Ejemplo n.º 1
0
    #	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)
Ejemplo n.º 2
0
		'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)
Ejemplo n.º 3
0
		},

		{
		'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)
Ejemplo n.º 4
0
	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)
Ejemplo n.º 5
0
            '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)