1.1 --- a/allpy/fileio.py	Thu Jul 21 18:34:27 2011 +0400
     1.2 +++ b/allpy/fileio.py	Mon Jul 25 14:40:41 2011 +0400
     1.3 @@ -3,6 +3,13 @@
     1.4  from tempfile import NamedTemporaryFile
     1.5  import util
     1.6  
     1.7 +bio_python = False
     1.8 +try:
     1.9 +    from Bio import Seq, SeqRecord, Align, SeqIO, AlignIO, Alphabet
    1.10 +    bio_python = True
    1.11 +except ImportError:
    1.12 +    pass
    1.13 +
    1.14  def get_markups_class(classname):
    1.15      """This ugly helper is to avoid bad untimely import loops."""
    1.16      import markups
    1.17 @@ -18,6 +25,8 @@
    1.18          elif format.startswith('markup:'):
    1.19              subformat = format.split(':',1)[1]
    1.20              return MarkupFile(file, format=subformat, **kw)
    1.21 +        elif bio_python and BioPythonFile.supports(format):
    1.22 +            return BioPythonFile(file, format, **kw)
    1.23          else:
    1.24              return EmbossFile(file, format, **kw)
    1.25  
    1.26 @@ -237,6 +246,34 @@
    1.27          if for_what == 'write':
    1.28              return string.strip().replace('_', '-').capitalize()
    1.29  
    1.30 +class BioPythonFile(AlignmentFile):
    1.31 +    """Parser & writer for file formats supporte by Bio python."""
    1.32 +
    1.33 +    @staticmethod
    1.34 +    def supports(format):
    1.35 +        """Tell what formats this method supports."""
    1.36 +        return (
    1.37 +            format in AlignIO._FormatToWriter
    1.38 +            or format in SeqIO._FormatToWriter
    1.39 +        )
    1.40 +
    1.41 +    def write_strings(self, sequences):
    1.42 +        """Write sequences to file."""
    1.43 +        aln = Align.MultipleSeqAlignment([
    1.44 +            SeqRecord.SeqRecord(
    1.45 +                Seq.Seq(body, Alphabet.single_letter_alphabet),
    1.46 +                id=name,
    1.47 +                description=description
    1.48 +            )
    1.49 +            for body, name, description in sequences
    1.50 +        ])
    1.51 +        AlignIO.write(aln, self.file, self.format)
    1.52 +
    1.53 +    def read_strings(self):
    1.54 +        """Read sequences from file."""
    1.55 +        for seq in AlignIO.read(self.file, self.format):
    1.56 +            yield seq.id, seq.description, str(seq.seq)
    1.57 +
    1.58  class EmbossFile(AlignmentFile):
    1.59      """Parser & writer for file formats supported by EMBOSS."""
    1.60  

     2.1 --- a/test/test_base.py	Thu Jul 21 18:34:27 2011 +0400
     2.2 +++ b/test/test_base.py	Mon Jul 25 14:40:41 2011 +0400
     2.3 @@ -122,4 +122,42 @@
     2.4      assert b.rows_as_strings() == ["A-C-D", "TGCGA"]
     2.5      assert b.sequences[0].source == o.name
     2.6  
     2.7 +def test_bio_io():
     2.8 +    """Test Bio python IO.
     2.9 +
    2.10 +    BioPython does not support msf, so it is not covered in many other tests.
    2.11 +    """
    2.12 +    file = (
    2.13 +        "# STOCKHOLM 1.0\n"
    2.14 +        "#=GS seqA  AC seqA123\n"
    2.15 +        "#=GS seqA  DR PDB; 1abc ; 1-42;\n"
    2.16 +        "#=GS seqB  AC seqB345\n"
    2.17 +        "SeqA             SEQVENCEHELLO\n"
    2.18 +        "#=GR SeqA  SS    -HHHHH---CHHH\n"
    2.19 +        "SeqB             SI-VENCE--LLO\n"
    2.20 +        "#=GR SeqB  SS    X-HHHHH--HHHH\n"
    2.21 +        "#=GC SS_cons     X-HHHHH--HHHH\n"
    2.22 +        "#=GC seq_cons    Si.VENCE.eLLo\n"
    2.23 +        "//\n"
    2.24 +    )
    2.25 +
    2.26 +    o = StringIO()
    2.27 +    o.write(file)
    2.28 +    o.seek(0)
    2.29 +
    2.30 +    aln = p.Alignment().append_file(o, "stockholm")
    2.31 +    assert len(aln.sequences) == 2
    2.32 +    assert len(aln.columns) == 13
    2.33 +    assert aln.sequences[1] not in aln.columns[2]
    2.34 +    assert aln.sequences[0][2].code1 == 'Q'
    2.35 +
    2.36 +    o = StringIO()
    2.37 +    aln.to_file(o, format='stockholm')
    2.38 +    o.seek(0)
    2.39 +    for line in o:
    2.40 +        hd = line.strip().split()[0]
    2.41 +        assert hd in ('#', '#=GS', '#=GF', '#=GC', 'SeqA', 'SeqB', '//')
    2.42 +    o.seek(0)
    2.43 +    assert iter(o).next() == "# STOCKHOLM 1.0\n"
    2.44 +
    2.45  # vim: set et ts=4 sts=4 sw=4: