blast2html: blast2html.py comparison

comparison blast2html.py @ 73:67b1a319c6dc py2.6

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

author	Jan Kanis <jan.code@jankanis.nl>
date	Wed, 18 Jun 2014 16:21:45 +0200
parents	6ecbfebb9dd9
children	03e044b5bcc2

comparison

equal deleted inserted replaced

-:6ecbfebb9dd9
+: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
+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 = {}
+_filters = dict()
 def filter(func_or_name):
 "Decorator to register a function as filter in the current jinja environment"
-if isinstance(func_or_name, str):
+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 {} has a Hsp_query-frame of {}. (should be 1 or -1)".format(nodeid(hsp), qframe))
+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 {} has a Hsp_hit-frame of {}. (should be 1 or -1)".format(nodeid(hsp), hframe))
+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  {:>7}  {}  {}\n".format(qfrom+offset*qframe, qs, qfrom+(offset+len(qs)-1)*qframe) +
+"Query  {0:>7}  {1}  {2}\n".format(qfrom+offset*qframe, qs, qfrom+(offset+len(qs)-1)*qframe) +
-"       {:7}  {}\n".format('', mid) +
+"       {0:7}  {1}\n".format('', mid) +
-"Subject{:>7}  {}  {}".format(hfrom+offset*hframe, hs, hfrom+(offset+len(hs)-1)*hframe)
+"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 {} qseq length mismatch: from {} to {} length {}".format(
+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 {} hseq length mismatch: from {} to {} length {}".format(
+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, str):
+if not isinstance(hit, six.string_types):
 hit = hitid(hit)
-link = "http://www.ncbi.nlm.nih.gov/nucleotide/{}?report={}&log$=nuclalign".format(hit, type)
+link = "http://www.ncbi.nlm.nih.gov/nucleotide/{0}?report={1}&log$=nuclalign".format(hit, type)
 if hsp != None:
-link += "&from={}&to={}".format(hsp['Hsp_hit-from'], hsp['Hsp_hit-to'])
+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 = str(value)
+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)
+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),
 )
-output.write(template.render(blast=self.blast,
+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))
+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 = "{:.1f}".format(max(hsp_val('Hsp_bit-score'))),
+maxscore = "{0:.1f}".format(max(hsp_val('Hsp_bit-score'))),
-totalscore = "{:.1f}".format(sum(hsp_val('Hsp_bit-score'))),
+totalscore = "{0:.1f}".format(sum(hsp_val('Hsp_bit-score'))),
-cover = "{:.0%}".format(cover_count / query_length),
+cover = "{0:.0%}".format(cover_count / query_length),
-e_value = "{:.4g}".format(min(hsp_val('Hsp_evalue'))),
+e_value = "{0:.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))),
+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="{} [-i] INPUT [-o OUTPUT]".format(sys.argv[0]))
+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')

Mercurial > repos > jankanis > blast2html

comparison blast2html.py @ 73:67b1a319c6dc py2.6