def run_bedtools():
params.i = infile
shell.grep('^#', infile, _stdout=outfile)
c = shell.Shell(dash='-', equal=' ', subcmd=True).bedtools
if unique:
c.sort(**params).pipe().uniq(__stdout=outfile).run()
else:
params.__stdout = outfile
c.sort(**params).run()
def run_bedops():
params['max-mem'] = args.mem
params.tmpdir = tmpdir
params._ = infile
shell.grep('^#', infile, _stdout=outfile)
c = shell.Shell(equal=' ')
if unique:
c.bedops(**params).pipe().uniq(__stdout=outfile).run()
else:
params.__stdout = outfile
c.bedops(**params).run()
def run_sort():
params.T = tmpdir
params.S = argsmem
params.u = unique
if sortby == 'coord':
params.k = ['1,1', '2,2n']
else:
params.k = '4'
shell.grep('^#', infile, _stdout=outfile)
shell.Shell().grep(v='^#',
infile).pipe(dash='-',
equal='=').sort(**params,
__stdout=outfile).run()
from pyppl import Box
from bioprocs.utils.shell import grep, zcat
infile = {{i.infile | quote}}
outfile = {{o.outfile | quote}}
params = {{args.params | repr}}
keyword = {{args.keyword | repr}}
if not keyword:
raise ValueError('A keyword (args.keyword) is required.')
params._stdout = outfile
if infile.endswith('.gz'):
zcat(infile).pipe().grep(_=keyword, **params)
else:
grep(_=[keyword, infile], **params)
from os import remove
from pyppl import Box
from bioprocs.utils import shell
infiles = {{i.infile | repr}}
params = {{args.params | repr}}
shell.TOOLS.bedtools = {{args.bedtools | quote}}
mergedtmp = '{{job.outdir}}/mergedtmp.bed'
mergedtmpsorted = '{{job.outdir}}/mergedtmp.sorted.bed'
shell.touch(mergedtmp)
for infile in infiles:
shell.grep(v='^#', _=infile, __stdout=mergedtmp)
shell.sort(k=['1,1', '2,2n'], _=mergedtmp, _stdout=mergedtmpsorted)
params.i = mergedtmpsorted
params._stdout = outfile
shell.Shell(subcmd=True, dash='-', equal=' ').bedtools.merge(**params).run()
shell.rm_rf(mergedtmp)
shell.rm_rf(mergedtmpsorted)