From f289883b43dbc202fb46249fd077933d8ed4fbd4 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Fri, 1 May 2015 11:54:16 +0200
Subject: [PATCH] Minor code cleanups
---
mutalyzer/entrypoints/mutalyzer.py | 10 ++++-
mutalyzer/extractor_loader.py | 37 -------------------
mutalyzer/test.py | 25 -------------
mutalyzer/website/templates/name-checker.html | 1 -
mutalyzer/website/views.py | 14 ++-----
5 files changed, 11 insertions(+), 76 deletions(-)
delete mode 100644 mutalyzer/extractor_loader.py
delete mode 100644 mutalyzer/test.py
diff --git a/mutalyzer/entrypoints/mutalyzer.py b/mutalyzer/entrypoints/mutalyzer.py
index c455ae1e..c04a112a 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 ee8b097e..00000000
--- 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 f733aec8..00000000
--- 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 c2c37d80..b58243d9 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 36327e18..0136564b 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'))
}
--
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