seandavi

plot(abs(baf(eset)[tmp,223]-baf(eset)[tmp,1]),pch='.')
plot(abs(baf(eset)[tmp,223]-baf(eset)[tmp,1]),pch='.',xlim=c(0,50000))
lines(x$Segmented,col='red')
plot(abs(baf(eset)[tmp,223]-baf(eset)[tmp,1]),pch='.',xlim=c(25000,50000))
lines(x$Segmented,col='red')
plot(abs(baf(eset)[tmp,223]-baf(eset)[tmp,1]),pch='.',xlim=c(27000,38000))
lines(x$Segmented,col='red')
x = haarSeg(abs(baf(eset)[tmp,223]-baf(eset)[tmp,1]),breaksFdrQ=0.000001,haarStartLevel=3,haarEndLevel=6)
lines(x$Segmented,col='green')
x = haarSeg(abs(baf(eset)[tmp,223]-baf(eset)[tmp,1]),breaksFdrQ=0.000001,haarStartLevel=4,haarEndLevel=6)

seandavi

#!/usr/bin/env python
from operator import itemgetter

class Transcript:
    def __init__(self,chromosome,name,exons,cds,strand):
        self.chromosome=chromosome
        self.name=name
        self.strand=strand
        self.exons=exons
        self.cds=cds

seandavi

phat <-
  function(x,n,error=0.01,hetprob=0.001) {
    #doesn't work as expected yet
    prv=hetprob
    pvv=(1-hetprob)/2
    phet = pbinom(x,n,0.5)*prv
    phomref=pbinom(x,n,error)*(1-prv-pvv)
    phomvar=pbinom(x,n,1-error)*pvv
    return(c(phomvar=phomvar,phet=phet,phomref=phomref))}

seandavi

 cat ${i} |  awk '/[RKYW]/ { if ( ( $8 > 9 ) && ( $5 > 30 ) ) print $1, $2 }' > ${i}.goodhetsites

seandavi

makeCuffDiffMatrix <- function(directory='.') {
  m = read.delim(file.path(directory,'genes.fpkm_tracking'),header=TRUE)
  d = read.delim(file.path(directory,'gene_exp.diff'),header=TRUE)
  x = seq(1,nrow(d),nrow(m))
  dt1 = m
  for(i in 1:length(x)) {
    dt = d[x[i]:(x[i]+nrow(m)-1),]
    dt$fdr=p.adjust(dt$p_value,method='fdr')
    colnames(dt)=paste(dt[1,4],dt[1,5],colnames(dt),sep="_")
    dt1 = cbind(dt1,dt[,-c(1:5,7,8)])

seandavi

<tool id="symd_tool" name="Perform SymD calculation on a PDB file">
  <description>Use this tool to run symd on a PDB file</description>
  <command interpreter="python">symd_wrapper.py $input $trfm_file $info_file ${input.name} </command>
  <inputs>
    <param format="txt" name="input" type="data" label="PDB file"/>
  </inputs>
  <outputs>
    <data format="txt" name="trfm_file" />
    <data format="txt" name="info_file" />
  </outputs>

seandavi

#!/usr/bin/env python
import csv
import itertools
import argparse

# File "refGene.txt" downloaded from UCSC and gunzipped
# must be in this directory
# Works only on "+" strand genes
# Minus strand genes left as an exercise

seandavi

#!/bin/bash
#
# Author: Sean Davis <seandavi@gmail.com>
#
# Uses named pipes (FIFO) to reduce storage needs
# to call varscan somatic
# Some details may need to be edited to meet particular needs
# call with the following parameters
# 1) The FASTA file containing the reference genome
# 2) The Normal bam file

seandavi

import sys
import os
import subprocess
import argparse
import tempfile
import csv

#liftoverChain = sys.argv[2]
#fname = sys.argv[1]

seandavi

#!/usr/bin/env python
import pysam
import argparse
import collections

parser = argparse.ArgumentParser()
parser.add_argument('bamfile',
                    help="bamfile for analysis")
parser.add_argument('-r','--region',
                    help="Limit to region chrN:XXX-YYY")