Commit 8d9f4c72 authored by aknecht2's avatar aknecht2
Browse files

Updated run_data to load individual chromsome files for a genome.

parent bdf3ba3c
......@@ -167,6 +167,17 @@ class RunData(object):
chrom_name = "%s_%s" % (assembly, os.path.basename(self.data["genomes"][assembly]["chrom.sizes"]))
self._add_file(chrom_name, self.data["genomes"][assembly]["chrom.sizes"], "local")
self.genomes[assembly]["chrom.sizes"] = chrom_name
self.genomes[assembly]["chr_fasta"] = []
# Load chromosome files here:
base_dir = os.path.dirname(os.path.dirname(self.data["genomes"][assembly]["chrom.sizes"] + "/"))
print "walking through base_dir: %s" % (base_dir,)
for root, dirs, files in os.walk(base_dir):
for f in files:
print "checking file %s" % (f,)
if f.startswith("chr"):
self._add_file(f, root + "/" + f, "local")
self.genomes[assembly]["chr_fasta"].append(f)
break
else:
print self.err
raise SystemExit(1)
......
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