| Previous changeset 3:e17a3470c70a (2017-03-03) Next changeset 5:c388666f58e0 (2017-03-24) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ commit 651fae48371f845578753052c6fe173e3bb35670 |
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modified:
GAFA.py GAFA.xml schema/gafa.mwb schema/gafa.png schema/gafa.svg test-data/test.gafa.sqlite |
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added:
test-data/gene.sqlite |
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removed:
test-data/gene.json |
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| 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 |
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| @@ -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) |
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| 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 |
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| @@ -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> |
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| diff -r e17a3470c70a -r 117fc7414307 schema/gafa.mwb |
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| Binary file schema/gafa.mwb has changed |
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| diff -r e17a3470c70a -r 117fc7414307 schema/gafa.png |
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| Binary file schema/gafa.png has changed |
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| 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 |
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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 |
| [ |
| b'@@ -1,9586 +0,0 @@\n-{\n- "ENSG00000171105": {\n- "assembly_name": "GRCh38", \n- "display_name": "INSR", \n- "description": "insulin receptor [Source:HGNC Symbol;Acc:HGNC:6091]", \n- "seq_region_name": "19", \n- "logic_name": "ensembl_havana_gene", \n- "object_type": "Gene", \n- "start": 7112255, \n- "id": "ENSG00000171105", \n- "source": "ensembl_havana", \n- "db_type": "core", \n- "version": 13, \n- "biotype": "protein_coding", \n- "end": 7294034, \n- "Transcript": [\n- {\n- "assembly_name": "GRCh38", \n- "display_name": "INSR-002", \n- "Parent": "ENSG00000171105", \n- "seq_region_name": "19", \n- "logic_name": "ensembl_havana_transcript", \n- "object_type": "Transcript", \n- "start": 7112255, \n- "id": "ENST00000341500", \n- "source": "ensembl_havana", \n- "version": 9, \n- "Exon": [\n- {\n- "assembly_name": "GRCh38", \n- "end": 7293931, \n- "start": 7293792, \n- "db_type": "core", \n- "object_type": "Exon", \n- "id": "ENSE00003071904", \n- "seq_region_name": "19", \n- "version": 1, \n- "species": "homosapiens", \n- "strand": -1\n- }, \n- {\n- "assembly_name": "GRCh38", \n- "end": 7267896, \n- "start": 7267345, \n- "db_type": "core", \n- "object_type": "Exon", \n- "id": "ENSE00003664284", \n- "seq_region_name": "19", \n- "version": 1, \n- "species": "homosapiens", \n- "strand": -1\n- }, \n- {\n- "assembly_name": "GRCh38", \n- "end": 7184637, \n- "start": 7184316, \n- "db_type": "core", \n- "object_type": "Exon", \n- "id": "ENSE00003682994", \n- "seq_region_name": "19", \n- "version": 1, \n- "species": "homosapiens", \n- "strand": -1\n- }, \n- {\n- "assembly_name": "GRCh38", \n- "end": 7174731, \n- "start": 7174583, \n- "db_type": "core", \n- "object_type": "Exon", \n- "id": "ENSE00003659630", \n- "seq_region_name": "19", \n- "version": 1, \n- "species": "homosapiens", \n- "strand": -1\n- }, \n- {\n- "assembly_name": "GRCh38", \n- "end": 7172434, \n- "start": 7172290, \n- "db_type": "core", \n- "object_type": "Exon", \n- "id": "ENSE00003580729", \n- "seq_region_name": "19", \n- "version": 1, \n- "species": "homosapiens", \n- "strand": -1\n- }, \n- {\n- "assembly_name": "GRCh38", \n- "end": 7170751, \n- "start": 7170537, \n- "db_type": "core", \n- "object_type": "Exon", \n- "id": "ENSE00003536394", \n- "seq_region_name": "19", \n- "version": 1, \n- "species": "homosapiens", \n- "strand": -1\n- }, \n- {\n- "assembly_name": "GRCh38", \n- "end": 7168094, \n- "start": 7167968, \n- "db_type": "core", \n- "object_type": "Exon", \n- "id": "ENSE00003613738", \n- "seq_region_name": "19", \n- "version": 1, \n- "speci'..b' "version": 1, \n- "species": "canisfamiliaris", \n- "strand": -1\n- }, \n- {\n- "assembly_name": "CanFam3.1", \n- "end": 14518681, \n- "start": 14518563, \n- "db_type": "core", \n- "object_type": "Exon", \n- "id": "ENSCAFE00000177706", \n- "seq_region_name": "6", \n- "version": 1, \n- "species": "canisfamiliaris", \n- "strand": -1\n- }, \n- {\n- "assembly_name": "CanFam3.1", \n- "end": 14518488, \n- "start": 14518302, \n- "db_type": "core", \n- "object_type": "Exon", \n- "id": "ENSCAFE00000177713", \n- "seq_region_name": "6", \n- "version": 1, \n- "species": "canisfamiliaris", \n- "strand": -1\n- }, \n- {\n- "assembly_name": "CanFam3.1", \n- "end": 14518095, \n- "start": 14518022, \n- "db_type": "core", \n- "object_type": "Exon", \n- "id": "ENSCAFE00000177726", \n- "seq_region_name": "6", \n- "version": 1, \n- "species": "canisfamiliaris", \n- "strand": -1\n- }, \n- {\n- "assembly_name": "CanFam3.1", \n- "end": 14517147, \n- "start": 14517045, \n- "db_type": "core", \n- "object_type": "Exon", \n- "id": "ENSCAFE00000177737", \n- "seq_region_name": "6", \n- "version": 1, \n- "species": "canisfamiliaris", \n- "strand": -1\n- }, \n- {\n- "assembly_name": "CanFam3.1", \n- "end": 14516938, \n- "start": 14516840, \n- "db_type": "core", \n- "object_type": "Exon", \n- "id": "ENSCAFE00000177744", \n- "seq_region_name": "6", \n- "version": 1, \n- "species": "canisfamiliaris", \n- "strand": -1\n- }, \n- {\n- "assembly_name": "CanFam3.1", \n- "end": 14516681, \n- "start": 14516506, \n- "db_type": "core", \n- "object_type": "Exon", \n- "id": "ENSCAFE00000177753", \n- "seq_region_name": "6", \n- "version": 1, \n- "species": "canisfamiliaris", \n- "strand": -1\n- }, \n- {\n- "assembly_name": "CanFam3.1", \n- "end": 14516182, \n- "start": 14515204, \n- "db_type": "core", \n- "object_type": "Exon", \n- "id": "ENSCAFE00000177757", \n- "seq_region_name": "6", \n- "version": 2, \n- "species": "canisfamiliaris", \n- "strand": -1\n- }\n- ], \n- "biotype": "protein_coding", \n- "species": "canisfamiliaris", \n- "end": 14529569, \n- "Translation": {\n- "end": 14528678, \n- "Parent": "ENSCAFT00000025950", \n- "db_type": "core", \n- "object_type": "Translation", \n- "id": "ENSCAFP00000024092", \n- "start": 14515481, \n- "length": 824, \n- "species": "canisfamiliaris"\n- }, \n- "is_canonical": "1", \n- "db_type": "core", \n- "strand": -1\n- }\n- ], \n- "species": "canisfamiliaris", \n- "strand": -1\n- }\n-}\n' |
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