def run(self, args):
if not args.index.endswith(".gem"):
raise CommandException("No valid GEM index specified, the file has to end in .gem")
if not os.path.exists(args.index):
raise CommandException("GEM index not found")
if not os.path.exists(args.annotation):
raise CommandException("Annotation not found")
name = args.name
if name is None:
name = os.path.basename(args.annotation)
junctions_out = name + ".junctions"
index_out = name + ".junctions.gem"
print "Loading Junctions"
junctions = set(gem.junctions.from_gtf(args.annotation))
print "%d Junctions loaded from annotation " % (len(junctions))
gem.junctions.write_junctions(junctions, junctions_out)
print "Junctions writen to %s " % (junctions_out)
print "Computing transcriptome..."
(transcriptome, keys) = gem.compute_transcriptome(args.maxlength, args.index, junctions_out)
print "Indexing transcriptome"
gem.index(transcriptome, index_out, threads=args.threads)
print "Done"
def run(self, args):
if not args.index.endswith(".gem"):
raise CommandException("No valid GEM index specified, the file has to end in .gem")
if not os.path.exists(args.index):
raise CommandException("GEM index not found")
if not os.path.exists(args.annotation):
raise CommandException("Annotation not found")
name = args.name
if name is None:
name = os.path.basename(args.annotation)
junctions_out = name + ".junctions"
index_out = name + ".junctions.gem"
print "Loading Junctions"
junctions = set(gem.junctions.from_gtf(args.annotation))
print "%d Junctions loaded from annotation " % (len(junctions))
gem.junctions.write_junctions(junctions, junctions_out)
print "Junctions writen to %s " % (junctions_out)
print "Computing transcriptome..."
(transcriptome, keys) = gem.compute_transcriptome(args.maxlength, args.index, junctions_out)
print "Indexing transcriptome"
gem.index(transcriptome, index_out, threads=args.threads)
print "Done"
def run(self, args):
input = args.input
output = os.path.basename(input)
if args.output is not None:
output = args.output
else:
output = output[:output.rfind(".")] + ".gem"
if not output.endswith(".gem"):
raise CommandException("Output file name has to end in .gem")
if not os.path.exists(input):
raise CommandException("Input file not found : %s" % input)
if input.endswith(".gz"):
raise CommandException("Compressed input is currently not supported!")
logging.gemtools.gt("Creating index")
gem.index(input, output, threads=args.threads)
def test_indexer_output_suffix():
result = results_dir + "/genome_index.gem"
input = testfiles["genome.fa"]
index = gem.index(input, result)
assert index == result, "Result should be %s.gem but is %s" % (result,
index)
assert os.path.exists(result)
def test_junction_filter():
result = results_dir + "/test_xs.gem"
index = gem.index(testfiles["test_xs.fa"], result)
jf = gem.splits.append_xs_filter(index)
of = open(testfiles["test_xs.sam"])
def get_xs(l):
for f in l.split("\t"):
if f.startswith("XS"):
return f[-1]
return None
for line in of:
if line[0] == "@": continue
source_xs = get_xs(line)
filter_xs = get_xs(jf.filter(line))
assert source_xs == filter_xs
#!/usr/bin/python
"""Example script that creates the example gem-index"""
import gem
import os
if __name__ == "__main__":
basedir = os.path.split(os.path.dirname(os.path.abspath(__file__)))[0]
target = "%s/results/chr21.gem" % basedir
source = "%s/data/chr21.fa" % basedir
print("Creating index for %s" % (source))
print("GEM index is created in %s" % (target))
if not os.path.exists(source):
print("Unable to find source file %s. "
"Please make sure you ran the bootstrap "
"script to download and prepare demo data" % (source))
exit(1)
index = gem.index(source, target)
print("Created index %s " % index)
def test_indexer_output_suffix():
result = results_dir + "/genome_index.gem"
input = testfiles["genome.fa"]
index = gem.index(input, result)
assert index == result, "Result should be %s.gem but is %s" % (result, index)
assert os.path.exists(result)
def test_indexer():
result = results_dir + "/genome_index"
input = testfiles["genome.fa"]
index = gem.index(input, result)
assert index == result+".gem"
assert os.path.exists(result+".gem")
def create_index():
"""Create the example index"""
print "Preparing index"
return gem.index("%s/chr21.fa" % data_dir, "%s/chr21.gem" % result_dir, threads=THREADS)
def test_indexer():
result = results_dir + "/genome_index"
input = testfiles["genome.fa"]
index = gem.index(input, result)
assert index == result + ".gem"
assert os.path.exists(result + ".gem")