avalind

MSMutect notes

I've run in to the following issues while trying to get MSMutect to work:

1. the path to the data folder in shell_for_all.sh needs to be absolute.
2. make a symlink with link name phobos in bin, pointing to the correct phobos binary.
3. bowtie2 needs to have its indices specified by the -x flag, so this needs to be added to the awk-oneliner invoking bowtie2 for each repeat.
4. Even when adding the -x flag bowtie2 complains about some missing reference files (using the Normal.bam) test data.

avalind

import fileinput

def fastaparse():
        fasta = {}
        current_id = None
        buf=""
        for line in fileinput.input():
                if line[0] == ">":
                        if current_id is None:
                                current_id = line[1:].strip()

avalind

generate.dataset <- function() {
	return(data.frame( 
		ccsk=runif(20, 2.5, 5.0),
		wt=runif(20, 1.5, 4.5),
		ak=runif(20, 1.0, 1.25),
		fk=runif(20, 0.5, 1.0)))
}

build.plot <- function() {
	synthetic <- generate.dataset()

avalind

Keybase proof

I hereby claim:

• I am avalind on github.
• I am andersvalind (https://keybase.io/andersvalind) on keybase.
• I have a public key whose fingerprint is 8760 6360 B509 DE1F 478B 0697 FE35 8E40 593B 0093

To claim this, I am signing this object:

avalind

#!/usr/bin/env python
# For simplicity, not efficiency.

class Graph(object):
  def __init__(self):
    self.nodes = {}

  def add_node(self, n):
    if n not in self.nodes:
      self.nodes[n] = []