mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-31 01:02:04 +08:00
James Taylor
44 lines
1.6 KiB
Python
44 lines
1.6 KiB
Python
#build list of available data
|
|
import os, sys
|
|
maf_sets = {}
|
|
|
|
try:
|
|
for line in open( "/cache/maf/maf_index.loc" ):
|
|
if line[0:1] == "#" : continue
|
|
|
|
fields = line.split('\t')
|
|
#read each line, if not enough fields, go to next line
|
|
try:
|
|
maf_desc = fields[0]
|
|
maf_uid = fields[1]
|
|
builds = fields[2]
|
|
build_list =[]
|
|
split_builds = builds.split(",")
|
|
for build in split_builds:
|
|
this_build = build.split("=")[0]
|
|
build_list.append(this_build)
|
|
paths = fields[3].replace("\n","").replace("\r","")
|
|
maf_sets[maf_uid]={}
|
|
maf_sets[maf_uid]['description']=maf_desc
|
|
maf_sets[maf_uid]['builds']=build_list
|
|
except:
|
|
continue
|
|
|
|
except Exception, exc:
|
|
print >>sys.stdout, 'interval2maf_code.py initialization error -> %s' % exc
|
|
|
|
#return available datasets for group and build, set None option as selected for hg16
|
|
def get_available_data( build ):
|
|
available_sets = []
|
|
for key in maf_sets:
|
|
if build in maf_sets[key]['builds']:
|
|
available_sets.append((maf_sets[key]['description'],key,False))
|
|
if len(available_sets) < 1:
|
|
available_sets.append(('No data available for this build','None',True))
|
|
return available_sets
|
|
|
|
|
|
def exec_before_job(trans,inp_data, out_data, param_dict, tool):
|
|
for name, data in out_data.items():
|
|
data.name = data.name + " [" + maf_sets[param_dict['mafType']]['description'] + "]"
|