if len(sys.argv) == 1:
print "Path to place chromInfo tables must be specified."
sys.exit(1)
dbpath = sys.argv[1]
builds = []
if len(sys.argv) > 2:
try:
buildfile = fileinput.FileInput(sys.argv[2])
for line in buildfile:
if line.startswith("#"):
continue
builds.append(line.split("\t")[0])
except:
print "Bad input file."
sys.exit(1)
else:
try:
for build in parse_builds.getbuilds("http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn"):
builds.append(build[0])
except:
print "Unable to retrieve builds."
sys.exit(1)
for build in builds:
if build == "?":
continue # no lengths for unspecified chrom
outfile = open(dbpath + build + ".len", "w")
print "Retrieving " + build
for chrominfo in getchrominfo("http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?", build):
print >> outfile, "\t".join(chrominfo)
outfile.close()
if len(sys.argv) == 1:
sys.exit("Path to place chromInfo tables must be specified.")
dbpath = sys.argv[1]
builds = []
if len(sys.argv) > 2:
try:
buildfile = fileinput.FileInput(sys.argv[2])
for line in buildfile:
if line.startswith("#"):
continue
builds.append(line.split("\t")[0])
except:
sys.exit("Bad input file.")
else:
try:
for build in parse_builds.getbuilds("http://genome.cse.ucsc.edu/cgi-bin/das/dsn"):
builds.append(build[0])
except:
sys.exit("Unable to retrieve builds.")
for build in builds:
if build == "?":
continue # no lengths for unspecified chrom
print("Retrieving " + build)
outfile_name = dbpath + build + ".len"
try:
with open(outfile_name, "w") as outfile:
for chrominfo in getchrominfo("http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?", build):
print("\t".join(chrominfo), file=outfile)
except Exception as e:
print("Failed to retrieve %s: %s" % (build, e))
os.remove(outfile_name)
