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)