1.1 --- a/allpy/structure.py	Wed Mar 16 22:15:19 2011 +0300
     1.2 +++ b/allpy/structure.py	Wed Mar 16 22:26:42 2011 +0300
     1.3 @@ -11,6 +11,7 @@
     1.4  import os.path
     1.5  import urllib2
     1.6  from copy import copy
     1.7 +import json
     1.8  
     1.9  from Bio.PDB import PDBParser
    1.10  from Bio.PDB import Select
    1.11 @@ -217,6 +218,41 @@
    1.12                  blocks[i].sequences.append(sequence)
    1.13          return [block for i, block in sorted(blocks.items())]
    1.14  
    1.15 +    def blocks_to_html(self, file, blocks, template):
    1.16 +        """ Write convenient html-file for viewing blocks
    1.17 +
    1.18 +        template -- str with template of html
    1.19 +            this template should contain substring 'self_js_text'
    1.20 +            to be replaced with information about blocks
    1.21 +        """
    1.22 +        column2pos = self.column2pos()
    1.23 +        js_blocks = []
    1.24 +        js_fasta_dict = {}
    1.25 +        for block in blocks:
    1.26 +            p_from = column2pos[block.columns[0]]
    1.27 +            p_to = column2pos[block.columns[-1]]
    1.28 +            js_block = {}
    1.29 +            js_block['start'] = p_from
    1.30 +            js_block['end'] = p_to
    1.31 +            js_block['IDs'] = []
    1.32 +            for sequence in block.sequences:
    1.33 +                js_block['IDs'].append(sequence.name)
    1.34 +            js_block['cores'] = []
    1.35 +            js_blocks.append(js_block)
    1.36 +        def char(monomer):
    1.37 +            if monomer:
    1.38 +                return monomer.code1
    1.39 +            return '-'
    1.40 +        for row in self.rows_as_lists():
    1.41 +            sequence = row.sequence
    1.42 +            line = "".join(map(char, row))
    1.43 +            js_fasta_dict[sequence.name] = line
    1.44 +        self_js_test = ("blocks = json('%(blocks)s');" +\
    1.45 +            "fasta_dict=json('%(fasta_dict)s');") %\
    1.46 +            {'blocks': json.dumps(js_blocks),
    1.47 +             'fasta_dict': json.dumps(js_fasta_dict)}
    1.48 +        file.write(template.replace('self_js_text', self_js_test))
    1.49 +
    1.50  class BlockMixin(base.Block, base.AlignmentMixin):
    1.51      """Mixin to add 3D properties to blocks.
    1.52  

     2.1 --- a/blocks3d/blocks3d.py	Wed Mar 16 22:15:19 2011 +0300
     2.2 +++ b/blocks3d/blocks3d.py	Wed Mar 16 22:26:42 2011 +0300
     2.3 @@ -6,7 +6,6 @@
     2.4  
     2.5  import argparse
     2.6  import os
     2.7 -import json
     2.8  
     2.9  from allpy import config
    2.10  from allpy import markup
    2.11 @@ -56,55 +55,9 @@
    2.12      timeout=args.t, timeout_2=args.T,
    2.13      min_width=args.m))
    2.14  
    2.15 -column2pos = alignment.column2pos()
    2.16 -
    2.17  if args.H:
    2.18 -    # html-file
    2.19 -    js_blocks = []
    2.20 -    js_fasta_dict = {}
    2.21 -    for b in blocks:
    2.22 -        p_from = column2pos[b.columns[0]]
    2.23 -        p_to = column2pos[b.columns[-1]]
    2.24 -        js_block = {}
    2.25 -        js_block['start'] = p_from
    2.26 -        js_block['end'] = p_to
    2.27 -        js_block['IDs'] = []
    2.28 -        for sequence in b.sequences:
    2.29 -            js_block['IDs'].append(sequence.name)
    2.30 -        js_block['cores'] = []
    2.31 -        js_blocks.append(js_block)
    2.32 -    def char(monomer):
    2.33 -        if monomer:
    2.34 -            return monomer.code1
    2.35 -        return '-'
    2.36 -    for row in block.rows_as_lists():
    2.37 -        sequence = row.sequence
    2.38 -        line = "".join(map(char, row))
    2.39 -        js_fasta_dict[sequence.name] = line
    2.40 -    self_js_test = ("blocks = json('%(blocks)s');" +\
    2.41 -        "fasta_dict=json('%(fasta_dict)s');") %\
    2.42 -        {'blocks': json.dumps(js_blocks),
    2.43 -         'fasta_dict': json.dumps(js_fasta_dict)}
    2.44 -    t = open(html_template).read()
    2.45 -    t = t.replace('self_js_text', self_js_test)
    2.46 -    args.H.write(t)
    2.47 +    alignment.blocks_to_html(args.H, blocks, open(html_template).read())
    2.48  
    2.49  if args.o:
    2.50 -    t = args.o
    2.51 -    # text output
    2.52 -    t.write("Block|from|to(exclusive)|gaps\n")
    2.53 -    for i, b in enumerate(blocks):
    2.54 -        p_from = column2pos[b.columns[0]]
    2.55 -        p_to = column2pos[b.columns[-1]] + 1
    2.56 -        width = p_to - p_from
    2.57 -        gaps = width - len(b.columns)
    2.58 -        t.write("%(i)i|%(from)i|%(to)i|%(gaps)i\n" %\
    2.59 -            {'i': i, 'from': p_from,
    2.60 -            'to': p_to, 'gaps': gaps})
    2.61 -    t.write('#\n')
    2.62 -    t.write("Block|Sequence\n")
    2.63 -    for i, b in enumerate(blocks):
    2.64 -        for sequence in b.sequences:
    2.65 -            t.write("%(i)i|%(sequence)s\n" %\
    2.66 -                {'i': i, 'sequence': sequence.name})
    2.67 +    alignment.blocks_to_file(args.o, blocks)
    2.68