace
import re
import sys
import os
import argparse
import json
sys.path.append(os.path.join(os.path.dirname(__file__), '..', '..', 'lib'))
sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
import common
import inputparser
#!/usr/bin/env python
# Usage: python blosum62.txt
# Then, enter input in "row col" format -- e..g, "s f".
import sys
class InvalidPairException(Exception):
class Matrix:
def __init__(self, matrix_filename):
#!/usr/bin/env python2
import subprocess
def move_window(oldpos, newpos):
return subprocess.check_output(['tmux', 'move-window', '-s', str(oldpos), '-t', str(newpos)])
def main():
output = subprocess.check_output(['tmux', 'list-windows'])
lines = [l.strip() for l in output.split('\n') if l.strip() != '']
frags = [line.strip().split(': ', 1) for line in output.split('\n') if line.strip() != '']
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
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
Caller: main()
Then: grouper.add_cnvs(cn_regions)
Called by grouper.add_cnvs()
View Output.PRJEB506.munged.fa-PRJNA205202.munged.fa
This file has been truncated, but you can view the full file.
24775 sequences in file PRJEB506.munged.fa
24942 sequences in file PRJNA205202.munged.fa
26312 sequences in file PRJNA13758.munged.fa
15408 sequences PRJEB506.munged.fa have homologs in dataset PRJNA205202.munged.fa
11651 sequences PRJNA205202.munged.fa have homologs in dataset PRJEB506.munged.fa
71943 PRJEB506.munged.fa-PRJEB506.munged.fa matches
25919 PRJNA205202.munged.fa-PRJNA205202.munged.fa matches
7008 groups of orthologs
You can’t perform that action at this time.