# if server == 'smc2': # return specL[-1] # else: # return specL return specL if __name__ == '__main__': optL, argL = getopt.getopt(sys.argv[1:], 'i:n:p:c:s:g:', []) optH = mybasic.parseParam(optL) pathL = optH['-i'] sN = optH['-n'] pN = optH['-p'] clean = optH['-c'] server = optH['-s'] genome = optH['-g'] mypipe.main(inputFilePathL=glob(pathL), genSpecFn=genSpec, sampN=sN, projectN=pN, clean=clean, server=server, genome=genome) #mypipe.main(inputFilePathL=glob('/home/heejin/practice/gatk/pipe_test/*.bam'), genSpecFn=genSpec, sampN='S647_splice', projectN='rsq_pipe_test2', clean=False)
'logExistsFn': lambda x: len(x)>0 and 'Uploaded run' in x[-1], 'outFilePostFix': ['recal.bam'] }, { 'name': 'Pileup', 'desc': 'recal.bam -> pileup', 'fun': pileup_batch.main, 'paramL': (baseDir, baseDir, False), 'paramH': {}, 'logPostFix': 'pileup.log', 'logExistsFn': lambda x: len(x)>0 and 'Set max' in x[-1], 'outFilePostFix': ['pileup'] }, # { # 'name': 'Cleanup', # 'desc': 'remove all, but logs and designated result file', # 'fun': cleanup.main, # 'paramL': (baseDir,), # 'paramH': {}, # 'logPostFix': 'cleanup.qlog', # 'logExistsFn': lambda x: False, # 'outFilePostFix': ['pileup'] # }, ] if __name__ == '__main__': mypipe.main(inputFilePathL=glob('/home/yenakim/YN/linked_fq/S780_T_SS/S780_T_SS.*.fq'), genSpecFn=genSpec, sampN='S780_T_SS', projectN='test', clean=False)
}, { 'name': 'build tree', 'desc': 'make phylogenetic tree', 'fun': make_phylotree.main, 'paramL': (baseDir, baseDir), 'paramH': {}, 'logPostFix': '.make_phylotree.log', 'logExistsFn': lambda x: 'done' in x[-1], 'outFilePostFix': ['.infile', '.outfile','.tree','.pars_tree.pdf','.outfile_report.txt'], 'clean': False, 'rerun': False }, ] if __name__ == '__main__': optL, argL = getopt.getopt(sys.argv[1:], 'i:n:p:c:s:g:') optH = mybasic.parseParam(optL) pathL = optH['-i'].split(',') sN = optH['-n'] pN = optH['-p'] clean = optH['-c'] server = optH['-s'] genome = optH['-g'] genSpecFN = genSpec if pathL != []: mypipe.main(inputFilePathL=pathL, genSpecFn=genSpecFN, sampN=sN, projectN=pN, clean=clean, server=server, genome=genome)
return [ ## PARAMETERS { 'name': 'determine mutation clonality', 'desc': 'mutect -> mutect_cl.dat', 'fun': mut_clonality_batch.main, 'paramL': (baseDir, baseDir, mysetting.cnaBaseDir, False, server), 'paramH': {}, 'logPostFix': '.mutect_cl.log', 'logExistsFn': lambda x: len(x)==0, 'outFilePostFix': ['mutect_cl.dat'], 'clean': False, 'rerun': False }, ] if __name__ == '__main__': optL, argL = getopt.getopt(sys.argv[1:],'i:n:p:c:s:',[]) optH = mybasic.parseParam(optL) pathL = optH['-i'] # cnPathL = optH['-k'] sN = optH['-n'] pN = optH['-p'] clean = optH['-c'] server = optH['-s'] # mypipe.main(inputFilePathL=glob(pathL)+glob(cnPathL), genSpecFn=genSpec, sampN=sN, projectN=pN, clean=clean, server=server) mypipe.main(inputFilePathL=glob(pathL), genSpecFn=genSpec, sampN=sN, projectN=pN, clean=clean, server=server)
'name': 'Pileup', 'desc': 'recal.bam -> pileup', 'fun': pileup_batch.main, 'paramL': (baseDir, baseDir, False), 'paramH': {}, 'logPostFix': 'pileup.log', 'logExistsFn': lambda x: len(x) > 0 and 'Set max' in x[-1], 'outFilePostFix': ['pileup'] }, # { # 'name': 'Cleanup', # 'desc': 'remove all, but logs and designated result file', # 'fun': cleanup.main, # 'paramL': (baseDir,), # 'paramH': {}, # 'logPostFix': 'cleanup.qlog', # 'logExistsFn': lambda x: False, # 'outFilePostFix': ['pileup'] # }, ] if __name__ == '__main__': mypipe.main(inputFilePathL=glob( '/home/yenakim/YN/linked_fq/S780_T_SS/S780_T_SS.*.fq'), genSpecFn=genSpec, sampN='S780_T_SS', projectN='test', clean=False)