diff --git a/mutalyzer/entrypoints/mutalyzer.py b/mutalyzer/entrypoints/mutalyzer.py index c455ae1ed8e290c8982d7883880c9950c613e0e0..c04a112a2ce1c8c2df0988f4ecd1a0e406d77d0e 100644 --- a/mutalyzer/entrypoints/mutalyzer.py +++ b/mutalyzer/entrypoints/mutalyzer.py @@ -17,7 +17,12 @@ from .. import output from .. import variantchecker -class MyEncoder(json.JSONEncoder): +# TODO: This seems like a bit of a weird trick. In any case, we should +# follow the pattern from the `json` documentation to call +# `JSONEncoder.default(self, o)` as a fallback. +# +# https://docs.python.org/2/library/json.html#json.JSONEncoder.default +class AlleleEncoder(json.JSONEncoder): def default(self, o): json_object = o.__dict__ json_object.update({"hgvs": unicode(o), "weight": o.weight()}) @@ -26,6 +31,7 @@ class MyEncoder(json.JSONEncoder): #default #MyEncoder + def check_name(description): """ Run the name checker. @@ -128,7 +134,7 @@ def check_name(description): print json.dumps({ #"reference_sequence": reference_sequence, #"sample_sequence": sample_sequence, - "allele_description": described_allele}, cls=MyEncoder) + "allele_description": described_allele}, cls=AlleleEncoder) def main(): diff --git a/mutalyzer/extractor_loader.py b/mutalyzer/extractor_loader.py deleted file mode 100644 index ee8b097e50518f008daafbde2bd7357da648bf37..0000000000000000000000000000000000000000 --- a/mutalyzer/extractor_loader.py +++ /dev/null @@ -1,37 +0,0 @@ -#!/usr/bin/env python - -from __future__ import unicode_literals - -import sys - -import json - -import describe - -class MyEncoder(json.JSONEncoder): - def default(self, o): - return o.__dict__ - -def main(): - if len(sys.argv) < 3: - print "usage: " + sys.argv[0] + " reference sample" - exit() - #if - - f = open(sys.argv[1], "r") - ref = f.read() - f.close() - f = open(sys.argv[2], "r") - alt = f.read() - f.close() - - extracted_allele = describe.describe_dna(ref, alt) - - #print "Description Extractor Version " + describe.extractor.VERSION - print extracted_allele - #print "JSON: " + json.dumps({"reference_sequence": ref, "sample_sequence": alt, "allele_description": extracted_allele}, cls=MyEncoder) - -#main - -if __name__ == "__main__": - main() diff --git a/mutalyzer/test.py b/mutalyzer/test.py deleted file mode 100644 index f733aec814afeda4f4c22ef9b8cabfaecb1b2221..0000000000000000000000000000000000000000 --- a/mutalyzer/test.py +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env python - -from __future__ import unicode_literals - -import json - -import describe - -class MyEncoder(json.JSONEncoder): - def default(self, o): - return o.__dict__ - -def main(): - ref = "ACGTCGATTCGCTAGCTTCGGGGGATAGATAGAGATATAGAGATATTTTT" - alt = "ACGTCGGTTCGCTAGCTTCGGGGGATAGATAGATATATAGAGATATTTTT" - - extracted_allele = describe.describe_dna(ref, alt) - - print extracted_allele - print json.dumps({"reference_sequence": ref, "sample_sequence": alt, - "allele_description": extracted_allele}, cls=MyEncoder) -#main - -if __name__ == "__main__": - main() diff --git a/mutalyzer/website/templates/name-checker.html b/mutalyzer/website/templates/name-checker.html index c2c37d8004a5cbc0316cf019af609a42e30112f5..b58243d9721cb834d202db63bc0ad7064435d38b 100644 --- a/mutalyzer/website/templates/name-checker.html +++ b/mutalyzer/website/templates/name-checker.html @@ -215,7 +215,6 @@ {% if extractedDescription %} <h4>Experimental services</h4> <p>Genomic description: <code>{{ extractedDescription }}</code></p> - <p>Protein description: <code>{{ extractedProtein }}</code></p> {% endif %} </div>{# class="col-md-8 name-checker-left-column" #} diff --git a/mutalyzer/website/views.py b/mutalyzer/website/views.py index 36327e1836c4589c610bd7d1c8bd062261fd05f4..0136564bf2b3311410cc1caf0d91b5f58058dfff 100644 --- a/mutalyzer/website/views.py +++ b/mutalyzer/website/views.py @@ -273,19 +273,12 @@ def name_checker(): output.getIndexedOutput('mutated', 0)): allele = extractor.describe_dna(output.getIndexedOutput('original', 0), output.getIndexedOutput('mutated', 0)) - #prot_allele = describe.describe_protein( - # output.getIndexedOutput('oldprotein', 0), - # output.getIndexedOutput('newprotein', 0, default='')) - prot_allele = '' - - extracted = extractedProt = '(skipped)' + extracted = '(skipped)' if allele: - extracted = unicode(allele) #describe.allele_description(allele) - if prot_allele: - extractedProt = unicode(prot_allele) #describe.allele_description(prot_allele) + extracted = unicode(allele) else: - extracted = extractedProt = '' + extracted = '' # Todo: Generate the fancy HTML views for the proteins here instead of in # `mutalyzer.variantchecker`. @@ -320,7 +313,6 @@ def name_checker(): 'reference_filename' : reference_filename, # Todo: Download link is not shown... 'browserLink' : browser_link, 'extractedDescription': extracted, - 'extractedProtein' : extractedProt, 'standalone' : bool(request.args.get('standalone')) } diff --git a/requirements.txt b/requirements.txt index 3942920811f24a6c0c015255333e09fa7fcc29ff..add9c97c442c2ac35daa22dd66187fafdc61b4a4 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ -e git+https://github.com/LUMC/magic-python.git#egg=Magic_file_extensions --e git+https://github.com/LUMC/extractor.git@f270ef101e909895d58e47420935f2bbfdb28a3b#egg=extractor +description-extractor==2.2.1 Flask==0.10.1 Jinja2==2.7.3 MySQL-python==1.2.5