# HG changeset patch
# User earlhaminst
# Date 1482323510 18000
# Node ID af9f72ddf7f9c4f2077d8a355e57ba80b76af2f7
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ commit 822c798d43a72724eeab174043fdaafcfdac845f-dirty
diff -r 000000000000 -r af9f72ddf7f9 GAFA.py
--- /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__()
diff -r 000000000000 -r af9f72ddf7f9 GAFA.xml
--- /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 @@
+
+ generates an SQLite database that can be visualised with Aequatus
+
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diff -r 000000000000 -r af9f72ddf7f9 datatypes_conf.xml
--- /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 @@
+
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diff -r 000000000000 -r af9f72ddf7f9 gafa_datatypes.py
--- /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})
diff -r 000000000000 -r af9f72ddf7f9 schema/gafa.mwb
Binary file schema/gafa.mwb has changed
diff -r 000000000000 -r af9f72ddf7f9 schema/gafa.png
Binary file schema/gafa.png has changed
diff -r 000000000000 -r af9f72ddf7f9 schema/gafa.svg
--- /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 @@
+
+
diff -r 000000000000 -r af9f72ddf7f9 test-data/cigar.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cigar.tabular Wed Dec 21 07:31:50 2016 -0500
@@ -0,0 +1,64 @@
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+ENSAMEP00000009909 4D22MD23M3D10MD13M2D39M3D21M4D9M3D5MD13M11D12M2D3MD53M2D5MD2M3D14M11D13MD9M4D4M3D6MD9M9D7MD10M2D14MD2MD7MD11M3D3MD24M4D8M3D2MD17MD11MD10M4D23MD33M82D21M3D6M9D23MD2M8D2M2D11MD20M2D17M2D18M2D6M2D22M4D17MDMD8M4D35MD44M29D2MD10M115D12MD7M4D2M6D14M2D7M4D15MD8MD8M7D2MD21M4D34M3D10MD16M3D8MD9MD21M2D22MDMD19M5D13MD14M14D2M3D42M4D16M9D10M2D8M36D31M8D34M2DM3D8MD6M4D22M8D12M8D7M8D13M11D4MD10M15D3M12D8MD25M5D15M2D10M3D4M4D42MD2M53D6MD5MDMD10MD14MD20M162DM4D11MD17MD19M2D25M6D30M11D19MD5MD24M2D25MD5MD20M2D27MD2M2DMD7MD19MD22MD43M2D6M2D14M8D3M8D22MD9M5D51MD9M24D26M2D3M2D3M5D43M2D10M2D3MD21MD10MD6M2D19M5D19M4D13M2D43MDM7D15MD21M82D33MD17M4D13M2D51MD12MD24M2D14MD13MD17M6D16MD5MD17M8D15MD7MD37MD16M3D2MD17MD11M2D31M2D24M6D7M3DM3D15MD16MDMD5M3D36MD139MD43M5D7M3D6MD79M2D84M2D14M2D27M2D45MD20M5D102M12D25M4D20M4D37MD41M5D6M2D32M7D6MD18MD23MD13MD3MD8M12D4MD6MD4MD43M17D17M2D16M3D4M19D17M2D
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
+ENSSSCP00000022872 3576DMD5M3D36MD139MD34MD8M5D7M3D6MD70MD18MD12M3D12M2D46M2D14M2D27M2D45MD20M5D102M12D25M4D20M4D37MD41M5D6M2D32M7D6MD18MD23MD13MD3MD8M12D4MD11MD43M17D15M65D
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
+ENSACAP00000004459 255D4M13D13M201D4M710D4M516D13M466D4M539D3M2DM486D15M6D24MD17M6D16M3D3MD17M8D14M5D42M4D13M3D20MD10M2D32M3D23M16DM3D14MD17M3D5M3D176MD43M5D7M3D86M2D83MD16M2D27M2D66M6D101M12D49M4D36MD42M5D6M2D32M7D6M4DM4D10MD23MD13MD3MD8M12D3M2D55M17D17M21D3M39D
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
+ENSFALP00000008821 4D22MD23M3D45M3D17M7D17M4D32M10D12M2D3MD38MD21MD2M3D14M11D13MD9M4D4M3D6MD36MD38M3D28M4D8M3D20MD9MDMD8M7D41MD14M82D29MD3MD3MD24MD2M11D49M5D18M2D6M2D42MD8M7D30M5D10M2D33M29D2MD10M115D26M6D23M4D15MD17M12D19M4D34M3DM6DM3D16M10DMD27M7D14M48D14M14D2M3D42M5D14M9D11M2D7M30DM6D73M5D9MD52M8D7M8D39M13D5M12D8MD25M4D16M2D64M81D35M162DM2D51M2D25M6D9M9D12M11D9M2D39M2D25M3D23M3D12M5D11M5D28M5D42MD19M2D6M2D5M28D32M5D30M3D18MD9M24D27MD2M2D3M5D5M22D27M3D4MD60M5D19M4D13MD46M7D35M16D4M57D40M6D12M4D12MD52M3D21M5D10M2D14MD13MD11MD5M6D16M4D2MD17M8D14MD7M2D37MD21MD17MD6MD3M2D58M6D7M3DM3D14MD11M9D5M3D36MD183M5D7M5D84M2D84M2D14M2D27M2D67M4D101M13D49M4D36MD42M5D6M4D25M12D6MD18MD23MD13MD3MD8M12D4MD55M18D14M4D12M49D
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diff -r 000000000000 -r af9f72ddf7f9 test-data/gene.json
--- /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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diff -r 000000000000 -r af9f72ddf7f9 test-data/test.gafa.sqlite
Binary file test-data/test.gafa.sqlite has changed
diff -r 000000000000 -r af9f72ddf7f9 test-data/tree.nhx
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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