diff --git a/INSTALL b/INSTALL
index 870d2b4afb597306ae488812a2bb4f1e792757bb..511ed443201ad7ebdb8f8011bcddee06e58c31ec 100644
--- a/INSTALL
+++ b/INSTALL
@@ -144,6 +144,12 @@ directory:
sudo bash extras/post-upgrade
If you installed Mutalyzer in a development environment, you don't have to
-do anything to upgrade except for running the automated migration scripts:
+do anything usually, except for the following situations.
+
+* If the database has changed, run:
for M in extras/migrations/*.migration; do sudo $M migrate; done
+
+* If the Mutalyzer version has changed, run:
+
+ sudo python setup.py develop
diff --git a/README b/README
index 1390caec4c4de2fb6a20c477ef9d13f1e4155c70..a10d1b298c5f2e5a61f3ab895ac8923a09a0f6cf 100644
--- a/README
+++ b/README
@@ -34,6 +34,80 @@ Or, if you are in a hurry, skip the long-running tests with:
MUTALYZER_ENV=test MUTALYZER_QUICK_TEST=1 nosetests -v
+Release management
+------------------
+
+The current Mutalyzer version is recorded in `mutalyzer/__init__.py`. See the
+comments in that file for more info of the versioning scheme.
+
+On the event of a new release, the following is done:
+
+ emacs mutalyzer/__init__.py
+
+Remove `'dev'` from `__version_info__` and set `RELEASE` to `True`.
+
+ svn commit -m 'Release 2.0.beta-11'
+ svn cp https://humgenprojects.lumc.nl/svn/mutalyzer/trunk \
+ https://humgenprojects.lumc.nl/svn/mutalyzer/tags/mutalyzer-2.0.beta-11 \
+ -m 'Tag 2.0.beta-11'
+ emacs mutalyzer/__init__.py
+
+Set `__version_info__` to a new version ending with `'dev'` and set `RELEASE`
+to `FALSE`.
+
+ svn commit -m 'Open development for 2.0.beta-12'
+
+Be sure to upgrade your installations to the new version as described in the
+INSTALL file (e.g. `sudo python setup.py develop` for development checkouts).
+
+
+Working with feature branches
+-----------------------------
+
+Some features are best developed isolated in a separate branch (a 'feature
+branch') before being merged into trunk. To make it easier to switch between
+branches, don't checkout the entire repository tree from its root. Instead,
+checkout the branch subdirectory (or trunk) directly and use `svn switch` to
+switch between them. Otherwise, you might need to update you Apache config and
+run `sudo python setup.py develop` every time you switch branches.
+
+To create the branch from current trunk:
+
+ svn cp https://humgenprojects.lumc.nl/svn/mutalyzer/trunk \
+ https://humgenprojects.lumc.nl/svn/mutalyzer/branches/my-feature-branch \
+ -m 'Create my-feature-branch from trunk'
+
+To work from this branch, switch your checkout to there:
+
+ svn switch https://humgenprojects.lumc.nl/svn/mutalyzer/branches/my-feature-branch
+
+To make it easier to reintegrate long-running branches, you can periodically
+merge trunk into them:
+
+ svn merge https://humgenprojects.lumc.nl/svn/mutalyzer/trunk
+
+Use `mergeinfo` to see which revisions are already merged. You can cherry-pick
+revisions to merge by using the `-c` option:
+
+ svn mergeinfo https://humgenprojects.lumc.nl/svn/mutalyzer/trunk \
+ --show-revs eligible
+ svn merge -c 354 https://humgenprojects.lumc.nl/svn/mutalyzer/trunk
+
+If you just want to mark a revision as being merged, you can use the
+`--record-only` switch.
+
+Reintegrating a branch into trunk is done from the trunk checkout:
+
+ svn switch https://humgenprojects.lumc.nl/svn/mutalyzer/trunk
+ svn merge --reintegrate --dry-run \
+ https://humgenprojects.lumc.nl/svn/mutalyzer/branches/my-feature-branch
+ svn rm https://humgenprojects.lumc.nl/svn/mutalyzer/branches/my-feature-branch \
+ -m 'Delete refactor-mutalyzer-branch'
+
+All `merge` operations taken an optional `--dry-run` switch. Use it to see
+what would happen without having to actually applying.
+
+
Development notes
-----------------
@@ -77,6 +151,8 @@ Todo list:
Good read: http://news.ycombinator.com/item?id=3002861
Suggestion: http://celeryproject.org/
- Have a normal 404 page.
+- Maintenance (and/or read-only) mode.
+- Cleanup this document.
Code style guide:
- Follow PEP 8 (code) and PEP 257 (docstrings).
diff --git a/extras/cron.d/mutalyzer-cache-sync b/extras/cron.d/mutalyzer-cache-sync
index c58ea7742d54a461e7a93ee102cd6c9a3274a492..02d3e0a349e261bdae898929d7629a768fdde4f5 100644
--- a/extras/cron.d/mutalyzer-cache-sync
+++ b/extras/cron.d/mutalyzer-cache-sync
@@ -1,2 +1,2 @@
# Synchronize the local cache with the live server every morning at 05:25
-#25 5 * * * www-data <MUTALYZER_BIN_CACHE_SYNC> 'http://www.mutalyzer.nl/2.0/services/?wsdl' 'http://www.mutalyzer.nl/2.0/Reference/{file}' 3
+#25 5 * * * www-data <MUTALYZER_BIN_CACHE_SYNC> 'https://mutalyzer.nl/services/?wsdl' 'https://mutalyzer.nl/Reference/{file}' 3
diff --git a/extras/migrations/001-db-gbinfo-add-created.migration b/extras/migrations/001-db-gbinfo-add-created.migration
index 26fd668a98012159486e81b7f6853f09cbf91e1e..686563ce39af39dddd5fe1e66afcab9e10a69721 100755
--- a/extras/migrations/001-db-gbinfo-add-created.migration
+++ b/extras/migrations/001-db-gbinfo-add-created.migration
@@ -36,6 +36,7 @@ def migrate():
ALTER TABLE GBInfo
ADD COLUMN created TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP,
ADD INDEX created (created);""")
+ cursor.execute('UPDATE GBInfo SET created = CURRENT_TIMESTAMP;')
connection.commit()
connection.close()
migration.info('Added column mutalyzer.GBInfo.created')
diff --git a/extras/post-install.sh b/extras/post-install.sh
index d9dfa1ea798a7e7d8038d1530687275a7b06e909..9f7550db04398da04c0dfd3a8fb09788776edcd9 100644
--- a/extras/post-install.sh
+++ b/extras/post-install.sh
@@ -46,8 +46,9 @@ for USERNAME in $(cut -f 1 -d : /etc/passwd); do
echo -e "${COLOR_INFO}Creating /home/${USERNAME}/.cache/mutalyzer${COLOR_END}"
su $USERNAME -c "mkdir -p /home/$USERNAME/.config/mutalyzer"
su $USERNAME -c "mkdir -p /home/$USERNAME/.cache/mutalyzer"
- su $USERNAME -c "cp extras/config.user.example /home/$USERNAME/.config/mutalyzer/config"
+ su $USERNAME -c "touch /home/$USERNAME/.config/mutalyzer/config"
su $USERNAME -c "touch /tmp/mutalyzer-$USERNAME.log"
+ cat extras/config.user.example > /home/$USERNAME/.config/mutalyzer/config
sed -i -e "s@<USERNAME>@${USERNAME}@g" /home/$USERNAME/.config/mutalyzer/config
fi
done
diff --git a/extras/pre-install.sh b/extras/pre-install.sh
index 8af0b585beae93da581e28719483aa4324ff0f79..a49e65bc0ac8b1d293f0dd915fd84d67e508acf5 100644
--- a/extras/pre-install.sh
+++ b/extras/pre-install.sh
@@ -20,6 +20,7 @@ COLOR_END='\033[0m'
echo -e "${COLOR_INFO}Installing packages with apt${COLOR_END}"
+apt-get update && \
apt-get install -y \
mysql-server \
python \
diff --git a/mutalyzer/Crossmap.py b/mutalyzer/Crossmap.py
index cd289e3ebd5e558886bc1204401f4e81cb759847..20fb8edc6147cb09c289a7754ab8dd2180b6ca1b 100644
--- a/mutalyzer/Crossmap.py
+++ b/mutalyzer/Crossmap.py
@@ -428,8 +428,7 @@ class Crossmap() :
@return: The converted notation (may be unaltered)
@rtype: integer
"""
-
- if s[0] == '*' :
+ if s[0] == '*':
return self.__STOP + int(s[1:])
return int(s)
diff --git a/mutalyzer/Retriever.py b/mutalyzer/Retriever.py
index d77f7fa63b00c933ff71d36a520e77822b32fced..ded70bcc034d797cbe7a16ff5f2e6b87c706f288 100644
--- a/mutalyzer/Retriever.py
+++ b/mutalyzer/Retriever.py
@@ -19,6 +19,7 @@ import StringIO # StringIO()
from Bio import SeqIO # read()
from Bio import Entrez # efetch(), read(), esearch(), esummary()
from Bio.Seq import UnknownSeq
+from Bio.Alphabet import ProteinAlphabet
from xml.dom import DOMException, minidom
from xml.parsers import expat
@@ -734,7 +735,15 @@ class GenBankRetriever(Retriever):
# Now we have the file, so we can parse it.
GenBankParser = genbank.GBparser()
- return GenBankParser.create_record(filename)
+ record = GenBankParser.create_record(filename)
+
+ # Todo: This will change once we support protein references
+ if isinstance(record.seq.alphabet, ProteinAlphabet):
+ self._output.addMessage(__file__, 4, 'EPROTEINREF',
+ 'Protein reference sequences are not supported.')
+ return None
+
+ return record
#loadrecord
#GenBankRetriever
diff --git a/mutalyzer/mapping.py b/mutalyzer/mapping.py
index 0cb27e7e41ce749205850e094546b0176889f5f6..afc5b837d5de2c95dbecdf76cda037da772549ac 100644
--- a/mutalyzer/mapping.py
+++ b/mutalyzer/mapping.py
@@ -254,15 +254,27 @@ class Converter(object) :
@rtype: triple (integer, integer, integer)
"""
if Type == 'c' :
- main = C.main2int(Loc.MainSgn + Loc.Main)
- offset = C.offset2int(Loc.OffSgn + Loc.Offset)
- g = C.x2g(main, offset)
- main, offset = C.g2x(g)
- #if
- else :
- g = int(Loc.Main)
+ if Loc.IVSLoc:
+ ivs_number = int(Loc.IVSLoc.IVSNumber)
+ if ivs_number < 1 or ivs_number > C.numberOfIntrons():
+ # Todo: Error handling in this entire module is 'suboptimal'
+ raise Exception('Invalid intron')
+ if Loc.IVSLoc.OffSgn == '+':
+ g = C.getSpliceSite(ivs_number * 2 - 1) + \
+ C.orientation * int(Loc.IVSLoc.Offset)
+ else:
+ g = C.getSpliceSite(ivs_number * 2) - \
+ C.orientation * int(Loc.IVSLoc.Offset)
+ main, offset = C.g2x(g)
+ else:
+ main = C.main2int(Loc.PtLoc.MainSgn + Loc.PtLoc.Main)
+ offset = C.offset2int(Loc.PtLoc.OffSgn + Loc.PtLoc.Offset)
+ g = C.x2g(main, offset)
+ main, offset = C.g2x(g)
+ else:
+ g = int(Loc.PtLoc.Main)
main, offset = C.g2x(g)
- #else
+
return (main, offset, g)
#_getcoords
@@ -285,13 +297,13 @@ class Converter(object) :
# Get the coordinates of the start position
startmain, startoffset, start_g = \
- self._getcoords(Cross, mutation.StartLoc.PtLoc,
+ self._getcoords(Cross, mutation.StartLoc,
self.parseTree.RefType)
# If there is an end position, calculate the coordinates.
if mutation.EndLoc :
endmain, endoffset, end_g = \
- self._getcoords(Cross, mutation.EndLoc.PtLoc,
+ self._getcoords(Cross, mutation.EndLoc,
self.parseTree.RefType)
else :
end_g, endmain, endoffset = start_g, startmain, startoffset
diff --git a/mutalyzer/parsers/genbank.py b/mutalyzer/parsers/genbank.py
index 247bcfbed4ba01f1e85b49b46822e95627702523..4dff2aba049b98bb0d0cc6f5ff0c151a3d4f9a68 100644
--- a/mutalyzer/parsers/genbank.py
+++ b/mutalyzer/parsers/genbank.py
@@ -6,6 +6,7 @@ mutalyzer GenRecord. Record populated with data from a GenBank file.
import bz2
from Bio import SeqIO, Entrez
+from Bio.Alphabet import ProteinAlphabet
from mutalyzer.config import Config
from mutalyzer import Db
@@ -457,6 +458,10 @@ class GBparser():
# Todo: also set organism in the LRG parser
record.organism = biorecord.annotations['organism']
+ # Todo: This will change once we support protein references
+ if isinstance(biorecord.seq.alphabet, ProteinAlphabet):
+ return record
+
exonList = []
geneDict = {}
diff --git a/tests/test_website.py b/tests/test_website.py
index 61a7206ba4c2565311161a0f544d720c7e79cbcc..97a67cd5d36950d722d41e0fd0e28039df257316 100644
--- a/tests/test_website.py
+++ b/tests/test_website.py
@@ -175,6 +175,19 @@ class TestWSGI():
'0 Warnings',
'Details of the parse error')
+ def test_check_protein_reference(self):
+ """
+ Submit the name checker form with a protein reference sequence (not
+ supported).
+ """
+ r = self.app.get('/check')
+ form = r.forms[0]
+ form['mutationName'] = 'BAA81889.1:c.274G>T'
+ r = form.submit()
+ r.mustcontain('1 Error',
+ '0 Warnings',
+ 'Protein reference sequences are not supported')
+
def test_check_noninteractive(self):
"""
Submit the name checker form non-interactively.
@@ -589,6 +602,15 @@ facilisi."""
expected = '\n'.join(['-612', '7720', '2016'])
assert_equal(r.body, expected)
+ def test_variantinfo_ivs(self):
+ """
+ Test the /Variant_info interface used by LOVD2 (with IVS positioning).
+ """
+ r = self.app.get('/Variant_info?LOVD_ver=2.0-33&build=hg19&acc=NM_000249.3&var=c.IVS10%2B3A%3EG')
+ assert_equal(r.content_type, 'text/plain')
+ expected = '\n'.join(['884', '3', '884', '3', '37059093', '37059093', 'subst'])
+ assert_equal(r.body, expected)
+
def test_upload_local_file(self):
"""
Test the genbank uploader.