[Biopython-dev] nodes in Martel tree

[Andrew Dalke]

Cayte wrote:
>   I wonder if with nested nodes, you need to use the leaf nodes to get it to
> work right.  I had the following structure.

No, you shouldn't need to.

> I had the following structure.

It's hard to evaluate that without the full format definition.  I've
attached a file which I used for testing.  The result when parsing
the data:

SEQTPA        107    98 gag GLU E
SEQTPA        108    99 tgg TRP W
SEQTPA        106   100 aaa XXX X bbb YYY Y

is (up to newlines)

<?xml version="1.0" encoding="iso-8859-1"?>
SEQTPA        <n1>107</n1>    <n2>98</n2><residue> <codon>gag</codon>
<three_letter>GLU</three_letter> <one_letter>E</one_letter></residue>
SEQTPA        <n1>108</n1>    <n2>99</n2><residue> <codon>tgg</codon>
<three_letter>TRP</three_letter> <one_letter>W</one_letter></residue>
SEQTPA        <n1>106</n1>   <n2>100</n2><residue> <codon>aaa</codon>
<three_letter>XXX</three_letter> <one_letter>X</one_letter></residue>
<residue> <codon>bbb</codon> <three_letter>YYY</three_letter>
<one_letter>Y</one_letter></residue>

As you can see in the last line, there are two "residue" fields.
I can't seem to reproduce the behaviour you are seeing.

> I have another question about residue notation.

That one I cannot answer - I don't know.  My guess agrees
with yours.

					Andrew
					dalke at acm.org
-------------- next part --------------
import Martel
from xml.sax import saxutils

blank_space = Martel.Str(" ")
codon = Martel.Re("(?P<codon>...)")
amino_3_letter_code = Martel.Re("(?P<three_letter>...)")
amino_1_letter_code = Martel.Re("(?P<one_letter>.)")

residue = Martel.Group( "residue",
                           blank_space +
                           codon +
                           blank_space +
                           amino_3_letter_code +
                           blank_space +
                           amino_1_letter_code )

spaces = Martel.Re(" +")

seqtpa = Martel.Str("SEQTPA") + \
         spaces + Martel.Integer("n1") + \
         spaces + Martel.Integer("n2") + \
         Martel.Rep1(residue) + \
         Martel.AnyEol()

format = Martel.Rep1(seqtpa)

data = """\
SEQTPA        107    98 gag GLU E
SEQTPA        108    99 tgg TRP W
SEQTPA        106   100 aaa XXX X bbb YYY Y
"""

parser = format.make_parser()
parser.setContentHandler(saxutils.XMLGenerator())
parser.parseString(data)