# HG changeset patch
# User earlhaminst
# Date 1489623658 14400
# Node ID 117fc741430706dfe2b2911728da8f8f86a6f656
# Parent  e17a3470c70a201c544a197f959edb14007eada9
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ commit 651fae48371f845578753052c6fe173e3bb35670

diff -r e17a3470c70a -r 117fc7414307 GAFA.py
--- a/GAFA.py	Fri Mar 03 07:20:23 2017 -0500
+++ b/GAFA.py	Wed Mar 15 20:20:58 2017 -0400
@@ -1,12 +1,12 @@
 from __future__ import print_function
 
 import collections
-import json
 import optparse
 import re
+import shutil
 import sqlite3
 
-version = "0.2.0"
+version = "0.3.0"
 
 Sequence = collections.namedtuple('Sequence', ['header', 'sequence'])
 
@@ -50,29 +50,19 @@
 
 def create_tables(conn):
     cur = conn.cursor()
-    cur.execute('PRAGMA foreign_keys = ON')
-    cur.execute('''CREATE TABLE meta (
-        version VARCHAR)''')
-
-    cur.execute('INSERT INTO meta (version) VALUES (?)',
+    # Check that the version of the input database is compatible
+    cur.execute('SELECT version FROM meta')
+    result = cur.fetchone()
+    input_meta_version = result[0]
+    if input_meta_version != '0.3.0':
+        raise Exception("Incompatible input meta version '%s'" % input_meta_version)
+    cur.execute('UPDATE meta SET version=?',
                 (version, ))
 
     cur.execute('''CREATE TABLE gene_family (
         gene_family_id INTEGER PRIMARY KEY,
         gene_tree VARCHAR NOT NULL)''')
 
-    cur.execute('''CREATE TABLE gene (
-        gene_id VARCHAR PRIMARY KEY NOT NULL,
-        gene_symbol VARCHAR,
-        gene_json VARCHAR NOT NULL)''')
-    cur.execute('CREATE INDEX gene_symbol_index ON gene (gene_symbol)')
-
-    cur.execute('''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))''')
-
     cur.execute('''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),
@@ -117,44 +107,23 @@
     conn.commit()
 
 
-def gene_json_to_db(conn, fname):
-    with open(fname) as f:
-        all_genes_dict = json.load(f)
-
-    cur = conn.cursor()
-    for gene_dict in all_genes_dict.values():
-        gene_id = gene_dict['id']
-        gene_symbol = gene_dict.get('display_name', None)
-        cur.execute("INSERT INTO gene (gene_id, gene_symbol, gene_json) VALUES (?, ?, ?)",
-                    (gene_id, gene_symbol, json.dumps(gene_dict)))
-
-        if "Transcript" in gene_dict:
-            for transcript in gene_dict["Transcript"]:
-                transcript_id = transcript['id']
-                if 'Translation' in transcript and 'id' in transcript['Translation']:
-                    protein_id = transcript["Translation"]["id"]
-                else:
-                    protein_id = None
-                cur.execute("INSERT INTO transcript (transcript_id, protein_id, gene_id) VALUES (?, ?, ?)",
-                            (transcript_id, protein_id, gene_id))
-    conn.commit()
-
-
 def __main__():
     parser = optparse.OptionParser()
     parser.add_option('-t', '--tree', action='append', help='Gene tree files')
     parser.add_option('-a', '--align', action='append', help='Protein alignments in fasta_aln format')
-    parser.add_option('-g', '--gene', help='Gene features file in JSON format')
+    parser.add_option('-g', '--gene', help='Gene features file in SQLite format')
     parser.add_option('-o', '--output', help='Path of the output file')
     options, args = parser.parse_args()
     if args:
         raise Exception('Use options to provide inputs')
 
+    if options.gene != options.output:
+        shutil.copyfile(options.gene, options.output)
+
     conn = sqlite3.connect(options.output)
+    conn.execute('PRAGMA foreign_keys = ON')
     create_tables(conn)
 
-    gene_json_to_db(conn, options.gene)
-
     for i, (tree, align) in enumerate(zip(options.tree, options.align), start=1):
         newicktree_to_db(conn, i, tree)
         align_to_db(conn, i, align)
diff -r e17a3470c70a -r 117fc7414307 GAFA.xml
--- a/GAFA.xml	Fri Mar 03 07:20:23 2017 -0500
+++ b/GAFA.xml	Wed Mar 15 20:20:58 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="gafa" name="Gene Align and Family Aggregator" version="0.2.0">
+<tool id="gafa" name="Gene Align and Family Aggregator" version="0.3.0">
     <description>generates an SQLite database that can be visualised with Aequatus</description>
     <command>
 <![CDATA[
@@ -16,7 +16,7 @@
     <inputs>
         <param name="treeFile" type="data" format="nhx" multiple="true" label="Gene tree" help="Gene tree in Newick format, e.g. generated from 'TreeBeST best' or 'Get gene tree by Ensembl ID' tool" />
         <param name="alignmentFile" type="data" format="fasta" multiple="true" label="Protein alignments" help="Protein alignments in fasta_aln format generated by T-Coffee" />
-        <param name="genesFile" type="data" format="json" label="Gene features" help="Gene features in JSON format generated by 'GFF3 to JSON' or 'Get features by Ensembl ID' tool" />
+        <param name="genesFile" type="data" format="sqlite" label="Gene features" help="Gene features in SQLite format generated by 'GSTF preparation' tool" />
     </inputs>
     <outputs>
         <data name="outputFile" format="gafa.sqlite" label="${tool.name} on ${on_string}" />
@@ -25,7 +25,7 @@
         <test>
             <param name="treeFile" ftype="nhx" value="tree1.nhx,tree2.nhx,tree3.nhx,tree4.nhx" />
             <param name="alignmentFile" ftype="fasta" value="align1.fasta,align2.fasta,align3.fasta,align4.fasta" />
-            <param name="genesFile" ftype="json" value="gene.json" />
+            <param name="genesFile" ftype="sqlite" value="gene.sqlite" />
             <output name="outputFile" file="test.gafa.sqlite" compare="sim_size" />
         </test>
     </tests>
diff -r e17a3470c70a -r 117fc7414307 schema/gafa.mwb
Binary file schema/gafa.mwb has changed
diff -r e17a3470c70a -r 117fc7414307 schema/gafa.png
Binary file schema/gafa.png has changed
diff -r e17a3470c70a -r 117fc7414307 schema/gafa.svg
--- a/schema/gafa.svg	Fri Mar 03 07:20:23 2017 -0500
+++ b/schema/gafa.svg	Wed Mar 15 20:20:58 2017 -0400
@@ -3,811 +3,865 @@
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diff -r e17a3470c70a -r 117fc7414307 test-data/gene.json
--- a/test-data/gene.json	Fri Mar 03 07:20:23 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9586 +0,0 @@
-{
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-      "display_name": "INSR", 
-      "description": "insulin receptor [Source:HGNC Symbol;Acc:HGNC:6091]", 
-      "seq_region_name": "19", 
-      "logic_name": "ensembl_havana_gene", 
-      "object_type": "Gene", 
-      "start": 7112255, 
-      "id": "ENSG00000171105", 
-      "source": "ensembl_havana", 
-      "db_type": "core", 
-      "version": 13, 
-      "biotype": "protein_coding", 
-      "end": 7294034, 
-      "Transcript": [
-         {
-            "assembly_name": "GRCh38", 
-            "display_name": "INSR-002", 
-            "Parent": "ENSG00000171105", 
-            "seq_region_name": "19", 
-            "logic_name": "ensembl_havana_transcript", 
-            "object_type": "Transcript", 
-            "start": 7112255, 
-            "id": "ENST00000341500", 
-            "source": "ensembl_havana", 
-            "version": 9, 
-            "Exon": [
-               {
-                  "assembly_name": "GRCh38", 
-                  "end": 7293931, 
-                  "start": 7293792, 
-                  "db_type": "core", 
-                  "object_type": "Exon", 
-                  "id": "ENSE00003071904", 
-                  "seq_region_name": "19", 
-                  "version": 1, 
-                  "species": "homosapiens", 
-                  "strand": -1
-               }, 
-               {
-                  "assembly_name": "GRCh38", 
-                  "end": 7267896, 
-                  "start": 7267345, 
-                  "db_type": "core", 
-                  "object_type": "Exon", 
-                  "id": "ENSE00003664284", 
-                  "seq_region_name": "19", 
-                  "version": 1, 
-                  "species": "homosapiens", 
-                  "strand": -1
-               }, 
-               {
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-                  "end": 7184637, 
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-                  "id": "ENSE00003682994", 
-                  "seq_region_name": "19", 
-                  "version": 1, 
-                  "species": "homosapiens", 
-                  "strand": -1
-               }, 
-               {
-                  "assembly_name": "GRCh38", 
-                  "end": 7174731, 
-                  "start": 7174583, 
-                  "db_type": "core", 
-                  "object_type": "Exon", 
-                  "id": "ENSE00003659630", 
-                  "seq_region_name": "19", 
-                  "version": 1, 
-                  "species": "homosapiens", 
-                  "strand": -1
-               }, 
-               {
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-                  "end": 7172434, 
-                  "start": 7172290, 
-                  "db_type": "core", 
-                  "object_type": "Exon", 
-                  "id": "ENSE00003580729", 
-                  "seq_region_name": "19", 
-                  "version": 1, 
-                  "species": "homosapiens", 
-                  "strand": -1
-               }, 
-               {
-                  "assembly_name": "GRCh38", 
-                  "end": 7170751, 
-                  "start": 7170537, 
-                  "db_type": "core", 
-                  "object_type": "Exon", 
-                  "id": "ENSE00003536394", 
-                  "seq_region_name": "19", 
-                  "version": 1, 
-                  "species": "homosapiens", 
-                  "strand": -1
-               }, 
-               {
-                  "assembly_name": "GRCh38", 
-                  "end": 7168094, 
-                  "start": 7167968, 
-                  "db_type": "core", 
-                  "object_type": "Exon", 
-                  "id": "ENSE00003613738", 
-                  "seq_region_name": "19", 
-                  "version": 1, 
-                  "species": "homosapiens", 
-                  "strand": -1
-               }, 
-               {
-                  "assembly_name": "GRCh38", 
-                  "end": 7166404, 
-                  "start": 7166154, 
-                  "db_type": "core", 
-                  "object_type": "Exon", 
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diff -r e17a3470c70a -r 117fc7414307 test-data/gene.sqlite
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diff -r e17a3470c70a -r 117fc7414307 test-data/test.gafa.sqlite
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