comparison blast2html.py @ 75:67b1a319c6dc draft py2.6

First go at 2.6 compatibility The tests are running without errors, but they don't produce the same output as python3

74:6ecbfebb9dd9

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

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

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:

    qseq = hsp.Hsp_qseq.text
    midline = hsp.Hsp_midline.text
    hseq = hsp.Hsp_hseq.text

    if not qframe in (1, -1):
        warnings.warn("Error in BlastXML input: Hsp node {} has a Hsp_query-frame of {}. (should be 1 or -1)".format(nodeid(hsp), qframe))
        qframe = -1 if qframe < 0 else 1
    if not hframe in (1, -1):
        warnings.warn("Error in BlastXML input: Hsp node {} has a Hsp_hit-frame of {}. (should be 1 or -1)".format(nodeid(hsp), hframe))
        hframe = -1 if hframe < 0 else 1
    
    def split(txt):
        return [txt[i:i+linewidth] for i in range(0, len(txt), linewidth)]

    for qs, mid, hs, offset in zip(split(qseq), split(midline), split(hseq), range(0, len(qseq), linewidth)):
        yield (
            "Query  {:>7}  {}  {}\n".format(qfrom+offset*qframe, qs, qfrom+(offset+len(qs)-1)*qframe) +
            "       {:7}  {}\n".format('', mid) +
            "Subject{:>7}  {}  {}".format(hfrom+offset*hframe, hs, hfrom+(offset+len(hs)-1)*hframe)
        )
        
    if qfrom+(len(qseq)-1)*qframe != qto:
        warnings.warn("Error in BlastXML input: Hsp node {} qseq length mismatch: from {} to {} length {}".format(
            nodeid(hsp), qfrom, qto, len(qseq)))
    if hfrom+(len(hseq)-1)*hframe != hto:
        warnings.warn("Error in BlastXML input: Hsp node {} hseq length mismatch: from {} to {} length {}".format(
            nodeid(hsp), hfrom, hto, len(hseq)))

    

@filter('len')

    elif frame == -1:
        return 'Minus'
    raise Exception("frame should be either +1 or -1")

def genelink(hit, type='genbank', hsp=None):
    if not isinstance(hit, str):
        hit = hitid(hit)
    link = "http://www.ncbi.nlm.nih.gov/nucleotide/{}?report={}&log$=nuclalign".format(hit, type)
    if hsp != None:
        link += "&from={}&to={}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to'])
    return link


# javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139
# I've removed the html escapes, since html escaping is already being performed by the template engine.

    Javascript string literal escape. Note that this only escapes data
    for embedding within javascript string literals, not in general
    javascript snippets.
    """

    value = str(value)

    for bad, good in _js_escapes:
        value = value.replace(bad, good)

    return value

    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)

                  ('Query length', self.blast["BlastOutput_query-len"]),
                  ('Program', self.blast.BlastOutput_version),
                  ('Database', self.blast.BlastOutput_db),
        )

        output.write(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))

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

            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?
                       ident = "{:.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')
    
    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')

75:67b1a319c6dc

#!/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__
            return func
        return inner
    else:

    qseq = hsp.Hsp_qseq.text
    midline = hsp.Hsp_midline.text
    hseq = hsp.Hsp_hseq.text

    if not qframe in (1, -1):
        warnings.warn("Error in BlastXML input: Hsp node {0} has a Hsp_query-frame of {1}. (should be 1 or -1)".format(nodeid(hsp), qframe))
        qframe = -1 if qframe < 0 else 1
    if not hframe in (1, -1):
        warnings.warn("Error in BlastXML input: Hsp node {0} has a Hsp_hit-frame of {1}. (should be 1 or -1)".format(nodeid(hsp), hframe))
        hframe = -1 if hframe < 0 else 1
    
    def split(txt):
        return [txt[i:i+linewidth] for i in range(0, len(txt), linewidth)]

    for qs, mid, hs, offset in zip(split(qseq), split(midline), split(hseq), range(0, len(qseq), linewidth)):
        yield (
            "Query  {0:>7}  {1}  {2}\n".format(qfrom+offset*qframe, qs, qfrom+(offset+len(qs)-1)*qframe) +
            "       {0:7}  {1}\n".format('', mid) +
            "Subject{0:>7}  {1}  {2}".format(hfrom+offset*hframe, hs, hfrom+(offset+len(hs)-1)*hframe)
        )
        
    if qfrom+(len(qseq)-1)*qframe != qto:
        warnings.warn("Error in BlastXML input: Hsp node {0} qseq length mismatch: from {1} to {2} length {3}".format(
            nodeid(hsp), qfrom, qto, len(qseq)))
    if hfrom+(len(hseq)-1)*hframe != hto:
        warnings.warn("Error in BlastXML input: Hsp node {0} hseq length mismatch: from {1} to {2} length {3}".format(
            nodeid(hsp), hfrom, hto, len(hseq)))

    

@filter('len')

    elif frame == -1:
        return 'Minus'
    raise Exception("frame should be either +1 or -1")

def genelink(hit, type='genbank', hsp=None):
    if not isinstance(hit, six.string_types):
        hit = hitid(hit)
    link = "http://www.ncbi.nlm.nih.gov/nucleotide/{0}?report={1}&log$=nuclalign".format(hit, type)
    if hsp != None:
        link += "&from={0}&to={1}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to'])
    return link


# javascript escape filter based on Django's, from https://github.com/dsissitka/khan-website/blob/master/templatefilters.py#L112-139
# I've removed the html escapes, since html escaping is already being performed by the template engine.

    Javascript string literal escape. Note that this only escapes data
    for embedding within javascript string literals, not in general
    javascript snippets.
    """

    value = six.text_type(value)

    for bad, good in _js_escapes:
        value = value.replace(bad, good)

    return value

    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)

                  ('Query length', self.blast["BlastOutput_query-len"]),
                  ('Program', self.blast.BlastOutput_version),
                  ('Database', self.blast.BlastOutput_db),
        )

        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)

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

            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():
    #import pdb; pdb.set_trace()
    default_template = path.join(path.dirname(__file__), 'blast2html.html.jinja')

    parser = argparse.ArgumentParser(description="Convert a BLAST XML result into a nicely readable html page",
                                     usage="{0} [-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')