1.1 --- a/allpy/protein.py	Mon Feb 07 22:00:55 2011 +0300
     1.2 +++ b/allpy/protein.py	Mon Feb 07 22:02:20 2011 +0300
     1.3 @@ -31,7 +31,7 @@
     1.4          self.save_fasta(tmp_file)
     1.5          tmp_file.close()
     1.6          os.system("muscle -in %(tmp)s -out %(tmp)s" % {'tmp': tmp_file.name})
     1.7 -        sequences, body = Alignment.from_file(open(tmp_file.name))
     1.8 +        sequences, body = Alignment().append_file(open(tmp_file.name))
     1.9          for sequence in self.sequences:
    1.10              try:
    1.11                  new_sequence = [i for i in sequences if sequence==i][0]

     2.1 --- a/test/usecase3.py	Mon Feb 07 22:00:55 2011 +0300
     2.2 +++ b/test/usecase3.py	Mon Feb 07 22:02:20 2011 +0300
     2.3 @@ -1,5 +1,5 @@
     2.4  from allpy import protein
     2.5 -alignment = protein.Alignment.from_file(open("aln.fasta"))
     2.6 +alignment = protein.Alignment().append_file(open("aln.fasta"))
     2.7  #conservative = [(10,20), (40,50)]
     2.8  conservative = [(0,6),(18,37)]
     2.9  
    2.10 @@ -30,7 +30,7 @@
    2.11      markup = ranges_to_markup(conservative)
    2.12      blocks = markup_to_blocks(markup)
    2.13      for block in blocks["-"]:
    2.14 -        block.flush_left()
    2.15 -    alignment.to_fasta(open("output.fasta", "w"))
    2.16 +        block.flush("left")
    2.17 +    alignment.to_file(open("output.fasta", "w"))
    2.18  
    2.19  main()

     3.1 --- a/utils/flush_left.py	Mon Feb 07 22:00:55 2011 +0300
     3.2 +++ b/utils/flush_left.py	Mon Feb 07 22:02:20 2011 +0300
     3.3 @@ -9,15 +9,15 @@
     3.4  from allpy import protein
     3.5  
     3.6  def main():
     3.7 -    alignment = protein.Alignment.from_file(open(options.in_file))
     3.8 +    alignment = protein.Alignment().append_file(open(options.in_file))
     3.9      if not options.begin:
    3.10          options.begin = 1
    3.11      if not options.end:
    3.12          options.end = len(alignment.columns)
    3.13      columns = alignment.columns[options.begin-1:options.end]
    3.14      block = protein.Block.from_alignment(alignment, columns=columns)
    3.15 -    block.flush_left()
    3.16 -    alignment.to_fasta(open(options.out_file, "w"))
    3.17 +    block.flush("left")
    3.18 +    alignment.to_file(open(options.out_file, "w"))
    3.19      if options.msf:
    3.20          os.system("seqret " + options.out_file + " msf::" + options.out_file.split(".")[0] + ".msf")
    3.21          os.system("rm " + options.out_file)

     4.1 --- a/utils/flush_left_vblock.py	Mon Feb 07 22:00:55 2011 +0300
     4.2 +++ b/utils/flush_left_vblock.py	Mon Feb 07 22:02:20 2011 +0300
     4.3 @@ -9,15 +9,15 @@
     4.4  from allpy import protein
     4.5  
     4.6  def main():
     4.7 -    alignment = protein.Alignment.from_file(open(options.in_file))
     4.8 +    alignment = protein.Alignment().append_file(open(options.in_file))
     4.9      if not options.begin:
    4.10          options.begin = 1
    4.11      if not options.end:
    4.12          options.end = len(alignment.columns)
    4.13      columns = alignment.columns[options.begin-1:options.end]
    4.14      block = protein.Block.from_alignment(alignment, columns=columns)
    4.15 -    block.flush_left()
    4.16 -    alignment.to_fasta(open(options.out_file, "w"))
    4.17 +    block.flush("left")
    4.18 +    alignment.to_file(open(options.out_file, "w"))
    4.19      if options.msf:
    4.20          os.system("seqret " + options.out_file + " msf::" + options.out_file.split(".")[0] + ".msf")
    4.21          os.system("rm " + options.out_file)

     5.1 --- a/utils/flush_left_vblocks.py	Mon Feb 07 22:00:55 2011 +0300
     5.2 +++ b/utils/flush_left_vblocks.py	Mon Feb 07 22:02:20 2011 +0300
     5.3 @@ -18,13 +18,13 @@
     5.4  from allpy import protein
     5.5  
     5.6  def main(ranges):
     5.7 -    alignment = protein.Alignment.from_file(open(options.in_file))
     5.8 +    alignment = protein.Alignment().append_file(open(options.in_file))
     5.9      for begin, end in ranges:
    5.10          columns = alignment.columns[begin-1:end]
    5.11          block = protein.Block.from_alignment(alignment, columns=columns)
    5.12 -        block.flush_left()
    5.13 +        block.flush("left")
    5.14  
    5.15 -    alignment.to_fasta(open(options.out_file, "w"))
    5.16 +    alignment.to_file(open(options.out_file, "w"))
    5.17      if options.msf:
    5.18          os.system("seqret " + options.out_file + " msf::" + options.out_file.split(".")[0] + ".msf")
    5.19          os.system("rm " + options.out_file)