New feature, query MySQL database directly

Tool to replace perl tool and query Ensembl MySQL database directly.
Initial commit, basic usage

MANIFEST.in

@@ -1,7 +1,7 @@
 include README.md
 include agfusion/data/agfusion.db
 include bin/agfusion
-include bin/build_db
+include bin/agfusion_builddb
 include test/test.py
 include test/test_mouse.sh
-include test/test_human.sh
+include test/test_human.sh

README.md

@@ -3,7 +3,7 @@ For a given gene fusion, AGFusion will predict the cDNA, CDS, and protein sequen
 
 Docs are at http://pythonhosted.org/agfusion/
 
-# Example Usage
+# Examples
 
 ### Basic Usage
 
@@ -101,6 +101,12 @@ agfusion \
 ![alt tag](https://github.com/murphycj/AGFusion/blob/master/doc/ENSMUST00000132176-ENSMUST00000002487-scale.png)
 ![alt tag](https://github.com/murphycj/AGFusion/blob/master/doc/ENSMUST00000120187-ENSMUST00000086074.png)
 
+# Advanced Usage
+
+### Building your own database
+
+You need to have mysql and the MySQLdb python package installed.
+
 # Installation
 
 First you need to install pyensembl (and the other dependencies listed at the bottom of this readme) and download the reference genome you will use by running one of the following.

agfusion/cli.py

@@ -8,9 +8,57 @@
 import agfusion
 import pyensembl
 
+
+def builddb():
+
+    parser = argparse.ArgumentParser(
+        description='Build the SQLite3 database for a reference ' +
+        'genomes by querying Biomart. The the database given by --database ' +
+        'already exists then that portion will be overwritten.'
+    )
+    parser.add_argument(
+        '--database',
+        type=str,
+        required=True,
+        help='Path to the database file (e.g. agfusion.db)'
+    )
+    parser.add_argument(
+        '--build',
+        type=str,
+        required=True,
+        help='homo_sapiens_core_84_38 (for GRCh38), ' +
+        'homo_sapiens_core_75_37 (for GRCh37), or ' +
+        'mus_musculus_core_75_38 (for GRCm38)'
+    )
+    parser.add_argument(
+        '--server',
+        type=str,
+        required=False,
+        default='ensembldb.ensembl.org',
+        help='(optional) Ensembl server (default ensembldb.ensembl.org)'
+    )
+    args = parser.parse_args()
+
+    db = agfusion.AGFusionDBBManager(args.database, args.build, args.server)
+
+    db.logger.info('Fetching alternative gene names...')
+
+    #db.fetch_gene_names()
+
+    db.logger.info('Fetching transcript tables...')
+
+    db.fetch_transcript_table()
+
+    db.logger.info('Fetching protein annotation data...')
+
+    db.fetch_protein_annotation()
+
+
 def main():
 
-    parser = argparse.ArgumentParser(description='Annotate Gene Fusion (AGFusion)')
+    parser = argparse.ArgumentParser(
+        description='Annotate Gene Fusion (AGFusion)'
+    )
     parser.add_argument(
         '--gene5prime',
         type=str,
@@ -27,16 +75,16 @@ def main():
         '--junction5prime',
         type=int,
         required=True,
-        help='Genomic location of predicted fuins for the 5\' gene partner. ' + \
-             'The 1-based position that is the last nucleotide included in ' + \
+        help='Genomic location of predicted fuins for the 5\' gene partner. ' +
+             'The 1-based position that is the last nucleotide included in ' +
              'the fusion before the junction.'
     )
     parser.add_argument(
         '--junction3prime',
         type=int,
         required=True,
-        help='Genomic location of predicted fuins for the 3\' gene partner. ' + \
-             'The 1-based position that is the first nucleotide included in ' + \
+        help='Genomic location of predicted fuins for the 3\' gene partner. ' +
+             'The 1-based position that is the first nucleotide included in ' +
              'the fusion after the junction.'
     )
     parser.add_argument(
@@ -56,26 +104,28 @@ def main():
         type=str,
         default=None,
         required=False,
-        help='(Optional) The SQLite3 database. Defaults to using the database provided by the package.'
+        help='(Optional) The SQLite3 database. Defaults to using the ' +
+             'database provided by the package.'
     )
     parser.add_argument(
         '--noncanonical',
         action='store_true',
         required=False,
         default=False,
-        help='(Optional) Include non-canonical gene transcripts in the analysis (default False).'
+        help='(Optional) Include non-canonical gene transcripts ' +
+             'in the analysis (default False).'
     )
     parser.add_argument(
         '--protein_databases',
         type=str,
         required=False,
         nargs='+',
-        default=['pfam','tmhmm'],
-        help='(Optional) Space-delimited list of one or more protein ' + \
-             'feature databases to include when visualizing proteins. ' + \
-             'Options are: pfam, tigrfam, prints, hmmpanther, ' + \
-             'blastprodom, gene3d, hamap, pirsf, ncoils, superfamily, seg, ' + \
-             'signalp, scanprosite, pfscan, tmhmm, and smart. ' + \
+        default=['pfam', 'tmhmm'],
+        help='(Optional) Space-delimited list of one or more protein ' +
+             'feature databases to include when visualizing proteins. ' +
+             'Options are: pfam, tigrfam, prints, hmmpanther, ' +
+             'blastprodom, gene3d, hamap, pirsf, ncoils, superfamily, seg, ' +
+             'signalp, scanprosite, pfscan, tmhmm, and smart. ' +
              '(default includes pfam and tmhmm).'
     )
     parser.add_argument(
@@ -84,10 +134,10 @@ def main():
         required=False,
         nargs='+',
         default=None,
-        help='(Optional) Space-delimited list of domain name and color to ' + \
-            'specify certain colors for domains. Format --color domain_name:color' + \
-            ' (e.g. --color Pkinase_Tyr:blue I-set:#006600). ' + \
-            'Can use specific color names for hex representation. Default ' + \
+        help='(Optional) Space-delimited list of domain name and color to ' +
+            'specify certain colors for domains. Format --color domain_name:color' +
+            ' (e.g. --color Pkinase_Tyr:blue I-set:#006600). ' +
+            'Can use specific color names for hex representation. Default ' +
             'blue for everything.'
     )
     parser.add_argument(
@@ -96,8 +146,8 @@ def main():
         required=False,
         nargs='+',
         default=None,
-        help='(Optional) Space-delimited list of domain name and new name to ' + \
-            'rename particular domains. Format --rename domain_name:new_domain_name' + \
+        help='(Optional) Space-delimited list of domain name and new name to ' +
+            'rename particular domains. Format --rename domain_name:new_domain_name' +
             ' (e.g. --rename Pkinase_Tyr:Kinase).'
     )
     parser.add_argument(