merged

README.md

@@ -1,32 +1,33 @@
-pita improves transcript annotation 
-===================================
-
-Pipeline to improve transcript annotation based on RNA-seq and ChIP-seq data.
-
-The current version has been used to annotate the Xenopus laevis genome based on experimental data.
-
-However, it is not yet easy to install and use as the documentation is incomplete. 
-In addition  the tools have not been thoroughly tested on a clean installation, 
-which means I'm not sure all dependencies have been correctly specified.
-
-Prerequisites
-------------
-The following Python modules are required:
-
-* GFF parser - http://github.com/chapmanb/bcbb/tree/master/gff
-* Biopython - http://biopython.org/
-* pysam (>= 0.7.4)
-* pyyaml
-* networkx (>= 1.9)
-* GimmeMotifs - http://github.com/simonvh/gimmemotifs
-* HTSeq - http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
-* numpy
-
-Installation
-------------
-
-    # install prerequisites
-    git clone [email protected]:simonvh/pita.git
-    cd pita
-    python setup.py test
-    sudo python setup.py install
+pita improves transcript annotation 
+===================================
+
+Pipeline to improve transcript annotation based on RNA-seq and ChIP-seq data.
+
+The current version has been used to annotate the Xenopus laevis genome based on experimental data.
+
+However, it is not yet easy to install and use as the documentation is incomplete. 
+In addition  the tools have not been thoroughly tested on a clean installation, 
+which means I'm not sure all dependencies have been correctly specified.
+
+Prerequisites
+------------
+The following Python modules are required:
+
+* GFF parser - http://github.com/chapmanb/bcbb/tree/master/gff
+* Biopython - http://biopython.org/
+* pysam (>= 0.7.4)
+* pyyaml
+* networkx (>= 1.9)
+* GimmeMotifs - http://github.com/simonvh/gimmemotifs
+* HTSeq - http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
+* numpy
+
+Installation
+------------
+
+    # install prerequisites
+    git clone [email protected]:simonvh/pita.git
+    cd pita
+    python setup.py test
+    sudo python setup.py install
+

config/example.yaml

@@ -1,5 +1,17 @@
 # Path to data files. Data files can be specified relative to this path
 data_path: /home/simon/prj/laevis/annotation/XENLA_JGI7b/pita/data
+genome: /usr/share/genome/XENLA_JGIv7b
+
+# Database connection details
+# 
+# For file-based sqlite connection:
+# database: sqlite:///database.db
+#
+# For mysql: mysql://user:password@server/database
+# For example:
+# database: mysql://pita:@localhost/pita
+
+database: sqlite:///pita_database.db
 
 # Comment to process all chromosomes
 chromosomes:

pita/__init__.py

@@ -0,0 +1,20 @@
+import sys
+import atexit
+from pita.db_backend import *
+
+def db_session(conn, new=False):
+    if not hasattr(db_session, 'session') or not db_session.session:
+        engine = create_engine(conn)
+        engine.raw_connection().connection.text_factory = str
+        db_session.engine = engine
+        if new:
+            Base.metadata.drop_all(db_session.engine)
+        Base.metadata.create_all(engine)
+        Base.metadata.bind = engine
+        db_session.session = scoped_session(sessionmaker(bind=engine))
+    elif new:
+        db_session.session.commit()
+        Base.metadata.drop_all(db_session.engine)
+        Base.metadata.create_all(db_session.engine)
+
+    return db_session.session