trim.rb

# :)

if __FILE__ == $0
  # Arguments
  input_fastq = ARGV[0]
  trimming_sequence = ARGV[1]
  head_or_tail = ARGV[2] || "HEAD"
  
  # Load data
  data = open(input_fastq).readlines
  
  # Modify input data
  out = data.each_slice(4).map do |read|
    # Parse fastq read lines
    read_id     = read[0].chomp
    sequence    = read[1].chomp
    comment     = read[2].chomp
    phred_score = read[3].chomp
    
    # Find pattern
    remove_positions = sequence.enum_for(:scan, /#{trimming_sequence}/).map{ Regexp.last_match.begin(0) }
    
    # Remove if pattern is found in sequence
    if !remove_positions.empty?
      case head_or_tail
      when "HEAD"
        cut_position = remove_positions.first + trimming_sequence.size
        [
          sequence.slice(cut_position, sequence.size),
          read_id,
          phred_score.slice(cut_position, sequence.size),
          comment
        ]
      when "TAIL"
        cut_position = remove_positions.last + trimming_sequence.size
        [
          sequence.slice(0, cut_position),
          read_id,
          phred_score.slice(0, cut_position),
          comment
        ]
      else
        puts "ERROR: Specify HEAD or TAIL"
        exit
      end
    else
      # if pattern is not found, output original read and quality
      [
        sequence,
        read_id,
        phred_score,
        comment
      ]
    end
  end
  
  # output trimmed fastq data
  puts out.flatten.join("\n")
end

How to execute:

Remove head of sequence until matching "ATCC"
$ ruby trim.rb data.fastq "ATCC" "HEAD"

Remove tail of sequence after matching "ATCC"
$ ruby trim.rb data.fastq "ATCC" "TAIL"