Mercurial > repos > iuc > sqlite_to_tabular
changeset 4:6e72fd26a9d3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
| author | iuc |
|---|---|
| date | Thu, 03 May 2018 10:17:22 -0400 |
| parents | f31bb1e5725d |
| children | 0b52ad240b2b |
| files | macros.xml query_db.py query_tabular.py test-data/psm_dbmod_output.tsv test-data/psm_dbmod_output1.tsv |
| diffstat | 5 files changed, 64 insertions(+), 9 deletions(-) [+] |
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--- a/macros.xml Mon Nov 06 23:20:41 2017 -0500 +++ b/macros.xml Thu May 03 10:17:22 2018 -0400 @@ -106,6 +106,13 @@ <when value="no"/> </conditional> </xml> + <xml name="sql_query_input"> + <param name="sqlquery" type="text" area="true" size="20x80" value="" optional="true" label="SQL Query to generate tabular output"> + <help>By default: tables are named: t1,t2,...,tn and columns in each table: c1,c2,...,cn</help> + <sanitizer sanitize="False"/> + <validator type="regex" message="">^(?ims)\s*select\s+.*\s+from\s+.*$</validator> + </param> + </xml> <xml name="macro_line_filters"> <repeat name="linefilters" title="Filter Tabular Input Lines"> <conditional name="filter">
--- a/query_db.py Mon Nov 06 23:20:41 2017 -0500 +++ b/query_db.py Thu May 03 10:17:22 2018 -0400 @@ -59,9 +59,13 @@ def run_query(conn, query, outputFile, no_header=False, comment_char='#'): cur = conn.cursor() results = cur.execute(query) - if not no_header: - outputFile.write("%s%s\n" % (comment_char, '\t'.join( - [str(col[0]) for col in cur.description]))) - for i, row in enumerate(results): - outputFile.write("%s\n" % '\t'.join( - [str(val) if val is not None else '' for val in row])) + if outputFile is not None: + if not no_header: + outputFile.write("%s%s\n" % (comment_char, '\t'.join( + [str(col[0]) for col in cur.description]))) + for i, row in enumerate(results): + outputFile.write("%s\n" % '\t'.join( + [str(val) if val is not None else '' for val in row])) + else: + conn.commit() + return results
--- a/query_tabular.py Mon Nov 06 23:20:41 2017 -0500 +++ b/query_tabular.py Thu May 03 10:17:22 2018 -0400 @@ -59,6 +59,9 @@ help='comment character to prefix column header line') parser.add_option('-o', '--output', dest='output', default=None, help='Output file for query results') + parser.add_option('-d', '--debug', dest='debug', default=False, + action='store_true', + help='Output info to stderr') (options, args) = parser.parse_args() # determine output destination @@ -109,9 +112,35 @@ try: with open(options.jsonfile) as fh: tdef = json.load(fh) + if options.debug: + print('JSON: %s' % tdef, file=sys.stderr) if 'tables' in tdef: for ti, table in enumerate(tdef['tables']): _create_table(ti, table) + if 'sql_stmts' in tdef: + for si, stmt in enumerate(tdef['sql_stmts']): + rowcount = run_query(get_connection(options.sqlitedb), stmt, None) + if options.debug: + print('\nDB modification: %s \nrowcount: %s' % + (stmt, rowcount), file=sys.stderr) + if 'queries' in tdef: + for qi, qstmt in enumerate(tdef['queries']): + if 'header' in qstmt: + no_header = False + comment_char = qstmt['header'] + else: + no_header = True + comment_char = None + with open(qstmt['result_file'], 'w') as fh: + query = qstmt['query'] + rowcount = run_query(get_connection(options.sqlitedb), + query, + fh, + no_header=no_header, + comment_char=comment_char) + if options.debug: + print('\nSQL: %s \nrowcount: %s' % + (query, rowcount), file=sys.stderr) except Exception as e: exit('Error: %s' % (e)) @@ -131,9 +160,13 @@ exit('Error: %s' % (e)) else: try: - run_query(get_connection(options.sqlitedb), query, outputFile, - no_header=options.no_header, - comment_char=options.comment_char) + rowcount = run_query(get_connection(options.sqlitedb), + query, outputFile, + no_header=options.no_header, + comment_char=options.comment_char) + if options.debug: + print('\nSQL: %s \nrowcount: %s' % + (query, rowcount), file=sys.stderr) except Exception as e: exit('Error: %s' % (e))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/psm_dbmod_output.tsv Thu May 03 10:17:22 2018 -0400 @@ -0,0 +1,5 @@ +#scan m/z Precursor m/z Error Sequence Protein(s) confidence +1 523.272583 -4.42404529799 PYANQPTVR NP_116558 99.999 +3 652.843567 4.02947892238 SSWAGLQFPVGR NP_066544_R21W 99.999 +4 788.87384 1.27277118312 AQACNLDQSGTNVAK NP_112092_rs7285167:R182C 99.999 +7 908.008545 0.740229025429 DMTVPVLVSKPPVFTGK NP_001909_rs72973763:I239V,rs12021720:S384G 94.7368421053
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/psm_dbmod_output1.tsv Thu May 03 10:17:22 2018 -0400 @@ -0,0 +1,6 @@ +scan Sequence Protein(s) Position m/z Precursor m/z Error confidence +1 PYANQPTVR NP_116558 2 523.272583 -4.42404529799 99.999 +3 SSWAGLQFPVGR NP_066544_R21W 19 652.843567 4.02947892238 99.999 +4 AQACNLDQSGTNVAK NP_112092_rs7285167:R182C 179 788.87384 1.27277118312 99.999 +6 LQLLPESFICK NP_001028196, NP_001244919, NP_036311 198; 163; 277 674.370911 0.341203679555 99.3865030675 +8 FGVSSESKPEEVK NP_001265138, NP_001265138_rs2274136:A858T,F879L, NP_001265139, NP_001265139_rs2274136:A785T,F806L, NP_005115, NP_005115_rs2274136:A827T,F848L 992; 992; 919; 919; 961; 961 711.858643 -0.766605567436 99.999