comparison blast_html.py @ 18:4434ffab721a

add a parameter for the template

17:8e61627a87f1

# License: GPL version 3 or higher

import sys
import math
import warnings
from itertools import repeat
import argparse
from lxml import objectify
import jinja2

    # (u'\u2028', r'\u2028'),
    # (u'\u2029', r'\u2029')
)

# Escape every ASCII character with a value less than 32. This is
# needed a.o. to prevent parsers from jumping out of javascript
# parsing mode.
_js_escapes = (_base_js_escapes +
               tuple(('%c' % z, '\\u%04X' % z) for z in range(32)))

@filter

    colors = ('black', 'blue', 'green', 'magenta', 'red')

    max_scale_labels = 10

    templatename = 'blast_html.html.jinja'

    def __init__(self, input):
        self.input = input

        self.blast = objectify.parse(self.input).getroot()
        self.loader = jinja2.FileSystemLoader(searchpath='.')
        self.environment = jinja2.Environment(loader=self.loader,
                                              lstrip_blocks=True, trim_blocks=True, autoescape=True)

        self.environment.filters['color'] = lambda length: match_colors[color_idx(length)]

        for name, filter in _filters.items():
            self.environment.filters[name] = filter

        self.query_length = int(self.blast["BlastOutput_query-len"])
        self.hits = self.blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit
        # sort hits by longest hotspot first
        self.ordered_hits = sorted(self.hits,

        if len(self.blast.BlastOutput_iterations.Iteration) > 1:
            warnings.warn("Multiple 'Iteration' elements found, showing only the first")

        output.write(template.render(blast=self.blast,
                                          length=self.query_length,
                                          hits=self.blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit,
                                          colors=self.colors,
                                          match_colors=self.match_colors(),
                                          queryscale=self.queryscale(),
                                          hit_info=self.hit_info(),
                                          genelink=genelink,
                                          params=params))
            

    def match_colors(self):
        """
        An iterator that yields lists of length-color pairs. 
        """

                       e_value = "{:.4g}".format(min(hsp_val('Hsp_evalue'))),
                       # FIXME: is this the correct formula vv?
                       ident = "{:.0%}".format(float(min(hsp.Hsp_identity / hsplen(hsp) for hsp in hsps))),
                       accession = hit.Hit_accession)


def main():

    parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",
                                     usage="{} [-i] INPUT [-o OUTPUT]".format(sys.argv[0]))
    input_group = parser.add_mutually_exclusive_group(required=True)

                             help='The input Blast XML file, same as -i/--input')
    input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'), 
                             help='The input Blast XML file')
    parser.add_argument('-o', '--output', type=argparse.FileType(mode='w'), default=sys.stdout,
                        help='The output html file')

    args = parser.parse_args()
    if args.input == None:
        args.input = args.positional_arg
    if args.input == None:
        parser.error('no input specified')

    b = BlastVisualize(args.input)
    b.render(args.output)


if __name__ == '__main__':
    main()

18:4434ffab721a

# License: GPL version 3 or higher

import sys
import math
import warnings
from os import path
from itertools import repeat
import argparse
from lxml import objectify
import jinja2

    # (u'\u2028', r'\u2028'),
    # (u'\u2029', r'\u2029')
)

# Escape every ASCII character with a value less than 32. This is
# needed a.o. to prevent html parsers from jumping out of javascript
# parsing mode.
_js_escapes = (_base_js_escapes +
               tuple(('%c' % z, '\\u%04X' % z) for z in range(32)))

@filter

    colors = ('black', 'blue', 'green', 'magenta', 'red')

    max_scale_labels = 10

    def __init__(self, input, templatedir, templatename):
        self.input = input
        self.templatename = templatename

        self.blast = objectify.parse(self.input).getroot()
        self.loader = jinja2.FileSystemLoader(searchpath=templatedir)
        self.environment = jinja2.Environment(loader=self.loader,
                                              lstrip_blocks=True, trim_blocks=True, autoescape=True)

        self.environment.filters.update(_filters)
        self.environment.filters['color'] = lambda length: match_colors[color_idx(length)]

        self.query_length = int(self.blast["BlastOutput_query-len"])
        self.hits = self.blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit
        # sort hits by longest hotspot first
        self.ordered_hits = sorted(self.hits,

        if len(self.blast.BlastOutput_iterations.Iteration) > 1:
            warnings.warn("Multiple 'Iteration' elements found, showing only the first")

        output.write(template.render(blast=self.blast,
                                     length=self.query_length,
                                     hits=self.blast.BlastOutput_iterations.Iteration.Iteration_hits.Hit,
                                     colors=self.colors,
                                     match_colors=self.match_colors(),
                                     queryscale=self.queryscale(),
                                     hit_info=self.hit_info(),
                                     genelink=genelink,
                                     params=params))
        

    def match_colors(self):
        """
        An iterator that yields lists of length-color pairs. 
        """

                       e_value = "{:.4g}".format(min(hsp_val('Hsp_evalue'))),
                       # FIXME: is this the correct formula vv?
                       ident = "{:.0%}".format(float(min(hsp.Hsp_identity / hsplen(hsp) for hsp in hsps))),
                       accession = hit.Hit_accession)

def main():

    parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",
                                     usage="{} [-i] INPUT [-o OUTPUT]".format(sys.argv[0]))
    input_group = parser.add_mutually_exclusive_group(required=True)

                             help='The input Blast XML file, same as -i/--input')
    input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r'), 
                             help='The input Blast XML file')
    parser.add_argument('-o', '--output', type=argparse.FileType(mode='w'), default=sys.stdout,
                        help='The output html file')
    # We just want the file name here, so jinja can open the file
    # itself. But it is easier to just use a FileType so argparse can
    # handle the errors. This introduces a small race condition when
    # jinja later tries to re-open the template file, but we don't
    # care too much.
    parser.add_argument('--template', type=argparse.FileType(mode='r'), default='blast_html.html.jinja',
                        help='The template file to use. Defaults to blast_html.html.jinja')

    args = parser.parse_args()
    if args.input == None:
        args.input = args.positional_arg
    if args.input == None:
        parser.error('no input specified')

    templatedir, templatename = path.split(args.template.name)
    args.template.close()
    if not templatedir:
        templatedir = '.'

    b = BlastVisualize(args.input, templatedir, templatename)
    b.render(args.output)


if __name__ == '__main__':
    main()