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)
args.reads1_files, args.reads2_files, args.output_shortname, args.symlink_dir, args.fetcher_dir
):
annoj_d = {
"aligner": aligner,
"dbhost": args.aj_dbhost,
"dbname": args.aj_dbname,
"dbuser": args.aj_dbuser,
"dbpass": args.aj_dbpass,
"dbtable": outf_short.replace("-", "").replace("(", "$").replace(")", "$"),
"bamfile": os.path.join(symlink_d, outf_short + ".sorted.bam"),
"fetcher": os.path.join(fetcher_d, outf_short + ".php"),
"title": args.aj_title,
"info": args.aj_info,
}
if reads2f == "":
annoj_d["pe"] = "--pe"
else:
annoj_d["pe"] = ""
calls.append(
'integrate_bam_annoj.py %(aligner) %(pe)s --dbhost=%(dbhost)s --dbname=%(dbname)s --dbuser=%(dbuser)s --dbpass=%(dbpass)s --dbtable=%(dbtable)s --bamfile=%(bamfile)s --fetcher=%(fetcher)s --title="%(title)s --info="%(info)s"'
% (annoj_d)
)
steps.append(PPS("Integrate with AnnoJ browser", calls, env=os.environ))
pipeline.add_steps(steps)
if args.auto and args.steplist is not None:
steplist = parse_steplist(args.steplist, pipeline)
else:
steplist = None
pipeline.run(interactive=not args.auto, steplist=steplist)