changeset 0:af9f72ddf7f9 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ commit 822c798d43a72724eeab174043fdaafcfdac845f-dirty
author earlhaminst
date Wed, 21 Dec 2016 07:31:50 -0500
parents
children fc8ca4ade638
files GAFA.py GAFA.xml datatypes_conf.xml gafa_datatypes.py schema/gafa.mwb schema/gafa.png schema/gafa.svg test-data/cigar.tabular test-data/gene.json test-data/test.gafa.sqlite test-data/tree.nhx
diffstat 11 files changed, 1060 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GAFA.py	Wed Dec 21 07:31:50 2016 -0500
@@ -0,0 +1,120 @@
+from __future__ import print_function
+
+import json
+import optparse
+import sqlite3
+
+version = "0.1.0"
+
+
+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 (?)',
+                (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,
+        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),
+        alignment VARCHAR NOT NULL,
+        PRIMARY KEY (gene_family_id, protein_id))''')
+    conn.commit()
+
+
+def cigar_to_db(conn, i, fname):
+    cur = conn.cursor()
+    with open(fname) as f:
+        for element in f.readlines():
+            seq_id, cigar = element.rstrip('\n').split('\t')
+            # Trim seq_id by removing everything from the first underscore
+            seq_id = seq_id.split('_', 1)[0]
+
+            cur.execute('SELECT transcript_id, protein_id FROM transcript WHERE transcript_id=? OR protein_id=?',
+                        (seq_id, seq_id))
+            results = cur.fetchall()
+            if len(results) == 0:
+                raise Exception("Sequence id '%s' could not be found among the transcript and protein ids" % seq_id)
+            elif len(results) > 1:
+                raise Exception("Searching sequence id '%s' among the transcript and protein ids returned multiple results" % seq_id)
+            transcript_id, protein_id = results[0]
+            if protein_id is None:
+                print("Skipping transcript '%s' with no protein id" % transcript_id)
+            else:
+                cur.execute('INSERT INTO gene_family_member (gene_family_id, protein_id, alignment) VALUES (?, ?, ?)',
+                            (i, protein_id, cigar))
+                conn.commit()
+
+
+def newicktree_to_db(conn, i, fname):
+    with open(fname) as f:
+        tree = f.read().replace('\n', '')
+
+    cur = conn.cursor()
+    cur.execute('INSERT INTO gene_family (gene_family_id, gene_tree) VALUES (?, ?)',
+                (i, tree))
+    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('-c', '--cigar', action='append', help='CIGAR alignments of CDS files in tabular format')
+    parser.add_option('-g', '--gene', help='Gene features file in JSON 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')
+
+    conn = sqlite3.connect(options.output)
+    create_tables(conn)
+
+    gene_json_to_db(conn, options.gene)
+
+    for i, (tree, cigar) in enumerate(zip(options.tree, options.cigar), start=1):
+        newicktree_to_db(conn, i, tree)
+        cigar_to_db(conn, i, cigar)
+
+
+if __name__ == '__main__':
+    __main__()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GAFA.xml	Wed Dec 21 07:31:50 2016 -0500
@@ -0,0 +1,45 @@
+<tool id="gafa" name="Gene Align and Family Aggregator" version="0.1.0">
+    <description>generates an SQLite database that can be visualised with Aequatus</description>
+    <command>
+<![CDATA[
+python '$__tool_directory__/GAFA.py'
+#for $dataset in $treeFile:
+    -t '$dataset'
+#end for
+#for $dataset in $alignmentFile:
+    -c '$dataset'
+#end for
+-g '$genesFile'
+-o '$outputFile'
+]]>
+    </command>
+    <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="tabular" multiple="true" label="CDS alignments" help="CDS alignments in tabular format generated by 'T-Coffee to CIGAR' tool" />
+        <param name="genesFile" type="data" format="json" label="Gene features" help="Gene features in JSON format generated by 'GFF3 to JSON' or 'Get Ensembl features by ID' tool" />
+    </inputs>
+    <outputs>
+        <data name="outputFile" format="gafa.sqlite" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="treeFile" ftype="nhx" value="tree.nhx" />
+            <param name="alignmentFile" ftype="tabular" value="cigar.tabular" />
+            <param name="genesFile" ftype="json" value="gene.json" />
+            <output name="outputFile" file="test.gafa.sqlite" compare="sim_size" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+Simple tool to generate an SQLite database that can be visualised with `Aequatus`_.
+
+Aequatus is an open-source homology browser developed with novel rendering approaches to visualise homologous, orthologous and paralogous gene structures.
+
+N.B.: The tool will modify the sequence identifiers found in the "CDS alignments" dataset by removing everything from the first underscore to the end of the string.
+
+.. _Aequatus: http://aequatus.earlham.ac.uk
+]]>
+    </help>
+    <citations>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Wed Dec 21 07:31:50 2016 -0500
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<datatypes>
+    <datatype_files>
+        <datatype_file name="gafa_datatypes.py"/>
+    </datatype_files>
+    <registration>
+        <datatype extension="gafa.sqlite" type="galaxy.datatypes.gafa_datatypes:GAFASQLite" mimetype="application/octet-stream" display_in_upload="True" />
+    </registration>
+    <sniffers>
+        <sniffer type="galaxy.datatypes.gafa_datatypes:GAFASQLite"/>
+    </sniffers>
+</datatypes>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gafa_datatypes.py	Wed Dec 21 07:31:50 2016 -0500
@@ -0,0 +1,51 @@
+import logging
+
+from galaxy.datatypes.binary import Binary, SQlite
+from galaxy.datatypes.metadata import MetadataElement, MetadataParameter
+from galaxy.util import sqlite
+
+log = logging.getLogger(__name__)
+
+
+class GAFASQLite(SQlite):
+    """Class describing a GAFA SQLite database"""
+    MetadataElement(name='gafa_schema_version', default='0.1.0', param=MetadataParameter, desc='GAFA schema version',
+                    readonly=True, visible=True, no_value='0.1.0')
+    file_ext = 'gafa.sqlite'
+
+    def set_meta(self, dataset, overwrite=True, **kwd):
+        super(GAFASQLite, self).set_meta(dataset, overwrite=overwrite, **kwd)
+        try:
+            conn = sqlite.connect(dataset.file_name)
+            c = conn.cursor()
+            version_query = 'SELECT version FROM meta'
+            results = c.execute(version_query).fetchall()
+            if len(results) == 0:
+                raise Exception('version not found in meta table')
+            elif len(results) > 1:
+                raise Exception('Multiple versions found in meta table')
+            dataset.metadata.gafa_schema_version = results[0][0]
+        except Exception as e:
+            log.warn("%s, set_meta Exception: %s", self, e)
+
+    def sniff(self, filename):
+        if super(GAFASQLite, self).sniff(filename):
+            gafa_table_names = frozenset(['gene', 'gene_family', 'gene_family_member', 'meta', 'transcript'])
+            conn = sqlite.connect(filename)
+            c = conn.cursor()
+            tables_query = "SELECT name FROM sqlite_master WHERE type='table' ORDER BY name"
+            results = c.execute(tables_query).fetchall()
+            found_table_names = frozenset(_[0] for _ in results)
+            return gafa_table_names <= found_table_names
+        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:
+# 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})
Binary file schema/gafa.mwb has changed
Binary file schema/gafa.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/schema/gafa.svg	Wed Dec 21 07:31:50 2016 -0500
@@ -0,0 +1,766 @@
+<?xml version="1.0" encoding="UTF-8"?>
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+ENSMUSP00000038576	4D22MD23M3D25MD21MD7M7D3M3D21M4D9M3D19M11D12M2D3MD37MD15M2D5MD2M3D14M11D13MD9M4D4M3D6MD9M9D7M3D8M2D17MD7MD11M3D13MD14M4D8M3D2MD17MD11MD10M4D13MD9MD18MD14M82D13MD7M3D6M9D23MD2M8D2M2D11MD39M2D18M2D6M2D22M4D17MDMD6M5D13M2D8M5D8MD44M29D2MD10M115D8M5D7M4D2M6D23M4D15M2D7MD8M7D2MD4MD4MD11M4D27MD6M3D10MD16M3D8MD9MD21M2D22MD21M5D12M3D13M14D2M3D42M4D15M9D11M2D8M36D13MD17M8D3MD30M2DM3D6MDMD6M4D22M8D2MD9M8D7M8D13M11D4MD10M15D3M12D8MD21MD3M5D15M2D10M3D3M4D42MD3M54D5MD2M2DMD12MD13M2D20M162DM4D11MD9MD6MD17M5D25M6D2M2D26M11D9M3D7MD5MD6MD17M2D25MD4M2D8MD9M5D13MD9M10D7MD5MD22M2D55M4D5M2D14M8D3M8D22MD9M5D36MD12M3D9M25D14MD11MD3M2D3M5D16M10D12M7D10M2D3MD14M4D3MD10MD6M4D17M5D18M7D10M3D43M8D16MD22M13D5M57D5MD33MD14MD2M4D12M2D26MD36M2D25M2D9M2D3MD13MD18M7D14MDM2D2MD17M8D15MD7MD37MD16M3D2MD17MD12M2D8M2DMD18M2D21M12D4M6D2MD10M23D5M3D36MD139MD42M5D8M3D6MD79M2D84M2D14M2D27M2D39MD5MD19M2DM4D101M12D25M4D2MD17M4D36MD53M2D32M7D6M2D17MD23MD13MD3MD7MD16M13D43M17D17M2D15M46D
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+ENSOGAP00000009477	4D22MD23M3D25MD21MD17M3D21M4D9M3D5MD13M11D12M2D3MD38MD14M2D5MD2M3D14M11D13MD9M4D4M3D6MD9M9D7MD10M2D9MD7MD7MD11M3D3MD9MD14M4D8M3D2MD17MD11MD10M4D4MD18MD18MD14M82D21M3D6M9D23MD2M8D2M2D11MD39M2D18M2D6M2D22M4D17MDMD6M5D36MD44M29D2MD10M115D12MD7M4D2M6D14M2D7M4D15MD8MD8M7D2MD21M4D11MD20M5D10MD13MD2M3D8MD9MD21M2D22MD21M5D13MD7MD6M14D2M3D42M4D16M9D10M2D8M36D31M8D34M2DM3D8MD6M4D18M12D12M8D7M8D13M11D4MD10M15D3M12D8MD25M5D15M2D10M3D3M5D18MD23MD2M53D6MD5MD12MD14MD20M162DM4D11MD17MD19M2D25M6D2MD8M2D17M11D9M2D8MD5MD24M2D25MD5MD5MD39MD6M2D9MD22MD63M3D5M2D7M17DM8D22MD9M5D9MD8M4D14MD14MD9M24D27MD3M2D3M5D16M10D29M2D3MD21MD9M2D6M3D18M5D3MD15M4D11M4D14MD28M8D28MD9M14D4M57D40MD17M4D12M2D52MD12MD24M2D14MD13MD17M6D16MD5MD17M8D15MD7MD37MD16M3D2MD17MD11M2D31M2D6MD8MD8M6D7M3DM5D13MD2M8D6MDMD5M3D36MD139MD43M5D7M3D6MD79M2D84M2D34M6D3M2D45MD20M5D102M3D2M7D25M4D20M4D37MD41M5D6M2D32M7D6MD18MD23MD13MD3MD8M12D4MD11MD43M17D17M2D16M3D4M19D7M12D
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+ENSSARP00000002541	4D22MD50M3D20MD17M6D18M4D9M3D19M11D12M2D3MD38MD14M2D5MD2M3D14M11D9MD3MD9M4D4M3D6MD9M9D7MD10M2D17MD7MD11M3D3MD24M4D8M3D2MD17MD11MD10M4D23MD18MD14M82D21M3D6M9D23MD2M8D2M2D11MD39M2D18M2D6M2D22M4D17MDMD6M10D31MD10M7D27M29D2MD9M116D12MD7M4D2M6D14M2D7M4D15MD8MD8M7D2MD10MD10M4D11M2D21M3D10MD16M3D8MD9MD21M2D22MDMD6MD12M5D9MD3MD14M14D2M3D42M4D16M9D10M2D8M36D31M8D34M2DM3D8MD6M4D17MD4M8D9MD2M8D7M8D13M11D4MD7MD2M15D3M12D8MD25M5D15M2D2M5D3M3D4M4D7M2D19MD13MDM54D6MD5MD12MD2M3D9MD20M162DM4D11MD17MD19M2D25M6D27MD2M11D9M2D8MD5MD4MD19M2D25MD5MD20M6D10MD12MD3M3D7MD86M2D6M2D7M26D18M2D2MD9M5D13MD37MD9M24D21MD5MD3M2D3M5D9M2D5M13D14MD11M2D3MD21MD10MD6M3D18M5D19M4D13M2D43MDM7D10MD26M83D32MD17M4D13M2D51MD12MD6MD17M2D14MD13MD17M6D8M9D5MD17M8D15MD7MD37MD16M3D2MD17MD11M2D31M2D24M6D7M3DM3D14M5D13MD7M3D36MD139MD43M5D7M3D6MD79M2D84M2D14M2D27M2D45MD20MDM4D101M12D25M4D20M4D37MD41M5D6M2D5M4D23M7D6MD2M2D14MD23MD13MD12M12D4MD11MD26MD6MD9M17D17M2D16M3D5M37D
+ENSEEUP00000008968	4D22MD23M3D24M4D14M2D3MD17M3D21M4D9M3D5MD13M11D12M2D4MD36MD15M2D5MD2M3D14M11D13MD9M4D4M3D6MD9M9D7MD10M2D17MD7MD11M3D3M4D21M4D8M3D2MD17MD11MD10M4D57M82D21M3D6M9D23MD2M8D2M2D11MD39M2D18M2D6M2D22M4D17MDMD6M11D27MD2MD30MD13M29D2M2D9M115D12MD7M4D2M6D14M2D7M4D15MD8MD8M7D2MD21M4D12MD21M4D9MD15M5D7MD9MD21M2D22MD9MD11M5D13MD14M14D2M3D42M4D15M11D9M2D8M36D31M8D34M2DM3D8MD6M4D17MD4M8D9MD2M8D7M8D13M11D15M15D3M12D8MD25M5D15M2D10M3D3M5D7M5D30MD2M53D6MD5MD12MD14MD20M166D2MD9MD16MD5MD14M2D25M6D30M11D9M2D8MD5MD24M2D25MD26M2D14MD12MD2M2DMD7M8D34M8D37M2D6M2D7M26D20M4D8M5D51MD8M25D21MD5MD3M2D3M5D16M10DM5D10M5D8M2D3MD21MD9M9D20M5D19M4D8MD4M2D45M7D15MD20M83D33MD17M4D4MD7M2D52MD37M2DM2D11MD13MD17M6D16MD5MD17M8D15MD8MD36M3D14M3D2MD17MD11M2DMD4MD24M2D4M5D15M6D7M3DM3D15MD2MD10MD2MDMD5M3D36MD139MD43M5D7M3D6MD79M2D84M2D15M2D26M2D45MD18MDMDM4D101M12D25M4D20M4D32MD4MD41M5D6M2D32M7D4M7D14MD23MD13MD3MD8M12D4MD9MDMD43M17D5MD11M2D16M3D4M19D6M13D
+ENSPVAP00000000225	28D22M3D24M2D21MD17M3D21M4D9M3D19M11D12M2D3MD37MD15M2D5MD2M3D14M11D13MD6M8D3M3D6MD9M9D7MD10M2D17MD7MD11M3D3MD24M4D8M3D2MD17MD11MD10M4D23MD18MD14M82D9M3D9M3D6M9D23MD2M8D2M2D11MD26MD12M2D18M2D6M2D22M4D17MDMD6MDM4D35MD44M29D2MD10M115D12MD7M4D2M6D14M2D7M4D15MD8MD8M7D2MD21M4D34M3D10MD16M3D8MD9MD21M7D18MD20M5D13MD14M14D2M3D42M4D16M9D10M2D8M36D31M8D34M2DM3D8MD6M4D22M8D12M8D4M12D12M11D4MD10M15D3M12D8MD25M5D15M2D10M3D3M5D42MD2M53D6MD5MD12MD14MD20M162DM4D11MD17MD19M2D25M6D5MD24M11D9M2D8MD5MD24M2D25MD5M2D19M2D27MD2M2DMD7MD86M2D6M2D7M26D22M2D8M5D51MD9M24D27MD3M2D3M5D16M10D17M2D10M2D3MD16M6D10MD6M6D15M5D19M4D13M2D43MDM7D36M83D33MD17M4D13M2D51MD12MD24M2D7MD4MDMD13MD17M6D10MD5MD5MD17M8D15MD7MD37MD16M3D2MD17MD11M2D6MD24M2D24M6D7M3DM3D15MD2MD13MDMD5M3D36MD139MD43M5D7M3D6MD79M2D84M2D14M2D27M2D45MD20M5DMD100M12D25M4D20M4D37MD41M5D6M2D32M7D6MD18MD23MD13MD3MD8M12D4MD11MD41MDM17D17M2D16M3D4M19D8M11D
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+ENSMPUP00000001928	4D22MD23M3D10MD13M2D39M3D21M4D9M3D5MD13M11D12M2D3MD37MD15M2D5MD2M3D14M11D13MD9M4D4M3D6MD9M9D7MD10M2D17MD7MD11M3D3MD24M4D8M3D2MD17MD11MD10M4D23MD33M82D21M3D6M9D23MD2M8D2M2D11MD20M2D17M2D18M2D6M2D22M4D17MDMD8M4D35MD44M29D2MD10M115D12MD7M4D2M6D14M3D6M4D15MD8MD8M7D2MD21M4D34M3D10MD16M3D8MD9MD21M2D22MDMD19M5D13MD14M14D2M3D42M4D16M9D10M2D8M36D31M8D34M2DM3D8MD6M4D22M8D12M8D7M8D13M11D4MD10M15D3M12D8MD25M5D15M2D10M3D4M4D42MD2M53D6MD5MDMD10MD6MD7MD20M162DM4D11MD17MD19M2D25M6D30M11D19MD5MD24M2D25MD5MD20M2D14MD12MD2M2DMD7MD42MD43M2D6M2D14M8D3M8D22MD9M5D47M2D2MD9M24D26M2D3M2D3M5D43M2D10M2D3MD21MD10MD6M2D19M5D19M4D13M2D43MDM7D10MD4MD21M82D33MD17M4D13M2D51MD12MD24M2D14MD13MD17M6D16MD5MD17M8D15MD7MD37MD16M3D2MD17MD11M2D31M2D24M6D7M3DM3D15MD2MD13MDMD5M3D36MD139MD43M5D7M3D6MD79M2D84M2D14M2D27M2D45MD20M5D139M4D20M4D37MD41M5D6M2D32M7D6MD18MD23MD13MD3MD8M12D4MD6MD4MD43M17D17M2D16M3D4M19D17M2D
+ENSAMEP00000009909	4D22MD23M3D10MD13M2D39M3D21M4D9M3D5MD13M11D12M2D3MD53M2D5MD2M3D14M11D13MD9M4D4M3D6MD9M9D7MD10M2D14MD2MD7MD11M3D3MD24M4D8M3D2MD17MD11MD10M4D23MD33M82D21M3D6M9D23MD2M8D2M2D11MD20M2D17M2D18M2D6M2D22M4D17MDMD8M4D35MD44M29D2MD10M115D12MD7M4D2M6D14M2D7M4D15MD8MD8M7D2MD21M4D34M3D10MD16M3D8MD9MD21M2D22MDMD19M5D13MD14M14D2M3D42M4D16M9D10M2D8M36D31M8D34M2DM3D8MD6M4D22M8D12M8D7M8D13M11D4MD10M15D3M12D8MD25M5D15M2D10M3D4M4D42MD2M53D6MD5MDMD10MD14MD20M162DM4D11MD17MD19M2D25M6D30M11D19MD5MD24M2D25MD5MD20M2D27MD2M2DMD7MD19MD22MD43M2D6M2D14M8D3M8D22MD9M5D51MD9M24D26M2D3M2D3M5D43M2D10M2D3MD21MD10MD6M2D19M5D19M4D13M2D43MDM7D15MD21M82D33MD17M4D13M2D51MD12MD24M2D14MD13MD17M6D16MD5MD17M8D15MD7MD37MD16M3D2MD17MD11M2D31M2D24M6D7M3DM3D15MD16MDMD5M3D36MD139MD43M5D7M3D6MD79M2D84M2D14M2D27M2D45MD20M5D102M12D25M4D20M4D37MD41M5D6M2D32M7D6MD18MD23MD13MD3MD8M12D4MD6MD4MD43M17D17M2D16M3D4M19D17M2D
+ENSECAP00000013146	4D22MD23M3D24M2D21MD17M3D21M4D9M3D19M11D12M2D3MD37MD15M2D5MD2M3D14M11D13MD9M4D4M3D6MD9M9D7MD10M2D17MD7MD11M3D3MD24M4D8M3D2MD17MD11MD10M4D23MD18MD14M82D21M3D6M9D23MD2M8D2M2D11MD39M2D18M2D6M2D22M4D17MDMD6MDM4D35MD44M29D2MD10M115D12MD7M4D2M6D14M2D7M4D15MD8MD8M7D2MD21M4D34M3D10MD16M3D8MD9MD21M2D22MD21M5D13MD14M14D2M3D42M4D16M9D10M7D3M36D31M8D34M2DM3D8MD6M4D17MD4M8D12M8D7M8D13M11D4MD10M15D3M12D8MD25M5D15M2D10M3D3M5D28MD13MD2M53D6MD5MD12MD14MD20M162DM4D11MD17MD19M2D25M6D30M11D9M2D8MD5MD24M2D25MD26M2D2MD11MD12MD2M2DMD7MD86M2D6M2D5M17D3M8D22MD9M5D51MD9M24D27MD3M2D3M5D16M10D17M2D10M2D3MD21MD10MD6M2D19M5D19M4D13M2D43MDM7D37M82D33MD17M4D13M2D51MD12MD22M6D12MD13MD17M6D16MD5MD17M8D15MD7MD37MD16M3D2MD17MD11M2D31M2D24M6D7M3DM3D15MD2MD13MDMD5M3D36MD139MD43M5D7M3D6MD79M2D84M2D14M2D27M2D45MD20M5D102M12D25M4D20M4D37MD41M5D6M2D32M7D6M2D17MD23MD13MD3MD8M12D4MD11MD43M17D17M2D16M3D4M19D4M15D
+ENSVPAP00000000821	4D22MD23M3D24M2D21MD17M3D21M4D9M3D6MD12M11D4MD7M2D42MD14M2D5MD2M3D14M11D6M2D5MD9M4D4M3D6MD9M9D7MD10M2D17MD7MD11M3D3MD24M4D8M3D2MD17MD11MD10M4D23MD18MD14M82D21M3D6M9D23MD2M8D2M2D10M2D39M2D18M2D6M2D22M4D17MDMD6MDM4D27M9D24MD19M29D2MD10M115D2M2D8M2D6M4D2M6D4MD9M2D7M5D14MD8MD8M7D2MD21M4D34M4D9MD16M3D8MD9MD21M2D23MD20M5D13MD14M14D2M3D42M4D16M9D10M2D8M36D22MD8M8D34M2DM3D8MD6M4D22M8D12M8D7M8D13M11D4MD10M15D3M12D8MD24M6D15M2D10M3D4M4D42MD2M53D5M4D3MD12MD14MD20M162DM4D11MD17MD19M2D25M6D30M11D9M2D8MD5MD24M2D25MD5MD20M2D14MD12MD3M3D7MD34MD51M2D6M2D7M26D22M2D8M5D4MD46MD9M24D27MD3M2D3M5D16M10D9M9D11M2D3MD21MD10MD6M2D19M5D19M4D13M2D43MDM7D23MD13M82D33MD17M4D13M2D51MD12MD24M2D14MD13MD17M6D16MD5MD17M8D15MD7MD37MD16M3D2MD17MD11M2D31M2D13M3D8M6D7M3DM5D13MD2MD13MDMD5M3D36MD20MD118MD43M5D7M3D6MD79M2D84M2D14M2D27M2D45MD20MDM4D101M12D25M4D20M4D37MD41M5D6M2D6MD25M7D6MD18MD23MD13MD3MD8M12D4MD11MD43M17D17M2D16M3D4M19D7M12D
+ENSTTRP00000010004	4D22MD23M3D24M2D21MD17M3D21M4D9M3D19M11D12M2D41MD15M2D2M2DMD2M3D8MD5M13D11MD9M4D4M3D6MD9M9D7MD10M2D17MD7MD11M3D3MD24M4D8M3D2MD17MD11MD10M4D12MD10MD18MD14M82D21M3D6M9D23MD2M8D2M2D11MD39M2D18M2D6M2D22M4D17MDMD6MDM4D35MD44M29D2MD10M115D12MDMD5M4D2M6D14M2D7M4D15MD8MD8M7D2MD21M4D34M3D10MD16M3D8MD9MD21M2D22MD21M5D13MD14M14D2M3D42M4D16M9D10M2D8M36D31M8D34M2DM3D8MD6M4D22M8D12M8D7M8D13M11D4MD10M15D3M12D8MD7MD17M5D15M2D10M3D3M5D42MD2M53D5M4D3MDMD10MD14MD20M162DM4D2MD8MD17MD19M2D25M6D5MD24M11D9M2D8MD5MD24M2D25MD5MD20M2D14MD12MD2M2DMD4MD2MD27MD58M2D6M2D7M26D22M2D8M5D4MD46MD9M24D27MD3M2D3M5D16M10D17M2D10M2D3MD21MD10MD6M2D19M5D19M4D13M2D43MDM7D37M82D33MD17M4D13M2D51MD12MD24M2D14MD13MD17M6D16MD5MD17M8D15MD7MD37MD16M3D2MD17MD11M2D31M2D24M6D7M3DM3D8M9DMD13MDMD5M3D36MD139MD43M5D7M3D6MD79M2D84M2D14M2D27M2D45MD20M5DM113D25M4D20M4D37MD41M5D6M2D32M7D6MD18MD23MD13MD3MD8M12D4MD11MD43M17D17M2D16M3D4M19D7M12D
+ENSSSCP00000028073	262DM2DMD2M3D14M11D13MD9M4D4M3D6MD8M16DMD10M2D17MD7MD11M3D3MD24M4D8M3D2MD17MD11MD10M4D23MD18MD14M82D21M3D6M9D23MD2M8D2M2D11MD39M2D18M2D6M2D22M4D17MD8MDM4D32MD2MD44M29D2MD10M115D12MDMD5M4D2M6D14M2D7M4D15MD8MD8M7D2MD21M4D34M3D10MD16M3D8MD9MD21M2D44M5D13MDMD12M14D2M3D42M4D16M9D10M2D8M36D31M8D34M2DM3D8MD6M4D22M8D12M8D7M8D13M11D4MD10M15D3M12D8MD25M5D15M2D10M3D4M4D42MD2M53D5M4D3MD12MD14MD2MD12M4DM162DM4D11MD16M2D19M2D25M6D30M11D9M2D8MD5MD24M2D25MD5MD20M2D14MD12MD2M2DMD7MD38M5D43M2D6M2D7M5D2M8D3M8D22M2D8M5D4MD46MD9M24D27MD3M2D3M5D16M10D5MD11M2D10M2D3MD21MD10MD6M2D19M5D19M4D13M2D43MDM7D10MD26M82D33MD17M4D13M2D50M2D12MD24M2D14MD13MD17M6D10MD5MD5MD17M8D15MD7MD37MD16M3D2MD17MD11M2D31M2D24M6D7M3DM3D8M9DMD13MDMD3M1073D
+ENSSSCP00000022872	3576DMD5M3D36MD139MD34MD8M5D7M3D6MD70MD18MD12M3D12M2D46M2D14M2D27M2D45MD20M5D102M12D25M4D20M4D37MD41M5D6M2D32M7D6MD18MD23MD13MD3MD8M12D4MD11MD43M17D15M65D
+ENSOARP00000011988	4D22MD23M3D24M2D21MD17M3D21M4D9M3D19M11D12M2D3MD37MD15M2D5MD2M3D8MD5M11D13MD9M4D4M3D6MD9M9D7MD10M2D17MD7MD11M3D3MD24M4D8M3D2MD17MD11MD10M4D4MD18MD18MD14M82D21M3D2M13D23MD2M8D2M2D11MD39M2D18M2D6M2D22M4D17MDMD6MDM4D35MD44M29D2MD10M115D12MDMD5M4D2M6D14M2D7M4D15MD8MD8M7D2MD21M4D34M3D10MD16M3D8MD9MD21M2D22MD21M5D13MD14M14D2M3D42M4D12M2D2M9D10M2D8M36D31M8D34M2DM3D8MD6M4D22M8D12M8D2MD4M8D13M11D4MD10M15D3M12D8MD25M5D15M2D10M3D4M4D42MD2M53D5M4D3MD12MD14MD20M162DM4D11MD9M2D6MD19M2D25M6D30M11D9M2D8MD5MD24M2D25MD5MD20M2D14MD12MD2M2DMD7MD86M2D6M2D14M8D3M8D22M2D8M5D4MD46MD9M24D27MD3M2D3M5D16M10D17M2D10M2D25MD10MD6M2D19M5D19M4D13M2D43MDM7D15MD21M82D33MD17M4D13M2D51MD12MD24M2D4MD9MD13MD17M6D16MD5MD17M8D15MD7MD37MD16M3D2MD17MD11M2D31M2D15MD8M6D7M3DM3D8M9DMD13MDMD5M3D36MD139MD43M5D7M3D6MD79M2D84M2D14M2D27M2D45MD20M5D102M12D25M4D20M4D37MD41M5D6M2D32M7D6MD18MD23MD13MD3MD8M12D4MD11MD43M17D17M2D16M3D4M19D17M2D
+ENSBTAP00000001311	4D22MD23M3D24M2D21MD8M7D2M3D21M4D9M3D19M11D12M2D3MD37MD15M2D5MD2M3D8MD5M11D13MD9M4D4M3D6MD9M9D7MD10M2D17MD7MD11M3D3MD24M4D8M3D2MD17MD11MD10M4D23MD18MD4M111D2M3D2M13D23MD2M8D2M2D11MD39M2D18M2D6M2D22M4D17MDMD6MDM4D35MD44M29D2MD10M115D12MDMD5M4D2M6D14M2D7M4D15MD8MD8M7D2MD21M4D34M3D10MD16M3D8MD9MD21M2D22MD21M5D13MD14M14D2M3D42M4D12M2D2M9D10M2D8M36D31M8D34M2DM3D8MD6M4D22M8D12M8D7M8D13M11D4MD10M15D3M12D8MD25M5D15M2D10M3D4M4D42MD2M53D5M4D3MD12MD14MD20M162DM4D11MD9M2D6MD19M2D25M6D30M11D9M2D8MD5MD24M2D25MD5MD20M2D14MD12MD2M2DMD7MD86M2D6M2D14M8D3M8D14MD7M2D8M5D4MD46MD9M24D27MD3M2D3M5D16M10D17M2D10M2D25MD10MD6M2D19M5D2MD16M4D13M2D43MDM7D37M82D33MD17M4D13M2D51MD12MD24M2D4MD9MD13MD17M6D16MD5MD17M8D15MD7MD37MD16M3D2MD17MD11M2D31M2D15MD8M6D7M3DM3D5M31D4M3D36MD139MD43M5D7M3D6MD79M2D84M2D14M2D27M2D45MD20M5D102M12D25M4D20M4D37MD41M5D6M2D32M7D6MD18MD23MD13MD3MD8M12D4MD11MD43M17D17M2D16M3D4M19DM18D
+ENSACAP00000004459	255D4M13D13M201D4M710D4M516D13M466D4M539D3M2DM486D15M6D24MD17M6D16M3D3MD17M8D14M5D42M4D13M3D20MD10M2D32M3D23M16DM3D14MD17M3D5M3D176MD43M5D7M3D86M2D83MD16M2D27M2D66M6D101M12D49M4D36MD42M5D6M2D32M7D6M4DM4D10MD23MD13MD3MD8M12D3M2D55M17D17M21D3M39D
+ENSPSIP00000012858	26MD23M3D47MD18MD21M9D5M3D20M10D12M2D3MD38MD21MD2M3D14M11D23M4D4M3D6MD10M3DM4D18M2D17MD25MD24M4D8M3D32MD31M7D18MD14M82D36M9D20M8D75M2D6M2D42MD2MD6M5D12MD23MD9M4D31M29D2MD10M115D12MD7M4D31M4D7M2D6MD8MD8M7D2MD59M2D11MD15M5D7MD9MD45MD16M2D3M5D13MD14M14D16MD30M4D35M2D7M30DM6D10M4D17M8D34M5D9MD52M8D7M8D13M11D33M12D8MD45M2D16M4D22MD23M53D6MD5MD7M10D10MD13MD6M162D33M5D12M7D22M8D30M11D9M6D4MD5MD22M4D25MD4M24D5M166D5M55D6M81D2MD3M2DM57D4M2D4M58D3M5D11M27D5M10D8M5D15MDM7D12M112D26M6D30M2D51M2D12MD24M6D24MD11MD5M6D16MD5MD17M8D14MDMD6MD37MD21MD17MD10M2D32M2D21MD2M6D7M3DM3D14MD25M3D36MD139MD43M5D7M3D6MD79M2D83M2D15M2D27M2D67M4D102M12D49M4D36MD44M3D6M2D26MD5M7D6MD4M4D34MD13MD3MD8M12D4MD49M5DM17D35M3D3M19D20M
+ENSTGUP00000012130	4D22MD23M3D47MD17M7D17M4D32M10D12M2D3MD38MD21MD2M3D14M11D13MD9M4D4M3D6MD36MD26MD11M7D24M4D8M3D20MD11MD8M7D41MD14M82D29MD3MD3MD24MD2M11D49M5D18M2D6M2D42M16D36MD43M29D2MD10M115D12M12D2M6D51M2D7M12D19M4D34M3D8M3D16M10DMD4M6D15MDM7D14M48D14M14D2M3D42M5D14M9D11M2D7M30DM13D66M5D8M2D6M6D40M8D7M8D39M13D5M12D8MD25M4D16M2D16MD48M80D14MD20M162DM2D32MD18M2D25M6D9M9D12M12D49M2D25M10D17M2D12MD14M17D17M5D2M2D42MD15M2D6M2D5M28D32M5D30M3D18MD9M24D27MD2M2D3M5D5M22D27M3D4MD60M5D19M4D13MD46M7D35M16D4M57D40M6D12M4D12MD52M3D21M5D10M2D14MD13MD11MD5M6D16M4D2MD17M8D14MDMD6MD37MD21MD17MD6MD3M2D58M6D7M3DM3D14MD11M9D5M3D36MD139MD43M5D7M5D84M2D84M2D14M2D27M2D67M4D101M13D49M4D36MD42M6D5M3D26M12D6MD18MD23MD13MD3MD8M12D4MD55M17D15M65D
+ENSFALP00000008821	4D22MD23M3D45M3D17M7D17M4D32M10D12M2D3MD38MD21MD2M3D14M11D13MD9M4D4M3D6MD36MD38M3D28M4D8M3D20MD9MDMD8M7D41MD14M82D29MD3MD3MD24MD2M11D49M5D18M2D6M2D42MD8M7D30M5D10M2D33M29D2MD10M115D26M6D23M4D15MD17M12D19M4D34M3DM6DM3D16M10DMD27M7D14M48D14M14D2M3D42M5D14M9D11M2D7M30DM6D73M5D9MD52M8D7M8D39M13D5M12D8MD25M4D16M2D64M81D35M162DM2D51M2D25M6D9M9D12M11D9M2D39M2D25M3D23M3D12M5D11M5D28M5D42MD19M2D6M2D5M28D32M5D30M3D18MD9M24D27MD2M2D3M5D5M22D27M3D4MD60M5D19M4D13MD46M7D35M16D4M57D40M6D12M4D12MD52M3D21M5D10M2D14MD13MD11MD5M6D16M4D2MD17M8D14MD7M2D37MD21MD17MD6MD3M2D58M6D7M3DM3D14MD11M9D5M3D36MD183M5D7M5D84M2D84M2D14M2D27M2D67M4D101M13D49M4D36MD42M5D6M4D25M12D6MD18MD23MD13MD3MD8M12D4MD55M18D14M4D12M49D
+ENSAPLP00000007411	4D46M3D5M4D38MD17M7D17M4D32M10D12M2D3MD38MD21MD2M3D14M11D13MD9M4D4M3D6MD36MD38M3D28M4D8M3D20MD11MD8M7D41MD14M82D21M3D5MD3MD28MD2M11D49M5D18M2D6M2D42MD8M10DM7D24MD9M2D33M29D2MD10M115D12MD7M4D5M3D51MD8M7D2MD4M4D13M3D16MD18M3D10MD14M12DMD27M7D14M48D14M14D2M3D42M5D14M9D11M2D7M30DM6D4M8D61M5D9MD52M8D7M8D11M13D4MD28M12D8MD25M5D33M5D41M72D10MD35M162D51MD11MD17M6D9MD20M14D6M5D5MD30M2D25MD26M2D10M5D6M6DM5D28M5D29M2D14MD16M2D6M2D5M28D32M5D51MD9M24D27MD7M5DM2D4M20D28M2D4MD39M2D20M4D19M4D58MDM7D25M4D8M14D4M57D40M6D12M4D12MD17MD33M8D7MD24M2D14MD13MD11MD5M6D10M2D4MD5MD17M8D14MDMD6MD37MD21MD17MD6MD3M2D58M6D7M3DM3D14MD11M9D5M3D36MD139MD42M9D4M3D86M2D113MD84M4D101M13D49M4D36MD44M3D6M2D27M12D6MD5M3D10MD23MD13MD3MD8M12D4MD54M18D41M19D20M
+ENSGALP00000027524	4D22MD23M3D15MD30M2D17M7D17M4D32M10D12M2D3MD38MD21MD2M3D14M11D13MD9M4D4M3D6MD17MD18MD38M3D28M4D8M3D20M2D10MD8M7D41MD14M82D21M3D5MD3MD28MD2M11D49M5D18M2D6M2D42MD8M10D28M5D9M2D33M29D2MD10M115D12MD7M4D5M3D51MD8M12D19M4D34M3D2M9D15M11DMD25MDM7D14M48D14M14D2M3D42M5D14M9D11M2D7M30DM6D4M8D61M5D9MD6M7D26MD12M8D7M8D12M12D33M12D8MD25M4D16M2D15M6D23M3D19M68D10MD35M162D54M2D25M6D7M9D14M11D19MD30M2D25MD20M8D26MDM5D28M5D45MD16M2D6M2D5M28D32M5D51MD9M24D27MD2M2D3M5D4M23D28M2D4MD60M6D18M4D29MD30M7D12M4D22M13D4M57D52M10D12MD52M3D22M3D11M2D14M5D9MD11MD5M6D16M5DMD17M8D14MDMD6MD37MD21MD17MD10M2DMD56M6D7M3DM3D14MD11M9D5M3D36MD139MD42M7D6M3D86M2D84M2D14M2D27M2D67M4D101M13D49M4D36MD44M3D6M3D26M12D6MD18MD23MD13MD3MD8M12D4MD107M3D3M19D20M
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene.json	Wed Dec 21 07:31:50 2016 -0500
@@ -0,0 +1,1 @@
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Binary file test-data/test.gafa.sqlite has changed
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