for f,rname in jobfiles[job.attrib['protocol']]:
resource_file = os.path.join(jdir,f)
if os.path.exists(resource_file):
pool_resources.append((resource_file,'%s_%s' % (job.attrib['protocol'],rname)))
igvfile = os.path.join(resultdir,'%s.igv.xml' % pool.attrib['name'])
with open(igvfile,'w') as outh:
print >>outh, igv_xml(refurl,pool_resources)
igvurls[pool.attrib['name']] = igvfile
#--- Summarize calls
calltable = merge_calls(analysis,reflens,poollist)
bestbets = best_calls(calltable)
#--- Create the excel file
excelfile = os.path.join(resultdir,'%s.xlsx' % analysis.attrib['name'])
create_result_workbook(refnames, poollist, calltable, bestbets, excelfile)
#--- Make the index.html file
htmlfile = os.path.join(adir,'index.html')
with open(htmlfile,'w') as outh:
print >>outh, make_index(analysis,'localhost',reflens,calltable,bestbets)
except (IOError,OSError) as e:
if e.args[1] == 'Read-only file system':
sys.exit('Destination "%s" is mounted as read-only.' % args.destination)
else: raise
finally:
os.umask(omask)
## generate the igv.xml file for each pool
igvfile = os.path.join(resultdir,'%s.igv.xml' % pool.attrib['name'])
with open(igvfile,'w') as outh:
print >>outh, igv_xml(refurl,pool_resources)
igvurls[pool.attrib['name']] = alias_filename(igvfile)
#--- Summarize calls
calltable = merge_calls(analysis,reflens,poollist)
bestbets = best_calls(calltable)
###################
#--- Create the excel file
excelfile = os.path.join(resultdir,'%s.xlsx' % analysis.attrib['name'])
create_result_workbook(refnames,poollist,calltable,bestbets,excelfile)
###################
#--- Make the index.html file
htmlfile = os.path.join(adir,'index.html')
with open(htmlfile,'w') as outh:
print >>outh, make_index(analysis,URLPATH,reflens,calltable,bestbets)
except (IOError,OSError) as e:
if e.args[1] == 'Read-only file system':
sys.exit('Destination "%s" is mounted as read-only.' % args.destination)
else: raise
finally:
os.umask(omask)
igvurls[pool.attrib['name']] = alias_filename(igvfile)
#--- Summarize calls
calltable = merge_calls(analysis, reflens, poollist)
bestbets = best_calls(calltable)
###################
#--- Create the excel file
excelfile = os.path.join(resultdir,
'%s.xlsx' % analysis.attrib['name'])
create_result_workbook(refnames, poollist, calltable, bestbets,
excelfile)
###################
#--- Make the index.html file
htmlfile = os.path.join(adir, 'index.html')
with open(htmlfile, 'w') as outh:
print >> outh, make_index(analysis, URLPATH, reflens, calltable,
bestbets)
except (IOError, OSError) as e:
if e.args[1] == 'Read-only file system':
sys.exit('Destination "%s" is mounted as read-only.' %
args.destination)
else:
raise
finally:
os.umask(omask)
