| Next changeset 1:fc8ca4ade638 (2017-02-20) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ commit 822c798d43a72724eeab174043fdaafcfdac845f-dirty |
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added:
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 |
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| 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 |
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| @@ -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__() |
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| 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 |
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| @@ -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> |
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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 |
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| @@ -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> |
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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 |
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| @@ -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}) |
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| diff -r 000000000000 -r af9f72ddf7f9 schema/gafa.mwb |
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| Binary file schema/gafa.mwb has changed |
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| diff -r 000000000000 -r af9f72ddf7f9 schema/gafa.png |
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| Binary file schema/gafa.png has changed |
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| 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 |
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| 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 |
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|
| b |
| 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 |
| [ |
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| b |
| diff -r 000000000000 -r af9f72ddf7f9 test-data/test.gafa.sqlite |
| b |
| Binary file test-data/test.gafa.sqlite has changed |
| b |
| diff -r 000000000000 -r af9f72ddf7f9 test-data/tree.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree.nhx Wed Dec 21 07:31:50 2016 -0500 |
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