changeset 6:c15476d4271c draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ commit af1fd308dde99cf40a9422c53dc680932be3765d

--- a/gafa_datatypes.py	Fri Mar 24 12:14:31 2017 -0400
+++ b/gafa_datatypes.py	Tue Mar 20 11:06:51 2018 -0400
@@ -40,12 +40,17 @@
         return False
 
 
-# Since Binary.register_sniffable_binary_format() ignores the sniff order declared in datatypes_conf.xml and put TS datatypes at the end, instead of simply doing:
+# Since in Galaxy < 18.01 Binary.register_sniffable_binary_format() ignores the
+# sniff order declared in datatypes_conf.xml and put TS datatypes at the end,
+# instead of simply doing:
 # Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite)
 # we need to register specialized SQLite datatypes before SQlite
-for i, format_dict in enumerate(Binary.sniffable_binary_formats):
-    if format_dict['class'] == SQlite:
-        break
-else:
-    i += 1
-Binary.sniffable_binary_formats.insert(i, {'type': 'gafa.sqlite', 'ext': 'gafa.sqlite', 'class': GAFASQLite})
+try:
+    for i, format_dict in enumerate(Binary.sniffable_binary_formats):
+        if format_dict['class'] == SQlite:
+            break
+    else:
+        i += 1
+    Binary.sniffable_binary_formats.insert(i, {'type': 'gafa.sqlite', 'ext': 'gafa.sqlite', 'class': GAFASQLite})
+except AttributeError:
+    pass

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/schema/gafa.sql	Tue Mar 20 11:06:51 2018 -0400
@@ -0,0 +1,25 @@
+CREATE TABLE meta (
+        version VARCHAR PRIMARY KEY NOT NULL);
+CREATE TABLE gene (
+        gene_id VARCHAR PRIMARY KEY NOT NULL,
+        gene_symbol VARCHAR,
+        species VARCHAR NOT NULL,
+        gene_json VARCHAR NOT NULL);
+CREATE INDEX gene_symbol_index ON gene (gene_symbol);
+CREATE TABLE transcript (
+        transcript_id VARCHAR PRIMARY KEY NOT NULL,
+        protein_id VARCHAR UNIQUE,
+        protein_sequence VARCHAR,
+        gene_id VARCHAR NOT NULL REFERENCES gene(gene_id));
+CREATE VIEW transcript_species as
+        SELECT transcript_id, species 
+        FROM transcript JOIN gene
+        ON transcript.gene_id = gene.gene_id;
+CREATE TABLE gene_family (
+        gene_family_id INTEGER PRIMARY KEY,
+        gene_tree VARCHAR NOT NULL);
+CREATE TABLE gene_family_member (
+        gene_family_id INTEGER NOT NULL REFERENCES gene_family(gene_family_id),
+        protein_id VARCHAR KEY NOT NULL REFERENCES transcript(protein_id),
+        protein_alignment VARCHAR NOT NULL,
+        PRIMARY KEY (gene_family_id, protein_id));