| Previous changeset 17:8e61627a87f1 (2014-05-13) Next changeset 19:67ddcb807b7d (2014-05-13) |
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Commit message:
add a parameter for the template |
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modified:
blast_html.py |
| b |
| diff -r 8e61627a87f1 -r 4434ffab721a blast_html.py --- a/blast_html.py Tue May 13 12:54:03 2014 +0200 +++ b/blast_html.py Tue May 13 15:26:20 2014 +0200 |
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| @@ -6,6 +6,7 @@ import sys import math import warnings +from os import path from itertools import repeat import argparse from lxml import objectify @@ -115,7 +116,7 @@ ) # Escape every ASCII character with a value less than 32. This is -# needed a.o. to prevent parsers from jumping out of javascript +# 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))) @@ -141,21 +142,18 @@ max_scale_labels = 10 - templatename = 'blast_html.html.jinja' - - def __init__(self, input): + def __init__(self, input, templatedir, templatename): self.input = input + self.templatename = templatename self.blast = objectify.parse(self.input).getroot() - self.loader = jinja2.FileSystemLoader(searchpath='.') + 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)] - 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 @@ -177,15 +175,15 @@ 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)) - + 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): """ @@ -253,7 +251,6 @@ 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", @@ -265,6 +262,13 @@ 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: @@ -272,7 +276,12 @@ if args.input == None: parser.error('no input specified') - b = BlastVisualize(args.input) + templatedir, templatename = path.split(args.template.name) + args.template.close() + if not templatedir: + templatedir = '.' + + b = BlastVisualize(args.input, templatedir, templatename) b.render(args.output) |