From 80db7b5bd194daf341f865be0a6a9a25eeb8c8a8 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Mon, 16 Jul 2012 11:55:39 +0000
Subject: [PATCH] Add chromAccession.py to SOAP tools
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@574 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
extras/soap-tools/chromAccession.py | 42 +++++++++++++++++++++++++++++
extras/soap-tools/mappingInfo.py | 4 +--
2 files changed, 43 insertions(+), 3 deletions(-)
create mode 100755 extras/soap-tools/chromAccession.py
diff --git a/extras/soap-tools/chromAccession.py b/extras/soap-tools/chromAccession.py
new file mode 100755
index 00000000..61494754
--- /dev/null
+++ b/extras/soap-tools/chromAccession.py
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+"""
+Get chromosome accession number from a Mutalyzer installation.
+
+Usage:
+ {command} chromosome [build]
+
+ chromosome: Chromosome to get accession number for, e.g. 'chr2'.
+ build: Human genome build, 'hg18' or 'hg19' (default: 'hg19').
+
+The accession number is retrieved from the Mutalyzer SOAP webservice and
+printed to standard output.
+"""
+
+
+from mutalyzer.util import monkey_patch_suds; monkey_patch_suds()
+
+import sys
+from suds.client import Client
+
+from mutalyzer.util import format_usage
+
+
+WSDL_LOCATION = 'http://localhost/mutalyzer/services/?wsdl'
+
+
+def main(chromosome, build='hg19'):
+ """
+ Get accession number and print it to standard output.
+ """
+ service = Client(WSDL_LOCATION, cache=None).service
+ result = service.chromAccession(build=build, name=chromosome)
+
+ if result:
+ print 'Chromosome accession number: %s' % str(result)
+
+
+if __name__ == '__main__':
+ if len(sys.argv) < 2:
+ print format_usage()
+ sys.exit(1)
+ main(*sys.argv[1:])
diff --git a/extras/soap-tools/mappingInfo.py b/extras/soap-tools/mappingInfo.py
index 9f5f724f..3fc0dda3 100755
--- a/extras/soap-tools/mappingInfo.py
+++ b/extras/soap-tools/mappingInfo.py
@@ -22,8 +22,7 @@ from suds.client import Client
from mutalyzer.util import format_usage
-#WSDL_LOCATION = 'http://localhost/mutalyzer/services/?wsdl'
-WSDL_LOCATION = 'https://mutalyzer.nl/services/?wsdl'
+WSDL_LOCATION = 'http://localhost/mutalyzer/services/?wsdl'
def main(transcript, variant, build='hg19'):
@@ -34,7 +33,6 @@ def main(transcript, variant, build='hg19'):
result = service.mappingInfo(LOVD_ver='3.0-beta-06', build=build,
accNo=transcript, variant=variant)
- print result
if result:
print 'Genomic start: %s' % result.start_g
print 'Genomic end: %s' % result.end_g
--
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