comparison blast2html.py @ 53:4217bb9cf1d3

depend on python 3; fix internal links with multiple iterations

52:d6c7b5de2833

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Actually runs under either python 2 or 3

# Copyright The Hyve B.V. 2014
# License: GPL version 3 or higher

from __future__ import unicode_literals

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



_filters = {}
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__
            return func
        return inner
    else:

    if node.tag == 'Hsp':
        return int(node['Hsp_align-len'])
    elif node.tag == 'Iteration':
        return int(node['Iteration_query-len'])
    raise Exception("Unknown XML node type: "+node.tag)
        

@filter
def asframe(frame):
    if frame == 1:
        return 'Plus'
    elif frame == -1:

    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, encoding='utf-8')
        self.environment = jinja2.Environment(loader=self.loader,
                                              lstrip_blocks=True, trim_blocks=True, autoescape=True)

        self._addfilters(self.environment)

                matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))
                last = table[i]
                count = 1
            matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))

            yield dict(colors=matches, link="#hit"+hit.Hit_num.text, defline=firsttitle(hit))

    @filter
    def queryscale(self, result):
        query_length = blastxml_len(result)
        skip = math.ceil(query_length / self.max_scale_labels)

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

            yield dict(hit = hit,
                       title = firsttitle(hit),
                       link_id = hit.Hit_num,
                       maxscore = "{:.1f}".format(max(hsp_val('Hsp_bit-score'))),
                       totalscore = "{:.1f}".format(sum(hsp_val('Hsp_bit-score'))),
                       cover = "{:.0%}".format(cover_count / query_length),
                       e_value = "{:.4g}".format(min(hsp_val('Hsp_evalue'))),
                       # FIXME: is this the correct formula vv?

    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)
    input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'),
                             help='The input Blast XML file, same as -i/--input')
    input_group.add_argument('-i', '--input', type=argparse.FileType(mode='r', encoding='utf-8'), 
                             help='The input Blast XML file')
    parser.add_argument('-o', '--output', type=argparse.FileType(mode='w', encoding='utf-8'), 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', encoding='utf-8'), default=default_template,
                        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

53:4217bb9cf1d3

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

# Copyright The Hyve B.V. 2014
# License: GPL version 3 or higher

from __future__ import unicode_literals

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



_filters = {}
def filter(func_or_name):
    "Decorator to register a function as filter in the current jinja environment"
    if isinstance(func_or_name, str):
        def inner(func):
            _filters[func_or_name] = func.__name__
            return func
        return inner
    else:

    if node.tag == 'Hsp':
        return int(node['Hsp_align-len'])
    elif node.tag == 'Iteration':
        return int(node['Iteration_query-len'])
    raise Exception("Unknown XML node type: "+node.tag)

@filter
def nodeid(node):
    id = []
    if node.tag == 'Hsp':
        id.insert(0, node.Hsp_num.text)
        node = node.getparent().getparent()
        assert node.tag == 'Hit'
    if node.tag == 'Hit':
        id.insert(0, node.Hit_num.text)
        node = node.getparent().getparent()
        assert node.tag == 'Iteration'
    if node.tag == 'Iteration':
        id.insert(0, node['Iteration_iter-num'].text)
        return '-'.join(id)
    raise ValueError("The nodeid filter can only be applied to Hsp, Hit or Iteration nodes in a BlastXML document")

    
@filter
def asframe(frame):
    if frame == 1:
        return 'Plus'
    elif frame == -1:

    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._addfilters(self.environment)

                matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))
                last = table[i]
                count = 1
            matches.append((count * percent_multiplier, self.colors[last] if last != 255 else 'transparent'))

            yield dict(colors=matches, hit=hit, defline=firsttitle(hit))

    @filter
    def queryscale(self, result):
        query_length = blastxml_len(result)
        skip = math.ceil(query_length / self.max_scale_labels)

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

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

    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)
    input_group.add_argument('positional_arg', metavar='INPUT', nargs='?', type=argparse.FileType(mode='r'),
                             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=default_template,
                        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