From 383b55f86e609d6244e840e61d2c59df2c3887d8 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Thu, 10 Nov 2011 15:25:58 +0000
Subject: [PATCH] Add restriction site effects to batch output
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@417 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
extras/config.example | 3 ++-
...5-config-batch-restriction-sites.migration | 25 +++++++++++++++++++
mutalyzer/util.py | 2 +-
mutalyzer/variantchecker.py | 11 ++++++++
tests/test_website.py | 20 +++++++++++++++
5 files changed, 59 insertions(+), 2 deletions(-)
create mode 100755 extras/migrations/005-config-batch-restriction-sites.migration
diff --git a/extras/config.example b/extras/config.example
index 4bbecc30..df98ac59 100644
--- a/extras/config.example
+++ b/extras/config.example
@@ -109,7 +109,8 @@ PIDfile = "/var/run/mutalyzer/mutalyzer-batchd.pid"
batchInputMaxSize = 5
# The output header for NameChecking
-nameCheckOutHeader = "Input", "Errors | Messages", "AccNo", "Genesymbol", "Variant", "Reference Sequence Start Descr.", "Coding DNA Descr.", "Protein Descr.", "GeneSymbol Coding DNA Descr.", "GeneSymbol Protein Descr.", "Genomic Reference", "Coding Reference", "Protein Reference", "Affected Transcripts", "Affected Proteins"
+# Todo: migration for restriction sites
+nameCheckOutHeader = "Input", "Errors | Messages", "AccNo", "Genesymbol", "Variant", "Reference Sequence Start Descr.", "Coding DNA Descr.", "Protein Descr.", "GeneSymbol Coding DNA Descr.", "GeneSymbol Protein Descr.", "Genomic Reference", "Coding Reference", "Protein Reference", "Affected Transcripts", "Affected Proteins", "Restriction Sites Created", "Restriction Sites Deleted"
# The output header for SyntaxChecking
syntaxCheckOutHeader = "Input", "Status"
diff --git a/extras/migrations/005-config-batch-restriction-sites.migration b/extras/migrations/005-config-batch-restriction-sites.migration
new file mode 100755
index 00000000..36a040fc
--- /dev/null
+++ b/extras/migrations/005-config-batch-restriction-sites.migration
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+# Add batch checker restriction sites headers to the configuration file.
+#
+# Usage:
+# ./005-config-batch-restriction-sites.migration [migrate]
+
+COLOR_INFO='\033[32m'
+COLOR_WARNING='\033[33m'
+COLOR_ERROR='\033[31m'
+COLOR_END='\033[0m'
+
+if [ -e /etc/mutalyzer/config ] && $(grep -q '^nameCheckOutHeader = "Input", "Errors | Messages", "AccNo", "Genesymbol", "Variant", "Reference Sequence Start Descr.", "Coding DNA Descr.", "Protein Descr.", "GeneSymbol Coding DNA Descr.", "GeneSymbol Protein Descr.", "Genomic Reference", "Coding Reference", "Protein Reference", "Affected Transcripts", "Affected Proteins"$' /etc/mutalyzer/config); then
+ echo -e "${COLOR_WARNING}This migration is needed.${COLOR_END}"
+ if [ "$1" = 'migrate' ]; then
+ echo 'Performing migration.'
+ echo -e "${COLOR_INFO}Copying /etc/mutalyzer/config to /etc/mutalyzer/config.backup${COLOR_END}"
+ cp /etc/mutalyzer/config /etc/mutalyzer/config.backup
+ sed -i 's/nameCheckOutHeader = "Input", "Errors | Messages", "AccNo", "Genesymbol", "Variant", "Reference Sequence Start Descr.", "Coding DNA Descr.", "Protein Descr.", "GeneSymbol Coding DNA Descr.", "GeneSymbol Protein Descr.", "Genomic Reference", "Coding Reference", "Protein Reference", "Affected Transcripts", "Affected Proteins"/nameCheckOutHeader = "Input", "Errors | Messages", "AccNo", "Genesymbol", "Variant", "Reference Sequence Start Descr.", "Coding DNA Descr.", "Protein Descr.", "GeneSymbol Coding DNA Descr.", "GeneSymbol Protein Descr.", "Genomic Reference", "Coding Reference", "Protein Reference", "Affected Transcripts", "Affected Proteins", "Restriction Sites Created", "Restriction Sites Deleted"/' /etc/mutalyzer/config
+ echo -e "${COLOR_INFO}Added batch checker restriction sites headers to /etc/mutalyzer/config${COLOR_END}"
+ echo 'Performed migration.'
+ fi
+else
+ echo -e "${COLOR_INFO}This migration is not needed.${COLOR_END}"
+fi
diff --git a/mutalyzer/util.py b/mutalyzer/util.py
index 8738bbca..e340ebe5 100644
--- a/mutalyzer/util.py
+++ b/mutalyzer/util.py
@@ -768,7 +768,7 @@ def slow(f):
and os.environ['MUTALYZER_QUICK_TEST'] == '1':
return
else:
- f(*args, **kwargs)
+ return f(*args, **kwargs)
return slow_f
#slow
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index 7ece5cbe..ab4f62a0 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -256,6 +256,17 @@ def _add_batch_output(O):
else:
outputline += "\t"*2
+ # Add effects on restriction sites as two columns (created and deleted).
+ # The value for each column is a semicolon-separated list of
+ # comma-separated lists: for each raw variant, a list of restriction
+ # sites.
+ sites_created = []
+ sites_deleted = []
+ for variant in O.getOutput("restrictionSites"):
+ sites_created.append(','.join(variant[0]))
+ sites_deleted.append(','.join(variant[1]))
+ outputline += "%s\t%s\t" % (';'.join(sites_created), ';'.join(sites_deleted))
+
#Link naar additional info:
#outputline+="http://localhost/mutalyzer2/redirect?mutationName=%s" %\
# "todovariant"
diff --git a/tests/test_website.py b/tests/test_website.py
index 97a67cd5..438b9e71 100644
--- a/tests/test_website.py
+++ b/tests/test_website.py
@@ -461,6 +461,26 @@ class TestWSGI():
size=len(variants)-1,
header='Input\tStatus')
+ @slow
+ def test_batch_namechecker_restriction_sites(self):
+ """
+ Submit the batch name checker form and see if restriction site effects
+ are added.
+
+ Note that we use the @slow decorator here even though it is already
+ applied to self._batch. The reason is that we use the result from
+ self._batch, which does not exist if @slow checks are disabled.
+ """
+ variants=['AB026906.1:c.274G>T',
+ 'AB026906.1:c.[274G>T;143A>G;15G>T]']
+ results = self._batch('NameChecker',
+ file='\n'.join(variants),
+ size=len(variants),
+ header='Input\tErrors | Messages')
+ assert 'Restriction Sites Created\tRestriction Sites Deleted' in results[0]
+ assert 'CviQI,RsaI\tBccI' in results[1]
+ assert 'CviQI,RsaI;HinP1I,HhaI;SfcI\tBccI;;BpmI,MnlI,BsaXI (2),Hpy188III' in results[2]
+
@slow
def test_batch_syntaxchecker_toobig(self):
"""
--
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