python script to convert plink bed/bim to qtdt format

import os

sdir = '/hapmap/'
basebedname = 'hapmap3'
ddir = '/erlotinib/'
temponame = 'tempo'
phenoname = 'erlotinib'

os.system('plink --bfile ' + sdir + basebedname + ' --recode12 --out ' + ddir + temponame )

## join tempo.ped with phenodata.txt 
## and generate pheno.ped file

shortfilename = ddir +  "phenodata.txt" ## FID,IID,dad,mom,sex,pheno1,...
longfilename = ddir +  temponame + ".ped" ## FID,IID,dad,mom,sex,pheno,snp1,...
outfilename = ddir + phenoname + ".ped"

index = {}
shortfile= open( shortfilename, "r" )
for row in shortfile:
    part = row.split(None,2)
    iid = part[1] ## IID is the second column in phenofile
    index[iid] = row.rstrip()
    ## rstrip gets rid of \n and other white spaces

shortfile.close()

outfile = open( outfilename, "w")
longfile= open( longfilename, "r" )

for row in longfile:
    part = row.split(None,6)
    iid = part[1]
    restofline = part[6]
    if iid in index:
        pheno = index[iid]
        outfile.write( pheno + ' ' + restofline)

longfile.close()
outfile.close()

## generate pheno.dat file

infilename = ddir + temponame + '.map'
outfilename = ddir + phenoname + '.dat'

infile = open(infilename,'r')
outfile = open(outfilename,'w')


## write covariates and phenotype names
outfile.write('C igrowth\n')
outfile.write('T logAUC\n')

## write one row per snp
for linea in infile:
 part = linea.split(None,2)
 newlinea = 'M ' + part[1] + '\n'
 outfile.write(newlinea)

infile.close()
outfile.close()

create new theme for ggplot

from: http://sape.inf.usi.ch/quick-reference/ggplot2/themes

theme_complete_bw <- function(base_size = 12) {
  structure(list(
    axis.line =         theme_blank(),
    axis.text.x =       theme_text(size = base_size * 0.8 , lineheight = 0.9, colour = "black", vjust = 1),
    axis.text.y =       theme_text(size = base_size * 0.8, lineheight = 0.9, colour = "black", hjust = 1),
    axis.ticks =        theme_segment(colour = "black"),
    axis.title.x =      theme_text(size = base_size, vjust = 0.5),
    axis.title.y =      theme_text(size = base_size, angle = 90, vjust = 0.5),
    axis.ticks.length = unit(0.15, "cm"),
    axis.ticks.margin = unit(0.1, "cm"),
 
    legend.background = theme_rect(colour=NA), 
    legend.key =        theme_rect(fill = NA, colour = "black", size = 0.25),
    legend.key.size =   unit(1.2, "lines"),
    legend.text =       theme_text(size = base_size * 0.8),
    legend.title =      theme_text(size = base_size * 0.8, face = "bold", hjust = 0),
    legend.position =   "right",
 
    panel.background =  theme_rect(fill = NA, colour = "black", size = 0.25), 
    panel.border =      theme_blank(),
    panel.grid.major =  theme_line(colour = "black", size = 0.05),
    panel.grid.minor =  theme_line(colour = "black", size = 0.05),
    panel.margin =      unit(0.25, "lines"),
 
    strip.background =  theme_rect(fill = NA, colour = NA), 
    strip.text.x =      theme_text(colour = "black", size = base_size * 0.8),
    strip.text.y =      theme_text(colour = "black", size = base_size * 0.8, angle = -90),
 
    plot.background =   theme_rect(colour = NA, fill = "white"),
    plot.title =        theme_text(size = base_size * 1.2),
    plot.margin =       unit(c(1, 1, 0.5, 0.5), "lines")
  ), class = "options")
}

# cdf: cd's to frontmost window of Finder (by Yarko)

copy the following in ~/.bash_profile

# cdf: cd's to frontmost window of Finder
cdf ()
{
    currFolderPath=$( /usr/bin/osascript <<"    EOT"
        tell application "Finder"
            try
                set currFolder to (folder of the front window as alias)
            on error
                set currFolder to (path to desktop folder as alias)
            end try
            POSIX path of currFolder
        end tell
    EOT
    )
    # ignore the cd if it's my desktop
    if [ "$currFolderPath" != "$HOME/Desktop/" ]
    then
        echo "cd to \"$currFolderPath\""
        cd "$currFolderPath"
    else
        echo "no finder path to cd to..."
    fi
}