CnrLwlss

import PIL, os, math
from PIL import Image

resizeWidth=500

allfiles=os.listdir(os.getcwd())
filelist=[f for f in allfiles if f[-4:] in ['.jpg','.JPG','.jpeg','.JPEG','.png','.PNG']]
Nimages=len(filelist)
im0=Image.open(filelist[0])
w,h=im0.size

CnrLwlss

#!/bin/bash
echo Making indices...

# Set up path to include bowtie2 and samtools
export PATH=$PATH:/home/username/bowtie2-2.1.0:/home/username/samtools:/home/username/samtools/bcftools:/home/username/samtools/misc

# Generate an index file from the reference genome
bowtie2-build reference_SGD/S288C_reference_genome_R64-1-1_20110203/S288C_reference_sequence_R64-1-1_20110203.fsa indices/SGD_S288C

roots=(

CnrLwlss

@echo off
:: Make indices
bowtie2-build reference_SGD/S288C_reference_genome_R64-1-1_20110203/S288C_reference_sequence_R64-1-1_20110203.fsa indices/SGD_S288C

for /f "tokens=*" %%x in (roots.txt) do (
  echo %%x
	:: Align reads
	bowtie2-align -x indices/SGD_S288C -1 data/%%x_1_sequence.fq -2 data/%%x_2_sequence.fq -S alignments/%%x.sam -p 12 --end-to-end
)

CnrLwlss

library(ShortRead)

# Root of .bam filename
sname="HG00100.unmapped.ILLUMINA.bwa.GBR.low_coverage.20130415"

# Construct path to file
fname=file.path("alignments",paste(sname,".bam",sep=""))

# Read alignments
bm=readGappedAlignments(fname)

CnrLwlss

#!/bin/bash

echo Generating consensus sequences

export PATH=$PATH:/home/username/bowtie2-2.1.0:/home/username/samtools:/home/username/samtools/bcftools:/home/username/samtools/misc

roots=(
SN7640178_10172_8183
SN7640178_10173_8265
SN7640178_10174_8266

CnrLwlss

#source("http://bioconductor.org/biocLite.R")
#biocLite("ecolitk")
#biocLite("ShortRead")
library(ecolitk)
library(plotrix)
library(ShortRead)

# Read in some alignments
getReads=function(fname,rad=1.5,readmax=29000,logb=10){
	bm=readGappedAlignments(fname)

CnrLwlss

# http://cnr.lwlss.net/seqConsensus

import os
from Bio import SeqIO

def checkMutations(ref_dict, roots, genedict,showSeq=False):
    '''Comparing a reference sequence (ref_dict) with a series of sample sequences.'''
    # Sample sequences are read in from .fastq files in a "pileups" directory.
    # Filenames are constructed from a list of roots (e.g. filenames without extensions).
    # A Python dictionary specifying genes to analyze connects gene labels (e.g. "HIS3") with a tuple of chromosome number, start position and stop position (e.g. (15,721946,722608)).

CnrLwlss

# Install and load ODE solver package
install.packages("deSolve")
library(deSolve)

# Named vector of parameter values
parameters=c(k1=0.15,k2=0.075,V=1.0)

# Named vector of initial conditions
state=c(A=4,B=2,AB=0)

CnrLwlss

<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
  <model id="ProteinExample">
    <listOfCompartments>
      <compartment id="cell" size="1"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="A" compartment="cell" initialAmount="4"/>
      <species id="B" compartment="cell" initialAmount="2"/>
      <species id="AB" compartment="cell" initialAmount="0"/>

CnrLwlss

@model:2.3.1=ProteinExample
@compartments
 cell=1
@species
 cell:A=4 
 cell:B=2
 cell:AB=0
 cell:NULL=0
@parameters
 k1=0.15