1.1 --- a/utils/mass_realign_blocks.py	Thu Feb 17 11:37:48 2011 +0300
     1.2 +++ b/utils/mass_realign_blocks.py	Thu Feb 17 18:35:59 2011 +0300
     1.3 @@ -36,13 +36,18 @@
     1.4          tasks.append((filename, int(begin), int(end)))
     1.5      return tasks
     1.6  
     1.7 +def sequences_excluded(sequences):
     1.8 +    exclude = map(str.strip, options.exclude.split(","))
     1.9 +    return [s for s in sequences if s.name not in exclude]
    1.10 +
    1.11  def main():
    1.12      tasks = read_task(open(options.task_file))
    1.13      for filename, begin, end in tasks:
    1.14          with open(filename) as in_file:
    1.15              alignment = protein.Alignment().append_file(in_file)
    1.16          columns = alignment.columns[begin-1:end]
    1.17 -        block = protein.Block.from_alignment(alignment, columns=columns)
    1.18 +        sequences = sequences_excluded(alignment.sequences)
    1.19 +        block = protein.Block.from_alignment(alignment, columns=columns, sequences=sequences)
    1.20          block.process(Muscle(), False, False)
    1.21          with open(filename, "w") as out_file:
    1.22              alignment.to_file(out_file)
    1.23 @@ -52,6 +57,8 @@
    1.24      parser = optparse.OptionParser(usage=usage)
    1.25      parser.add_option("-t", "--task-file",
    1.26          help="Task description file. Each line has filename, start position, end position, separated with tabs.")
    1.27 +    parser.add_option("-x", "--exclude",
    1.28 +        help="Comma-separated list of sequence names to exclude when realigning.")
    1.29      options, args = parser.parse_args()
    1.30  
    1.31      if args: