From 42e2f88a0777b7a05e8fc5f49ebd5aca13740e38 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Wed, 25 Mar 2015 17:11:03 +0100
Subject: [PATCH] Use esummary 2.0 response format
---
mutalyzer/Retriever.py | 27 ++++++++++++++++++---------
1 file changed, 18 insertions(+), 9 deletions(-)
diff --git a/mutalyzer/Retriever.py b/mutalyzer/Retriever.py
index e22536e3..cc6f9193 100644
--- a/mutalyzer/Retriever.py
+++ b/mutalyzer/Retriever.py
@@ -585,24 +585,33 @@ class GenBankRetriever(Retriever):
'Could not get mapping information for gene %s.' % gene)
return None
- if unicode(summary[0]["NomenclatureSymbol"]).lower() == gene.lower() : # Found it.
- if not summary[0]["GenomicInfo"] :
+ try:
+ document = summary['DocumentSummarySet']['DocumentSummary'][0]
+ except (KeyError, IndexError):
+ self._output.addMessage(__file__, -1, 'INFO',
+ 'Error parsing Entrez esummary result.')
+ self._output.addMessage(__file__, 4, 'ERETR',
+ 'Could not get mapping information for gene %s.' % gene)
+ return None
+
+ if unicode(document["NomenclatureSymbol"]).lower() == gene.lower() : # Found it.
+ if not document["GenomicInfo"] :
self._output.addMessage(__file__, 4, "ENOMAPPING",
"No mapping information found for gene %s." % gene)
return None
#if
- ChrAccVer = unicode(summary[0]["GenomicInfo"][0]["ChrAccVer"])
- ChrLoc = unicode(summary[0]["GenomicInfo"][0]["ChrLoc"])
- ChrStart = int(summary[0]["GenomicInfo"][0]["ChrStart"])
- ChrStop = int(summary[0]["GenomicInfo"][0]["ChrStop"])
+ ChrAccVer = unicode(document["GenomicInfo"][0]["ChrAccVer"])
+ ChrLoc = unicode(document["GenomicInfo"][0]["ChrLoc"])
+ ChrStart = int(document["GenomicInfo"][0]["ChrStart"])
+ ChrStop = int(document["GenomicInfo"][0]["ChrStop"])
break
#if
# Collect official symbols that has this gene as alias in case we
# can not find anything.
- if gene in [unicode(a) for a in summary[0]["OtherAliases"]] and \
- summary[0]["NomenclatureSymbol"] :
- aliases.append(unicode(summary[0]["NomenclatureSymbol"]))
+ if gene in [unicode(a) for a in document["OtherAliases"]] and \
+ document["NomenclatureSymbol"] :
+ aliases.append(unicode(document["NomenclatureSymbol"]))
#for
if not ChrAccVer : # We did not find any genes.
--
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