steps.append(PPS('Map peaks to genes',calls,env=os.environ))
# THEME
# extract foreground and generate background sequences
fg_fn = "%s_peaks.fa"%opts.exp_name
bg_fn = "%s_bg.fa"%opts.exp_name
nib_dir = org_settings['genome_dir']
calls = ["peaks_to_fasta.py %(opts)s --output=%(fg_fn)s --bg-fn=%(bg_fn)s %(organism)s %(peaks_fn)s"%{'opts':opts.pk_to_fa_args,'organism':organism,'fg_fn':fg_fn,'bg_fn':bg_fn,'peaks_fn':peaks_fn}]
steps.append(PPS('Peaks to Fasta',calls,env=os.environ))
# run THEME on fg
motif_fn = '%s_motifs.txt'%opts.exp_name
hyp_fn = org_settings['theme_hypotheses']
markov_fn = org_settings['theme_markov']
calls = ["THEME.py %(opts)s --motif-file=%(motif_fn)s %(fg_fn)s %(bg_fn)s %(hyp)s %(markov)s"%{'opts':opts.theme_args,'motif_fn':motif_fn,'fg_fn':fg_fn,'bg_fn':bg_fn,'hyp':hyp_fn,'markov':markov_fn}]
steps.append(PPS('Run THEME on foreground',calls,env=os.environ))
# run THEME randomization
random_motif_fn = '%s_motifs_rand.txt'%opts.exp_name
calls = ["THEME.py %(opts)s --randomization --motif-file=%(motif_fn)s %(fg_fn)s %(bg_fn)s %(hyp)s %(markov)s"%{'opts':opts.theme_args,'motif_fn':random_motif_fn,'fg_fn':fg_fn,'bg_fn':bg_fn,'hyp':hyp_fn,'markov':markov_fn}]
steps.append(PPS('Run THEME randomization',calls,env=os.environ))
# cleanup
rm_str = "rm -f %(d)s/*.out %(d)s/*.err %(d)s/*.script %(d)s/*.stats %(d)s/*.bed"
calls = [rm_str%{'d':exp_wrk_dir},
rm_str%{'d':cnt_wrk_dir}]
steps.append(PPS('Clean up',calls,env=os.environ))
pipeline.add_steps(steps)
pipeline.run(interactive=not opts.auto)
ls_fn = 'ls_out.txt'
steps.append(ProcessPypeStep('Get directory file list','ls -1d > %s'%ls_fn))
# step 2 - do a word count
wc_fn = 'wc_out.txt'
steps.append(ProcessPypeStep('Get wordcount','wc %s > %s'%(ls_fn,wc_fn)))
# step 3 - sort the file and output
steps.append(ProcessPypeStep('Sort wordcount','sort -n %s'%wc_fn))
# step 4 - cleanup files
def rm_stuff() :
import glob
from subprocess import call
txt_fns = glob.glob('*.txt')
for fn in txt_fns :
call('rm %s'%fn,shell=True)
return True
steps.append(PythonPypeStep('Cleanup',rm_stuff))
# step 5 - intentionally fail
def epic_fail() :
return False
steps.append(PythonPypeStep('Cheerfully Ignore Failure',epic_fail))
# step 6 - whistle a happy tune
steps.append(ProcessPypeStep('Whistle a Happy Tune','echo Whistling a happy tune'))
pipeline.add_steps(steps)
pipeline.run(interactive=True)
meme_d = {'meme_args':opts.meme_args,
'meme_log':meme_log,
'fg_fn':fg_fn,
#'bg_fn':bg_fn,
#'bg_markov':meme_bg_markov,
'meme_oc':meme_oc
}
calls = ["meme-chip -oc %(meme_oc)s %(meme_args)s %(fg_fn)s 2>&1 | tee %(meme_log)s"%meme_d]
steps.append(PPS("Run MEME-ChIP",calls,env=os.environ))
#############################################################################
# build infosite
#############################################################################
calls = ['build_chipseq_infosite.py %s'%opts.infosite_args]
steps.append(PPS('Build infosite',calls,env=os.environ))
# cleanup
rm_str = "rm -f %(d)s/*.out %(d)s/*.err %(d)s/*.script %(d)s/*.stats %(d)s/*.bed"
calls = [rm_str%{'d':exp_wrk_dir}]
if control_fn :
calls.append(rm_str%{'d':cnt_wrk_dir})
#steps.append(PPS('Clean up',calls,env=os.environ))
pipeline.add_steps(steps)
if opts.auto and opts.steplist is not None :
steplist = parse_steplist(opts.steplist,pipeline)
else :
steplist = None
pipeline.run(interactive=not opts.auto,steplist=steplist)
