_bash_aliases

# Some user added aliases in order of addition.
# If something breaks consider removing the most recent additions.

# SSH
hpcc="smithby1@hpcc.msu.edu"
alias hpcc-ssh="ssh $hpcc"
alias hpcc-sshx="ssh -X $hpcc"
lyorn="smithby1@lyorn.idyll.org"
alias lyorn-ssh="ssh $lyorn"
alias lyorn-sshx="ssh -X $lyorn"
z61t="bjsmith@smithby1-4.user.msu.edu"
alias z61t-ssh="ssh $z61t"
alias z61t-sshx="ssh -X $z61t"
webhost="byronjsm@byronjsmith.com"
alias webhost-ssh="ssh $webhost"
flux="bjsm@flux-login.engin.umich.edu"
alias flux-ssh="ssh $flux"
alias flux-sshx="ssh -X $flux"


# What else?
# Safe copy, mv, and rm
alias cp="cp -i"
alias mv="mv -i"
alias rm="rm -i"
alias rmv="rm -fr"
alias psu="ps -u $USER"
alias ..="cd .."
alias ll="ls -alFh"
alias nmsq="grep -c '^>'"
alias now="date +%r%n%a%t%D"
alias calc="bc -l <<<"
alias view="vim -R"
alias topu="top -u $USER"

function commsrunning {
    ps -u $USER -o comm=
}

function name2proc {
    echo `ps -u $USER | grep $1 | awk '{print($1)}'`
}
complete -W "`commsrunning`" name2proc

function namekill {
    kill `name2proc $1`
}
complete -W "`commsrunning`" namekill

alias cl="column -s '	' -t"

function tab {
    cl $1 | less -S
}

function fastq2fasta {
    cat $1 | perl -e '$i=0;while(<>){if(/^\@/&&$i==0){s/^\@/\>/;print;
    }elsif($i==1){print;$i=-3}$i++;}'
}

function to_csv {
    awk '{for (i=1; i<=(NF - 1); i++) printf $i ","; printf $NF "\n"}' <&0
}

function to_tsv {
    awk '{for (i=1; i<=(NF - 1); i++) printf $i "\t"; printf $NF "\n"}' <&0
}