From 4db71666f8d86dd7b6a8db83561369f2b539d58a Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Fri, 18 Dec 2015 18:04:52 +0100
Subject: [PATCH] Create legend only after gene model enrichment
This fixes a bug where transcripts created from CDS by construction did
not show up in the legend because the legend was created before that
construction.
---
mutalyzer/variantchecker.py | 36 +++++++++++++++++++-----------------
tests/test_variantchecker.py | 12 ++++++++++++
2 files changed, 31 insertions(+), 17 deletions(-)
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index 9da54db8..a47d80e9 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -1773,23 +1773,6 @@ def check_variant(description, output):
record = GenRecord.GenRecord(output)
record.record = retrieved_record
- # Create the legend.
- for gene in record.record.geneList:
- for transcript in sorted(gene.transcriptList, key=attrgetter('name')):
- if not transcript.name:
- continue
- output.addOutput('legends',
- ['%s_v%s' % (gene.name, transcript.name),
- transcript.transcriptID, transcript.locusTag,
- transcript.transcriptProduct,
- transcript.linkMethod])
- if transcript.translate:
- output.addOutput('legends',
- ['%s_i%s' % (gene.name, transcript.name),
- transcript.proteinID, transcript.locusTag,
- transcript.proteinProduct,
- transcript.linkMethod])
-
# Note: The GenRecord instance is carrying the sequence in .record.seq.
# So is the Mutator instance in .mutator.orig.
@@ -1802,6 +1785,25 @@ def check_variant(description, output):
process_variant(mutator, parsed_description, record, output)
except _VariantError:
return
+ finally:
+ # The legend needs to be created after processing the variant (which
+ # enriches the gene model by calling record.checkRecord), but we can
+ # create it regardless of success or failure.
+ for gene in record.record.geneList:
+ for transcript in sorted(gene.transcriptList, key=attrgetter('name')):
+ if not transcript.name:
+ continue
+ output.addOutput('legends',
+ ['%s_v%s' % (gene.name, transcript.name),
+ transcript.transcriptID, transcript.locusTag,
+ transcript.transcriptProduct,
+ transcript.linkMethod])
+ if transcript.translate:
+ output.addOutput('legends',
+ ['%s_i%s' % (gene.name, transcript.name),
+ transcript.proteinID, transcript.locusTag,
+ transcript.proteinProduct,
+ transcript.linkMethod])
output.addOutput('original', unicode(mutator.orig))
output.addOutput('mutated', unicode(mutator.mutated))
diff --git a/tests/test_variantchecker.py b/tests/test_variantchecker.py
index 1f9cd1c2..897a3e08 100644
--- a/tests/test_variantchecker.py
+++ b/tests/test_variantchecker.py
@@ -1578,3 +1578,15 @@ def test_start_codon_alt_start_yield_start(output, checker):
assert output.getOutput('oldProtein')[0].startswith('M')
assert 'ATG' in output.getOutput('altStart')
assert output.getOutput('altProtein')[0].startswith('M')
+
+
+@with_references('AB026906.1')
+def test_legend_mrna_by_construction(output, checker):
+ """
+ Transcript created from CDS by construction should be in the legend.
+ """
+ checker('AB026906.1:g.7872G>T')
+ assert output.getOutput('legends') == [
+ ['SDHD_v001', None, None, None, 'construction'],
+ ['SDHD_i001', 'BAA81889.1', None, 'small subunit of cytochrome b of succinate dehydrogenase', 'construction']
+ ]
--
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