rcgrep

#!/bin/bash

if [[ ! -n $1 ]]; then
  cat <<EOH
Usable only as a pipe. This wraps around zegrep and adds the reverse complement
of the specified search pattern. Character classes [] and group/branching ( | )
will work. Backslash patterns will fail. Use '-' to stretch between patterns.
The augmented zegrep command is output on STDERR.
  - Usage:
    rcgrep PATTERN [grep options]

  - Multiline sequences are combined into a single line (numbered lines not supported)
  - The stretch wildcard character is '-' (it will be translated to .*).
  - The grep options -i and --color=always are provided already.
  - When piping to less use less -R .
EOH
  exit 0
fi

seq=$1
shift 1

qes=$(echo $seq | tr GCATUgcatu CGTAAcgtaa | rev | tr '][)(' '[]()' | perl -pe 's/\-/\.\*/g');
seq=$(echo $seq | perl -pe 's/\-/\.\*/g');

options=( "-i" "--color=always" "$@" )

echo "___ Command used: zegrep \"${options[@]}\" \"($seq|$qes)\" ___" >&2

perl -ne 'chomp;print;print"\n"unless/^[acgtnxu\- \~]+$/i;END{print"\n"}' | zegrep "${options[@]}" "($seq|$qes)"