Mercurial > repos > greg > genotype_population_info
changeset 0:0b7555cd19f3 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 15 Aug 2019 10:58:24 -0400 |
| parents | |
| children | 4943d9b12222 |
| files | .shed.yml genotype_population_info.py genotype_population_info.xml |
| diffstat | 3 files changed, 144 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Thu Aug 15 10:58:24 2019 -0400 @@ -0,0 +1,11 @@ +name: genotype_population_info +owner: greg +description: | + Contains a tool that generates the genotype population information file for use as input to the coral_multilocus_genotype tool. +homepage_url: http://baumslab.org +long_description: | + Contains a tool that generates the genotype population information file for use as input to the coral_multilocus_genotype tool. +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/corals/genotype_population_info +type: unrestricted +categories: + - Micro-array Analysis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genotype_population_info.py Thu Aug 15 10:58:24 2019 -0400 @@ -0,0 +1,93 @@ +#!/usr/bin/env python +import argparse +import sys + +import psycopg2 +from sqlalchemy import create_engine, MetaData +from sqlalchemy.engine.url import make_url + + +class GenotypeInfoGenerator(object): + def __init__(self): + self.args = None + self.conn = None + self.parse_args() + self.outfh = open(self.args.output, "w") + self.connect_db() + self.engine = create_engine(self.args.database_connection_string) + self.metadata = MetaData(self.engine) + + def parse_args(self): + parser = argparse.ArgumentParser() + parser.add_argument('--database_connection_string', dest='database_connection_string', help='Postgres database connection string'), + parser.add_argument('--input_partial_info', dest='input_partial_info', help='Tabular file containing part of the genotype info') + parser.add_argument('--output', dest='output', help='Output dataset'), + self.args = parser.parse_args() + + def connect_db(self): + url = make_url(self.args.database_connection_string) + args = url.translate_connect_args(username='user') + args.update(url.query) + assert url.get_dialect().name == 'postgresql', 'This script can only be used with PostgreSQL.' + self.conn = psycopg2.connect(**args) + + def run(self): + sql = """ + SELECT sample.user_specimen_id, + reef.region + FROM sample + LEFT OUTER JOIN colony + ON sample.colony_id = colony.id + LEFT OUTER JOIN reef + ON reef.id = colony.reef_id + WHERE sample.affy_id = '%s'; + """ + with open(self.args.input_partial_info, "r") as fh: + for line in fh: + line = line.strip() + out_items = [] + items = line.split('\t') + # Item number. + out_items.append(items[0]) + affy_id = items[1] + out_items.append(affy_id) + if len(items) == 2: + # Example line: + # 1 a100000-4368120-060520-256_I07.CEL + # The line is missing the user_specimen_id and + # region, so retrieve it from the database. + query = sql % affy_id + cur = self.conn.cursor() + cur.execute(query) + try: + missing_items = cur.fetchone() + # user_specimen_id + out_items.append(missing_items[0]) + # region + out_items.append(missing_items[1]) + except Exception as e: + msg = "Error retrieving user_specimen_id and region from the database for affy_id %s: %s" % (affy_id, e) + self.stop_err(msg) + else: + # The line contains all of the information we need. + # user_specimen_id + out_items.append(items[3]) + # region + out_items.append(items[9]) + self.outfh.write("%s\n" % "\t".join(out_items)) + self.outfh.close() + + def shutdown(self): + self.conn.close() + + def stop_err(self, msg): + sys.stderr.write(msg) + self.outfh.flush() + self.outfh.close() + sys.exit(1) + + +if __name__ == '__main__': + gig = GenotypeInfoGenerator() + gig.run() + gig.shutdown()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genotype_population_info.xml Thu Aug 15 10:58:24 2019 -0400 @@ -0,0 +1,40 @@ +<tool id="genotype_population_info" name="Generate genotype population" version="1.0.0"> + <description>information from a partial dataset</description> + <command detect_errors="exit_code"><![CDATA[ +python $__tool_directory__/genotype_population_info.py +--database_connection_string '$__app__.config.corals_database_connection' +--input_partial_info '$input_partial_info' +--output '$output' +]]></command> + <inputs> + <param name="input_partial_info" type="data" format="tabular" label="Partial genotype population file"/> + </inputs> + <outputs> + <data name="output" format="tabular"/> + </outputs> + <tests> + <test> + <!--Testing this tool is a bit difficult at the current time.--> + </test> + </tests> + <help> +**What it does** + +Accepts a file that contains Affymetrix identifiers and a subset of the user specimen identifiers and +regions for genotyping. The corals (stag) database is queried to retrieve the user specimen identifiers +and regions that are missing for each Affymetrix identifier, and a complete set of genotype population +information is produced for use as input to the Coral Multilocus Genotype tool. This tool must be able +to access the corals (stag) database. + </help> + <citations> + <citation type="bibtex"> + @misc{None, + journal = {None}, + author = {Baums I}, + title = {Manuscript in preparation}, + year = {None}, + url = {http://baumslab.org} + </citation> + </citations> +</tool> +