def install_jbrowse(install_dir,
root_url,
rename_to=None,
conf_file=None):
if not conf_file:
conf_file = config.get_default_conf_file()
install_dir = util.abspath(install_dir)
pkg_data_dir = config.get_pkg_data_dir()
jbrowse_zip = glob(pjoin(pkg_data_dir,"JBrowse*"))
assert len(jbrowse_zip) == 1, "Expected a single JBrowse archive "+\
"stored within the package data dir: %s" % (pkg_data_dir,)
jbrowse_zip = jbrowse_zip[0]
util.makedir(install_dir)
#context manager only works for zipfile in Python 2.7
f = zipfile.ZipFile(jbrowse_zip, 'r')
try:
install_name = os.path.dirname(f.namelist()[0])
assert (install_name not in (".","..")) and \
os.path.dirname(install_name) == "",\
"Unsafe path detected in JBrowse archive: {}".format(f.namelist()[0])
install_home = pjoin(install_dir,install_name)
#JBrowse setup script will not install Pelr modules
#if it is executed in a directory where it was ran before,
#even unsuccessfuly.
#Wack the existing directory:
if os.path.exists(install_home):
shutil.rmtree(install_home)
#somehow zipfile module wacks executable bits
#f.extractall(path=install_dir)
#unsafe:
check_call(["unzip","-q","-o",jbrowse_zip],cwd=install_dir)
finally:
f.close()
if rename_to:
install_home_new = pjoin(install_dir,rename_to)
if os.path.exists(install_home_new):
shutil.rmtree(install_home_new)
os.rename(install_home,install_home_new)
install_home = install_home_new
check_call(["./setup.sh"],cwd=install_home)
for line in fileinput.input(pjoin(install_home,"index.html"),inplace=True):
#Galaxy Web server intercepts 'data' in URL params, we need to use another name
print line.replace('queryParams.data','queryParams.jbrowse_data'),
conf = util.load_config_json(conf_file)
conf["jbrowse_bin_dir"] = util.abspath(pjoin(install_home,"bin"))
conf["jbrowse_url"] = util.urljoin_path(root_url,
os.path.basename(install_home))
util.save_config_json(conf,conf_file)
return conf_file
def to_jbrowse(
genome_name,
annot_inp_fasta,
annot_out,
index_html,
data_dir_out,
conf_file=None):
args = locals()
args.pop("conf_file")
if not conf_file:
conf_file = config.get_default_conf_file()
opt = util.load_config_json(conf_file)
args["annot_inp_fasta"] = util.none_from_str(args["annot_inp_fasta"])
args["genome_name"] = util.none_from_str(args["genome_name"])
return galaxy_jbrowse(**opt).vicvb_to_jbrowse(**args)
def install_jbrowse(install_dir, root_url, rename_to=None, conf_file=None):
if not conf_file:
conf_file = config.get_default_conf_file()
install_dir = util.abspath(install_dir)
pkg_data_dir = config.get_pkg_data_dir()
jbrowse_zip = glob(pjoin(pkg_data_dir, "JBrowse*"))
assert len(jbrowse_zip) == 1, "Expected a single JBrowse archive "+\
"stored within the package data dir: %s" % (pkg_data_dir,)
jbrowse_zip = jbrowse_zip[0]
util.makedir(install_dir)
#context manager only works for zipfile in Python 2.7
f = zipfile.ZipFile(jbrowse_zip, 'r')
try:
install_name = os.path.dirname(f.namelist()[0])
assert (install_name not in (".","..")) and \
os.path.dirname(install_name) == "",\
"Unsafe path detected in JBrowse archive: {}".format(f.namelist()[0])
install_home = pjoin(install_dir, install_name)
#JBrowse setup script will not install Pelr modules
#if it is executed in a directory where it was ran before,
#even unsuccessfuly.
#Wack the existing directory:
if os.path.exists(install_home):
shutil.rmtree(install_home)
#somehow zipfile module wacks executable bits
#f.extractall(path=install_dir)
#unsafe:
check_call(["unzip", "-q", "-o", jbrowse_zip], cwd=install_dir)
finally:
f.close()
if rename_to:
install_home_new = pjoin(install_dir, rename_to)
if os.path.exists(install_home_new):
shutil.rmtree(install_home_new)
os.rename(install_home, install_home_new)
install_home = install_home_new
check_call(["./setup.sh"], cwd=install_home)
for line in fileinput.input(pjoin(install_home, "index.html"),
inplace=True):
#Galaxy Web server intercepts 'data' in URL params, we need to use another name
print line.replace('queryParams.data', 'queryParams.jbrowse_data'),
conf = util.load_config_json(conf_file)
conf["jbrowse_bin_dir"] = util.abspath(pjoin(install_home, "bin"))
conf["jbrowse_url"] = util.urljoin_path(root_url,
os.path.basename(install_home))
util.save_config_json(conf, conf_file)
return conf_file
def gff_to_jbrowse(self,
gff_file,
index_html,
data_dir_out,
jbrowse_url=None
):
opt = self.opt
if jbrowse_url is None:
jbrowse_url = opt["jbrowse_url"]
env = None
if self.opt.get("jbrowse_bin_dir",None):
env = os.environ.copy()
util.add_to_path(opt["jbrowse_bin_dir"],
prepend=True,
env=env)
if not os.path.exists(data_dir_out):
os.makedirs(data_dir_out)
gff_file = util.abspath(gff_file)
#fasta_file = util.abspath(fasta_file)
jbrowse_out_dir = os.path.join(data_dir_out,opt["jbrowse_data_subdir"])
#can use os.devnull to discard all output
jbrowse_conv_log_base = os.path.join(os.getcwd(),"jbrowse_conv_log")
with nested( open(jbrowse_conv_log_base+".out","w"),\
open(jbrowse_conv_log_base+".err","w") ) as ( stdout, stderr ):
check_call(["prepare-refseqs.pl","--gff",gff_file,"--out",jbrowse_out_dir],
env=env,
stdout=stdout,
stderr=stderr)
#@todo use biodb-to-json instead with flat file input, and accept config
#file as a parameter (provide a default one too). See volvox.json config
#in the distribution. Also add dropped_features param to load everything
#unique in field 3 of GFF and check that only dropped_features are missing
#from the config
check_call(["flatfile-to-json.pl","--gff",gff_file,"--out",jbrowse_out_dir,
"--trackLabel","Genes",
"--cssClass","feature5",
"--type","gene",
"--autocomplete","all"
"--getLabel",
"--getType"
],
env=env,
stdout=stdout,
stderr=stderr)
check_call(["flatfile-to-json.pl","--gff",gff_file,"--out",jbrowse_out_dir,
"--trackLabel","CDS",
"--cssClass","generic_parent",
"--subfeatureClasses",'{ "exon" : "exon" }',
"--type","CDS",
"--type","exon",
"--autocomplete","all"
"--getLabel",
"--getType",
"--getSubs",
"--getPhase"
],
env=env,
stdout=stdout,
stderr=stderr)
check_call(["flatfile-to-json.pl","--gff",gff_file,"--out",jbrowse_out_dir,
"--trackLabel","Peptides",
"--cssClass","est",
"--subfeatureClasses",'{ "mat_peptide" : "transcript-CDS" }',
"--type","mat_peptide",
"--autocomplete","all"
"--getLabel",
"--getType",
"--getSubs",
"--getPhase"
],
env=env,
stdout=stdout,
stderr=stderr)
check_call(["flatfile-to-json.pl","--gff",gff_file,"--out",jbrowse_out_dir,
"--trackLabel","Misc",
"--cssClass","feature3",
"--type","misc_feature",
"--autocomplete","all"
"--getLabel",
"--getType",
"--getSubs",
"--getPhase"
],
env=env,
stdout=stdout,
stderr=stderr)
check_call(["generate-names.pl","--out",jbrowse_out_dir],
env=env,
stdout=stdout,
stderr=stderr)
tracks_conf_file = os.path.join(jbrowse_out_dir,"trackList.json")
tracks_conf = util.load_config_json(tracks_conf_file)
tracks_conf["refSeqDropdown"] = True #show pull-down even for very many sequences
util.save_config_json(tracks_conf,tracks_conf_file)
#create index.html that redirects to JBrowse index.html with correct data param etc
_jbrowse_dataset_index_html = \
config.get_data_string(self.opt["jbrowse_galaxy_index_html_tpl"],
"galaxy.index.html")
jbrowse_url_params = util.to_url_params(dict(
tracks=",".join(("DNA","Genes","CDS","Peptides","Misc")),
tracklist=0
))
with open(index_html,"w") as f:
f.write(_jbrowse_dataset_index_html.\
format(jbrowse_url=jbrowse_url.rstrip("/"),
jbrowse_data_subdir=opt["jbrowse_data_subdir"],
jbrowse_url_params=jbrowse_url_params))