comparison blast2html.py @ 99:02b795b784e1 draft

fix bug; add comments

98:4378d11f0ed7

        s += '0'
    return s

@filter
def firsttitle(hit):
    return hit.Hit_def.text.split('>')[0]

@filter
def othertitles(hit):
    """Split a hit.Hit_def that contains multiple titles up, splitting out the hit ids from the titles."""
    id_titles = hit.Hit_def.text.split('>')

    titles = []
    for t in id_titles[1:]:
        id, title = t.split(' ', 1)
        titles.append(argparse.Namespace(Hit_id = id,

                       # float(...) because non-flooring 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))))

    @filter
    def genelink(self, hit, text=None, clas=None, display_nolink=True):
        if text is None:
            text = hitid(hit)
        db = hit.getroottree().getroot().BlastOutput_db
        if isinstance(self.genelinks, six.string_types):
            template = self.genelinks
        else:
            template = self.genelinks.get(db)
        if template is None:

        try:
            link = template.format(**args)
        except Exception as e:
            warnings.warn('Error in formatting gene bank link {} with {}: {}'.format(template, args, e))
            return text if display_nolink else ''
        classattr = 'class="{}" '.format(jinja2.escape(clas)) if clas is not None else ''
        return jinja2.Markup("<a {}href=\"{}\">{}</a>".format(classattr, jinja2.escape(link), jinja2.escape(text)))


def read_genelinks(dir):

99:02b795b784e1

        s += '0'
    return s

@filter
def firsttitle(hit):
    return str(hit.Hit_def).split('>')[0]

@filter
def othertitles(hit):
    """Split a hit.Hit_def that contains multiple titles up, splitting out the hit ids from the titles."""
    id_titles = str(hit.Hit_def).split('>')

    titles = []
    for t in id_titles[1:]:
        id, title = t.split(' ', 1)
        titles.append(argparse.Namespace(Hit_id = id,

                       # float(...) because non-flooring 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))))

    @filter
    def genelink(self, hit, text=None, clas=None, display_nolink=True):
        """Create a html link from a hit node to a configured gene bank webpage.
        text: The text of the link, defaults to the hit_id
        clas: extra css classes that will be added to the <a> element
        display_nolink: boolean, if false don't display anything if no link can be created. Default True.
        """
        
        if text is None:
            text = hitid(hit)

        db = hit.getroottree().getroot().BlastOutput_db

        if isinstance(self.genelinks, six.string_types):
            template = self.genelinks
        else:
            template = self.genelinks.get(db)
        if template is None:

        try:
            link = template.format(**args)
        except Exception as e:
            warnings.warn('Error in formatting gene bank link {} with {}: {}'.format(template, args, e))
            return text if display_nolink else ''

        classattr = 'class="{}" '.format(jinja2.escape(clas)) if clas is not None else ''
        return jinja2.Markup("<a {}href=\"{}\">{}</a>".format(classattr, jinja2.escape(link), jinja2.escape(text)))


def read_genelinks(dir):