From a03ab8f29407ddbdfc70e3eb60c3fb2fe105e9fd Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Wed, 26 Mar 2014 14:34:16 +0100
Subject: [PATCH] In LRG, ignore transcripts without a fixed id
Because we don't know how to name them anyway. We also ignore genes
without any transcripts.
---
mutalyzer/parsers/lrg.py | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/mutalyzer/parsers/lrg.py b/mutalyzer/parsers/lrg.py
index d8f742c8..d3624360 100644
--- a/mutalyzer/parsers/lrg.py
+++ b/mutalyzer/parsers/lrg.py
@@ -254,6 +254,9 @@ def genesFromUpdatable(updParsed):
transcripts = transcriptsFromParsed(geneData["transcripts"])
if not transcripts:
transcripts = _emptyTranscripts(geneData)
+ # Todo: For now we skip genes for which we have no transcripts
+ # since we don't know how to name them anyway.
+ continue
gene.transcriptList = transcripts
genes.append(gene)
#for
@@ -286,8 +289,10 @@ def transcriptsFromParsed(parsedData):
# Second add the transcripts not linked
# FIXME: How to name these transcripts?
- for trData in nofixed:
- transcripts.append(_transcriptPopulator("", trData))
+ # Todo: For now we skip these transcripts since we don't know how to name
+ # them.
+ #for trData in nofixed:
+ # transcripts.append(_transcriptPopulator("", trData))
return transcripts
#transcriptsFromParsed
--
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