def index(args):
if not os.path.exists(args.indexdir):
print "Index_dir %s does not exist!" % (args.indexdir)
sys.exit(1)
fasta_dir = args.fastadir
index_dir = os.path.join(args.indexdir, args.indexname)
g = GenomeIndex()
g.create_index(fasta_dir, index_dir)
# Create genome FASTA file for use with bedtools
with open(os.path.join(index_dir, "genome.fa"), 'w') as out:
for f in find_by_ext(fasta_dir, FASTA_EXT):
for line in open(f):
out.write(line)
test_chr = g.get_chromosomes()[0]
tmp = NamedTemporaryFile()
tmp.write("{}\t1\t2\n".format(test_chr))
tmp.flush()
b = pybedtools.BedTool(tmp.name)
try:
b.nucleotide_content(fi=os.path.join(index_dir, "genome.fa"))
except pybedtools.helpers.BEDToolsError as e:
if str(e).find("generating") == -1:
raise
