1.1 --- a/utils/mass_realign_blocks.py	Tue Feb 15 21:03:19 2011 +0300
     1.2 +++ b/utils/mass_realign_blocks.py	Tue Feb 15 21:11:17 2011 +0300
     1.3 @@ -1,7 +1,12 @@
     1.4  #!/usr/bin/python
     1.5 -"""Realign given part of alignment.
     1.6 +"""Realign parts of multiple sequences.
     1.7  
     1.8 -All position indexes are counting from 1.
     1.9 +Realignment task is given as a file of the following format:
    1.10 +    * each line has filename, first column number and last column number, separated with tabs
    1.11 +    * empty lines and lines beginning with # are ignored
    1.12 +    * index of first column is 1
    1.13 +
    1.14 +All column ranges for each file are joined to be realined as a single alignment.
    1.15  """
    1.16  import optparse
    1.17  import sys
    1.18 @@ -13,9 +18,11 @@
    1.19      task = {}
    1.20      for line in file:
    1.21          line = line.rstrip("\n\r")
    1.22 +        if line.strip() == "" or line.strip()[0] == "#":
    1.23 +            continue
    1.24          filename, begin, end = line.split("\t")
    1.25          task[filename] = task.get(filename, [])
    1.26 -        task[filename].append((begin, end))
    1.27 +        task[filename].append((int(begin), int(end)))
    1.28      return task
    1.29  
    1.30  def main():