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Query fix

This commit is contained in:
Arnar Flatberg 2007-07-05 18:49:24 +00:00
parent 850deeec0d
commit dd04e28a62
1 changed files with 21 additions and 9 deletions
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30
workflows/smokers.py
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@ -229,15 +229,24 @@ class ModKernelFunction(workflow.Function):
class NCBIQuery(workflow.Function):
def __init__(self):
def __init__(self, gene_id_name='gene_id'):
self._gene_id_name = gene_id_name
workflow.Function.__init__(self, 'query', 'NCBI')
def run(self, selection):
if not selection.has_key(self._gene_id_name):
logger.log("notice", "Expected gene ids: %s, but got: %s" %(self._gene_id_name, selection.keys()))
return None
if len(selection[self._gene_id_name])==0:
logger.log("notice", "No selected genes to query")
return None
logger.log("notice", "No selected genes to query")
base = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?'
options = {r'&db=' : 'gene',
r'&cmd=' : 'retrieve',
r'&dopt=' : 'full_report'}
gene_str = ''.join([gene + "+" for gene in selection['gene_id']])
gene_str = ''.join([gene + "+" for gene in selection[self._gene_id_name]])
options[r'&list_uids='] = gene_str[:-1]
opt_str = ''.join([key+value for key,value in options.items()])
web_str = base + opt_str
@ -245,20 +254,23 @@ class NCBIQuery(workflow.Function):
class KEGGQuery(workflow.Function):
def __init__(self):
def __init__(self, org='hsa', gene_id_name='gene_id'):
self._org=org
self._gene_id_name = gene_id_name
workflow.Function.__init__(self, 'query', 'KEGG')
def run(self, selection):
if not selection.has_key('genes') \
or not selection.has_key('orfs'):
if not selection.has_key(self._gene_id_name):
logger.log("notice", "Expected gene ids: %s, but got. %s" %(self._gene_id_name, selection.keys()))
return None
if len(selection[self._gene_id_name])==0:
logger.log("notice", "No selected genes to query")
return None
base = r'http://www.genome.jp/dbget-bin/www_bget?'
options = {'org' : 'gene'}
org = 'hsa'
gene_str = ''.join([gene + "+" for gene in selection['gene_id']])
gene_str = ''.join([gene + "+" for gene in selection[self._gene_id_name]])
gene_str = gene_str[:-1]
gene_str = org + "+" + gene_str
gene_str = self._org + "+" + gene_str
web_str = base + gene_str
webbrowser.open(web_str)