Mercurial > repos > shellac > sam_consensus_v3
diff env/lib/python3.9/site-packages/bioblend/galaxy/genomes/__init__.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.9/site-packages/bioblend/galaxy/genomes/__init__.py Mon Mar 22 18:12:50 2021 +0000 @@ -0,0 +1,104 @@ +""" +Contains possible interactions with the Galaxy Histories +""" +from bioblend.galaxy.client import Client + + +class GenomeClient(Client): + + def __init__(self, galaxy_instance): + self.module = 'genomes' + super().__init__(galaxy_instance) + + def get_genomes(self): + """ + Returns a list of installed genomes + + :rtype: list + :return: List of installed genomes + """ + genomes = self._get() + return genomes + + def show_genome(self, id, num=None, chrom=None, low=None, high=None): + """ + Returns information about build <id> + + :type id: str + :param id: Genome build ID to use + + :type num: str + :param num: num + + :type chrom: str + :param chrom: chrom + + :type low: str + :param low: low + + :type high: str + :param high: high + + :rtype: dict + :return: Information about the genome build + """ + params = {} + if num: + params['num'] = num + if chrom: + params['chrom'] = chrom + if low: + params['low'] = low + if high: + params['high'] = high + return self._get(id, params) + + def install_genome(self, func='download', source=None, dbkey=None, + ncbi_name=None, ensembl_dbkey=None, url_dbkey=None, + indexers=None): + """ + Download and/or index a genome. + + + :type dbkey: str + :param dbkey: DB key of the build to download, ignored unless 'UCSC' is specified as the source + + :type ncbi_name: str + :param ncbi_name: NCBI's genome identifier, ignored unless NCBI is specified as the source + + :type ensembl_dbkey: str + :param ensembl_dbkey: Ensembl's genome identifier, ignored unless Ensembl is specified as the source + + :type url_dbkey: str + :param url_dbkey: DB key to use for this build, ignored unless URL is specified as the source + + :type source: str + :param source: Data source for this build. Can be: UCSC, Ensembl, NCBI, URL + + :type indexers: list + :param indexers: POST array of indexers to run after downloading (indexers[] = first, indexers[] = second, ...) + + :type func: str + :param func: Allowed values: 'download', Download and index; 'index', Index only + + :rtype: dict + :return: dict( status: 'ok', job: <job ID> ) + If error: + dict( status: 'error', error: <error message> ) + """ + payload = {} + if source: + payload['source'] = source + if func: + payload['func'] = func + if dbkey: + payload['dbkey'] = dbkey + if ncbi_name: + payload['ncbi_name'] = ncbi_name + if ensembl_dbkey: + payload['ensembl_dbkey'] = ensembl_dbkey + if url_dbkey: + payload['url_dbkey'] = url_dbkey + if indexers: + payload['indexers'] = indexers + return self._post(payload)