def __init__(self, opts):
if not os.path.exists(opts.jar):
raise ValueError, 'jar file does not exist'
self.jar = opts.jar
self.tmp_dir = opts.tmp_dir
self.log_suffix = opts.suffix_tmpl % (timestamp(), 'log')
self.maxjheap = opts.maxjheap
self.output_dir = os.path.dirname(opts.output)
self.runs = []
self.logs = []
def __init__(self, opts):
if not os.path.exists(opts.jar):
raise ValueError, "jar file does not exist"
self.jar = opts.jar
self.tmp_dir = opts.tmp_dir
self.log_suffix = opts.suffix_tmpl % (timestamp(), "log")
self.maxjheap = opts.maxjheap
self.output_dir = os.path.dirname(opts.output)
self.runs = []
self.logs = []
op.add_option('-n', '--title', default='')
op.add_option('-v', '--verbose', action='store_true')
opts, args = op.parse_args()
assert opts.input <> None
assert os.path.isfile(opts.input)
assert os.path.isfile(opts.jar)
if not os.path.exists(opts.tmp_dir): os.makedirs(opts.tmp_dir)
suffix_tmpl = 'rgTempFixMate_%s.%s'
opts.suffix_tmpl = suffix_tmpl
# Picard tools always produces bam files. Naming accordingly...
ifd, intermediate_filename = tempfile.mkstemp(suffix=suffix_tmpl %
(timestamp(), 'bam'),
dir=opts.tmp_dir)
fm = fixMate(opts)
fm.run(os.path.abspath(opts.input), output_file=intermediate_filename)
if opts.verbose:
for run, log in zip(fm.runs, fm.logs):
print 'Call to \n%s\n produced the following output:\n%s' % (run,
log)
intermediate = Bam(intermediate_filename)
# Picard tool produced intermediate bam file. Depending on the
# desired format, we either just move to final location or create
# a sam version of it.
op.add_option("-n", "--title", default="")
op.add_option("-v", "--verbose", action="store_true")
opts, args = op.parse_args()
assert opts.input <> None
assert os.path.isfile(opts.input)
assert os.path.isfile(opts.jar)
if not os.path.exists(opts.tmp_dir):
os.makedirs(opts.tmp_dir)
suffix_tmpl = "rgTempFixMate_%s.%s"
opts.suffix_tmpl = suffix_tmpl
# Picard tools always produces bam files. Naming accordingly...
ifd, intermediate_filename = tempfile.mkstemp(suffix=suffix_tmpl % (timestamp(), "bam"), dir=opts.tmp_dir)
fm = fixMate(opts)
fm.run(os.path.abspath(opts.input), output_file=intermediate_filename)
if opts.verbose:
for run, log in zip(fm.runs, fm.logs):
print "Call to \n%s\n produced the following output:\n%s" % (run, log)
intermediate = Bam(intermediate_filename)
# Picard tool produced intermediate bam file. Depending on the
# desired format, we either just move to final location or create
# a sam version of it.
if opts.newformat == "sam":
sam_file = intermediate.to_sam(os.path.abspath(opts.output))