terdon's bashrc

# .bashrc
pathmunge () {
        if ! echo $PATH | /bin/egrep -q "(^|:)$1($|:)" ; then
           if [ "$2" = "after" ] ; then
              PATH=$PATH:$1
           else
              PATH=$1:$PATH
           fi
        fi
}
setWindowTitle() {
    echo -ne "\e]2;$*\a"
}
updateWindowTitle() {
    setWindowTitle "$USER@${HOSTNAME%%.*}:${PWD/$HOME/~}"
}
#better autocomplete
if [ -f /etc/bash_completion ] && ! shopt -oq posix; then
   . /etc/bash_completion
fi

## beep
xset b off

#Make Bash append rather than overwrite the history on disk:
shopt -s histappend
#Whenever displaying the prompt, write the previous line to disk:
#PROMPT_COMMAND='history -a'

#A new shell gets the history lines from all previous shells
PROMPT_COMMAND='history -a; updateWindowTitle'

PS1='${debian_chroot:+($debian_chroot)}\[\033[01;33m\]\u@\h\[\033[01;34m\] \W \\$\[\033[00m\] '

eval `dircolors -b $HOME/.mycolors`

export TERM=xterm;
PERL5LIB=${PERL5LIB}:${HOME}/Setups/ensembl_API/src/bioperl-live
PERL5LIB=${PERL5LIB}:${HOME}/Setups/ensembl_API/src/ensembl/modules
PERL5LIB=${PERL5LIB}:${HOME}/Setups/ensembl_API/src/ensembl-compara/modules
PERL5LIB=${PERL5LIB}:${HOME}/Setups/ensembl_API/src/ensembl-variation/modules
PERL5LIB=${PERL5LIB}:${HOME}/Setups/ensembl_API/src/ensembl-functgenomics/modules
export PERL5LIB="$HOME/Setups/PfamScan/:$HOME/.cpan/build/:$HOME/scripts:$PERL5LIB"
export HISTCONTROL=ignoredups
export HISTSIZE=9999
export HISTFILESIZE=999999
export HISTFILE="$HOME/.bash_history"
export EDITOR='/usr/bin/emacs';
pathmunge /home/terdon/bin
pathmunge /home/terdon/scripts
pathmunge /home/terdon/research/data/python
pathmunge /home/terdon/Setups/PfamScan
pathmunge /usr/sbin
pathmunge /usr/local/sbin
pathmunge /sbin

alias eog='eom'
alias gping='ping www.google.com'
alias nocolor='sed -r "s/\x1B\[([0-9]{1,3}((;[0-9]{1,3})*)?)?[m|K]//g"'
alias ls='ls --color=tty'
alias kls='ls'
alias sls='ls'
alias dir='dir --color=yes'
alias l='ls -lh'
alias la='ls -a'
alias cl='clear; ls'
alias ..='cd ..'
alias ...='cd ../../'
alias mroe='more'
alias m='more'
alias ll='less -R'
alias c='clear'
alias rmr='rm -r'
alias wtf='apropos'
alias sl="ls"
alias geneid2fasta='perl -ne "print unless /^#/ || /gene/ || /^\s+$/ || /\d/; print if /^>/;"'
alias sru='sort -u'
alias src='sort -u | wc -l'
alias grprint='html2text $1'
alias aterm='aterm -sl 10000'
alias grep='grep --color'
alias gerp='grep'
alias clean_latex='rm .mtc .aux *.log *.bbl *.blg *.glo *.idx *.ilg *.ind *.maf *.out *.toc */.mtc* /.aux /.log /.bbl /.blg /.glo /.idx /.ilg /.ind /.maf /.out *.toc'
function multi7z () {
    for n in $@; do 7zr x $n; done
}

function pdfconcat () { gs -q -sPAPERSIZE=a4 -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sOutputFile=/dev/stdout "$@" ;}
function bigdiff() {
    for ((i=1; i<=$len; i++)); do
    #echo "i:$i $len";
    a=`gawk -v num=$i 'NR==num{print; exit}' $1`;
    b=`gawk -v num=$i 'NR==num{print; exit}' $2`;
    if [ "$a" != "$b" ];
    then
        echo -e "> $a\n< $b";
    fi;
    done

}
function netnames() {
    if [ $1 ]; then
    gawk '{print $1"\n"$2}' $1 | sort -u
    else
    echo -e "NETNAMES: Prints the unique names in a.gr file.\n\nUSAGE: netnames NET.gr"
    fi
}