Given output of tdc-diff.py (https://gist.github.com/standage/10765999), extract sequences warranting further exploration.

tdc-extract.py

#!/usr/bin/env python
import getopt, os, re, sys

class Seq:
  def __init__(self, defline, seq):
    self.defline = defline
    self.seq = seq
    match = re.match("^>(\S+)", defline)
    self.id = match.group(1)

def parse_fasta(fp):
  """
  Stolen shamelessly from http://stackoverflow.com/a/7655072/459780.
  """
  name, seq = None, []
  for line in fp:
    line = line.rstrip()
    if line.startswith(">"):
      if name: yield (name, ''.join(seq))
      name, seq = line, []
    else:
      seq.append(line)
  if name: yield (name, ''.join(seq))

def print_usage(outstream):
  usage = ("\nUsage: tdc-extract [options] s1.cds.fa s2.cds.fa < tdc-diff.txt\n"
           "  Options:\n"
           "    -h|--help:             print this help message and exit\n"
           "    -o|--out: FILE         file to which output will be printed;\n"
           "                           default is terminal (stdout)\n"
           "    -x|--label1: STRING    label for sample 1 in the output;\n"
           "                           default is 's1'\n"
           "    -y|--label2: STRING    label for sample 2 in the output;\n"
           "                           default is 's2'\n")
  print >> outstream, usage

def parse_options(argv):
  params = {
    'l1': 's1',
    'l2': 's2',
    'outstream': sys.stdout,
  }
  optstr = "ho:x:y:"
  longopts = ["help", "out", "label1", "label2"]
  (options, args) = getopt.getopt(argv[1:], optstr, longopts)
  for key, value in options:
    if key in ('-h', '--help'):
      print_usage(sys.stdout)
      sys.exit(0)
    elif key in ('-o', '--out'):
      params['outstream'] = open(value, 'w')
    elif key in ('-x', '--label1'):
      params['l1'] = value
    elif key in ('-y', '--label2'):
      params['l2'] = value
    else:
      print_usage(sys.stderr)
      assert False, "unsupported option '%s'" % key

  if len(args) != 2:
    print_usage(sys.stderr)
    assert False, "expected 2 arguments, %d provided" % len(args)
  params['fa1']  = os.path.abspath(args[0])
  params['fa2']  = os.path.abspath(args[1])

  return params

if __name__ =='__main__':
  params = parse_options(sys.argv)

  s1seqs = {}
  s2seqs = {}

  for line in sys.stdin:
    line = line.rstrip()
    matches = re.search("^\S+\tcds\.(TCONS_\d+)\|\S+\tcds\.(TCONS_\d+)\|\S+", line)
    if matches:
      s1seqs[matches.group(1)] = 1
      s2seqs[matches.group(2)] = 1

  with open(params['fa1'], 'r') as fp:
    for defline, seq in parse_fasta(fp):
      record = Seq(defline, seq)
      if record.id in s1seqs:
        record.id = params['l1'] +"."+ record.id
        print >> params['outstream'], ">%s\n%s" % (record.id, record.seq)

  with open(params['fa2'], 'r') as fp:
    for defline, seq in parse_fasta(fp):
      record = Seq(defline, seq)
      if record.id in s2seqs:
        record.id = params['l2'] +"."+ record.id
        print >> params['outstream'], ">%s\n%s" % (record.id, record.seq)