.functions

# .functions

# ==============================================================================
# Move fastq.gz files into directories based on sample number
# ==============================================================================

function folders() {
  for F in *.fastq.gz; do
    mkdir -p Sample_`expr match "$F" '.*_S\([0-9]\{1,2\}\)'`
    mv $F Sample_`expr match "$F" '.*_S\([0-9]\{1,2\}\)'`
  done
}

# ==============================================================================
# List directory contents after changing to it
# ==============================================================================

function cd() {
  builtin cd $1 && ls -la
}

# ==============================================================================
# Compress file with the appropriate command
# ==============================================================================

compress() {
  FILE=$1
  shift
  case $FILE in
    *.tar.bz2) tar cjf $FILE $*  ;;
    *.tar.gz)  tar czf $FILE $*  ;;
    *.tgz)     tar czf $FILE $*  ;;
    *.zip)     zip $FILE $*      ;;
    *.rar)     rar $FILE $*      ;;
    *)         echo "Filetype not recognized" ;;
  esac
}

# ==============================================================================
# Extract file with the appropriate command
# ==============================================================================

extract () {
  if [ -f $1 ] ; then
    case $1 in
      *.tar.bz2)   tar xjf $1     ;;
      *.tar.gz)    tar xzf $1     ;;
      *.bz2)       bunzip2 $1     ;;
      *.rar)       unrar e $1     ;;
      *.gz)        gunzip $1      ;;
      *.tar)       tar xf $1      ;;
      *.tbz2)      tar xjf $1     ;;
      *.tgz)       tar xzf $1     ;;
      *.zip)       unzip $1       ;;
      *.Z)         uncompress $1  ;;
      *.7z)        7z x $1        ;;
      *)     echo "'$1' cannot be extracted via extract()" ;;
    esac
    else
        echo "'$1' is not a valid file"
    fi
}