comparison blast2html.py @ 77:4d2c25baf5a3 draft py2.6

Fix rounding errors

76:03e044b5bcc2

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

# Actually this program works with both python 2 and 3

# Copyright The Hyve B.V. 2014
# License: GPL version 3 or (at your option) any higher version

from __future__ import unicode_literals, division

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



_filters = dict()
def filter(func_or_name):
    "Decorator to register a function as filter in the current jinja environment"
    if isinstance(func_or_name, six.string_types):
        def inner(func):
            _filters[func_or_name] = func.__name__

    def _addfilters(self, environment):
        for filtername, funcname in _filters.items():
            try:
                environment.filters[filtername] = getattr(self, funcname)
            except AttributeError:
                environment.filters[filtername] = globals()[funcname]

    def render(self, output):
        template = self.environment.get_template(self.templatename)

        params = (('Query ID', self.blast["BlastOutput_query-ID"]),

        )

        result = template.render(blast=self.blast,
                                 iterations=self.blast.BlastOutput_iterations.Iteration,
                                 colors=self.colors,
                                 # match_colors=self.match_colors(),
                                 # hit_info=self.hit_info(),
                                 genelink=genelink,
                                 params=params)
        if six.PY2:
            result = result.encode('utf-8')
        output.write(result)

            def hsp_val(path):
                return (float(hsp[path]) for hsp in hsps)

            yield dict(hit = hit,
                      title = firsttitle(hit),
                       maxscore = "{0:.1f}".format(max(hsp_val('Hsp_bit-score'))),
                       totalscore = "{0:.1f}".format(sum(hsp_val('Hsp_bit-score'))),
                       cover = "{0:.0%}".format(cover_count / query_length),
                       e_value = "{0:.4g}".format(min(hsp_val('Hsp_evalue'))),
                       # FIXME: is this the correct formula vv?
                       ident = "{0:.0%}".format(float(min(hsp.Hsp_identity / blastxml_len(hsp) for hsp in hsps))),
                       accession = hit.Hit_accession)


def main():
    default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja')

77:4d2c25baf5a3

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

# Actually this program works with both python 2 and 3, tested against python 2.6

# Copyright The Hyve B.V. 2014
# License: GPL version 3 or (at your option) any higher version

from __future__ import unicode_literals, division

import sys
import math
import warnings
import six, codecs
from six.moves import builtins
from os import path
from itertools import repeat
import argparse
from lxml import objectify
import jinja2



_filters = dict(int='int', float='float')
def filter(func_or_name):
    "Decorator to register a function as filter in the current jinja environment"
    if isinstance(func_or_name, six.string_types):
        def inner(func):
            _filters[func_or_name] = func.__name__

    def _addfilters(self, environment):
        for filtername, funcname in _filters.items():
            try:
                environment.filters[filtername] = getattr(self, funcname)
            except AttributeError:
                try:
                    environment.filters[filtername] = globals()[funcname]
                except KeyError:
                    environment.filters[filtername] = getattr(builtins, funcname)

    def render(self, output):
        template = self.environment.get_template(self.templatename)

        params = (('Query ID', self.blast["BlastOutput_query-ID"]),

        )

        result = template.render(blast=self.blast,
                                 iterations=self.blast.BlastOutput_iterations.Iteration,
                                 colors=self.colors,
                                 genelink=genelink,
                                 params=params)
        if six.PY2:
            result = result.encode('utf-8')
        output.write(result)

            def hsp_val(path):
                return (float(hsp[path]) for hsp in hsps)

            yield dict(hit = hit,
                       title = firsttitle(hit),
                       maxscore = "{0:.1f}".format(max(hsp_val('Hsp_bit-score'))),
                       totalscore = "{0:.1f}".format(sum(hsp_val('Hsp_bit-score'))),
                       cover = "{0:.0%}".format(cover_count / query_length),
                       e_value = "{0:.4g}".format(min(hsp_val('Hsp_evalue'))),
                       # FIXME: is this the correct formula vv?
                       # float(...) because non-rounding division doesn't work with lxml elements in python 2.6
                       ident = "{0:.0%}".format(float(min(float(hsp.Hsp_identity) / blastxml_len(hsp) for hsp in hsps))),
                       accession = hit.Hit_accession)


def main():
    default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja')