From 7de1296953a817d174f9d4ade5b77b5f20b38bf5 Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Sat, 12 Apr 2014 20:14:15 +0200
Subject: [PATCH] Added JSON encoder.
---
mutalyzer/entrypoints/mutalyzer.py | 26 ++++++++++++++++++--------
1 file changed, 18 insertions(+), 8 deletions(-)
diff --git a/mutalyzer/entrypoints/mutalyzer.py b/mutalyzer/entrypoints/mutalyzer.py
index b9af312f..b499142c 100644
--- a/mutalyzer/entrypoints/mutalyzer.py
+++ b/mutalyzer/entrypoints/mutalyzer.py
@@ -8,7 +8,7 @@ Mutalyzer command-line name checker.
from __future__ import unicode_literals
import argparse
-import sys
+import json
from . import _cli_string
from .. import describe
@@ -16,6 +16,10 @@ from .. import output
from .. import variantchecker
+class MyEncoder(json.JSONEncoder):
+ def default(self, o):
+ return o.__dict__
+
def check_name(description):
"""
Run the name checker.
@@ -93,13 +97,16 @@ def check_name(description):
for i in O.getOutput("legends") :
print i
- extracted_allele = describe.describe(
- O.getIndexedOutput("original", 0),
- O.getIndexedOutput("mutated", 0))
- extracted_protein_allele = describe.describe(
- O.getIndexedOutput("oldprotein", 0),
- O.getIndexedOutput("newprotein", 0, default=""),
- DNA=False)
+ reference_sequence = O.getIndexedOutput("original", 0)
+ sample_sequence = O.getIndexedOutput("mutated", 0)
+
+ extracted_allele = describe.describe(reference_sequence,
+ sample_sequence)
+ #extracted_protein_allele = describe.describe(
+ # O.getIndexedOutput("oldprotein", 0),
+ # O.getIndexedOutput("newprotein", 0, default=""),
+ # DNA=False)
+ extracted_protein_allele = ""
extracted = extracted_protein = '(skipped)'
@@ -112,6 +119,9 @@ def check_name(description):
print extracted
print extracted_protein
#print "+++ %s" % O.getOutput("myTranscriptDescription")
+ print json.dumps({"reference_sequence": reference_sequence,
+ "sample_sequence": sample_sequence, "allele_description":
+ extracted_allele}, cls=MyEncoder)
def main():
--
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