def main(argv):
try:
config, args = bam_config.parse_config(argv)
if args and args[0].startswith("dry"):
config.dry_run = True
except bam_config.ConfigError, error:
print_err(error)
return 1
def main(argv):
try:
config, args = bam_config.parse_config(argv)
if args and args[0].startswith("dry"):
config.dry_run = True
except bam_config.ConfigError, error:
print_err(error)
return 1
def main(argv):
config, args = parse_options(argv)
if config is None:
return 1
# Get default options for bam_pipeline
bam_config, _ = bam_cfg.parse_config(args)
makefiles = bam_pipeline.read_makefiles(bam_config, args)
# Build .fai files for reference .fasta files
bam_pipeline.index_references(bam_config, makefiles)
for makefile in makefiles:
mkfile_fname = makefile["Statistics"]["Filename"]
bam_config.destination = os.path.dirname(mkfile_fname)
tasks = bam_pipeline.build_pipeline_full(bam_config,
makefile,
return_nodes=False)
make_dirs(config.destination)
makefile_name = add_postfix(makefile["Statistics"]["Filename"],
config.postfix)
makefile_path = reroot_path(config.destination, makefile_name)
if samefile(makefile["Statistics"]["Filename"], makefile_path):
sys.stderr.write("ERROR: Would overwrite source makefile at %r\n" %
(makefile_path, ))
sys.stderr.write(
" Please set --destination and/or --output-name-postfix\n"
)
sys.stderr.write(" before continuing.\n")
return 1
print("Writing makefile", makefile_path)
found_prefix = False
for prefix in makefile["Prefixes"]:
if prefix != config.prefix:
print("%sSkipping %s" % (_INDENTATION, prefix))
else:
found_prefix = True
if not found_prefix:
sys.stderr.write("\nERROR:\n")
sys.stderr.write("Could not find prefix %r in %r! Aborting ...\n" %
(config.prefix, mkfile_fname))
return 1
with open(makefile_path, "w") as makefile_handle:
bam_mkfile.print_header(dst=makefile_handle)
makefile_handle.write("\n" * 3)
for target in tasks:
target_name = add_postfix(target.name, config.postfix)
print("%sTarget: %s -> %s" %
(_INDENTATION, target.name, target_name))
makefile_handle.write('%s"%s":\n' %
(_INDENTATION * 0, target_name))
for prefix in target.prefixes:
if prefix.name != config.prefix:
continue
for sample in prefix.samples:
print("%sSample: %s" % (_INDENTATION * 2, sample.name))
makefile_handle.write('%s"%s":\n' %
(_INDENTATION * 1, sample.name))
for library in sample.libraries:
print("%sLibrary: %s" %
(_INDENTATION * 3, library.name))
makefile_handle.write(
'%s"%s":\n' % (_INDENTATION * 2, library.name))
sink_cache = {}
destination = os.path.join(target_name, "reads",
sample.name,
library.name)
for lane in library.lanes:
convert_reads(config, destination, lane,
sink_cache)
ReadSink.close_all_sinks()
for lane_name in sorted(sink_cache):
makefile_handle.write(
'%s"%s":\n' %
(_INDENTATION * 3, lane_name))
for (reads_type, sink) in sorted(
sink_cache[lane_name].items()):
makefile_handle.write(
'%s%s "%s"\n' %
(_INDENTATION * 4,
("%s:" % (reads_type, )).ljust(20),
sink.filename))
makefile_handle.write("\n")
print("\tDone ...")
print()
return 0
def main(argv):
config, args = parse_options(argv)
if config is None:
return 1
# Get default options for bam_pipeline
bam_config, _ = bam_cfg.parse_config(args)
makefiles = bam_pipeline.read_makefiles(bam_config, args)
# Build .fai files for reference .fasta files
bam_pipeline.index_references(bam_config, makefiles)
for makefile in makefiles:
mkfile_fname = makefile["Statistics"]["Filename"]
bam_config.destination = os.path.dirname(mkfile_fname)
tasks = bam_pipeline.build_pipeline_full(bam_config, makefile,
return_nodes=False)
make_dirs(config.destination)
makefile_name = add_postfix(makefile["Statistics"]["Filename"],
config.postfix)
makefile_path = reroot_path(config.destination, makefile_name)
if samefile(makefile["Statistics"]["Filename"], makefile_path):
sys.stderr.write("ERROR: Would overwrite source makefile at %r\n" % (makefile_path,))
sys.stderr.write(" Please set --destination and/or --output-name-postfix\n")
sys.stderr.write(" before continuing.\n")
return 1
print("Writing makefile", makefile_path)
found_prefix = False
for prefix in makefile["Prefixes"]:
if prefix != config.prefix:
print("%sSkipping %s" % (_INDENTATION, prefix))
else:
found_prefix = True
if not found_prefix:
sys.stderr.write("\nERROR:\n")
sys.stderr.write("Could not find prefix %r in %r! Aborting ...\n"
% (config.prefix, mkfile_fname))
return 1
with open(makefile_path, "w") as makefile_handle:
bam_mkfile.print_header(dst=makefile_handle)
makefile_handle.write("\n" * 3)
for target in tasks:
target_name = add_postfix(target.name, config.postfix)
print("%sTarget: %s -> %s" % (_INDENTATION,
target.name,
target_name))
makefile_handle.write('%s"%s":\n' % (_INDENTATION * 0,
target_name))
for prefix in target.prefixes:
if prefix.name != config.prefix:
continue
for sample in prefix.samples:
print("%sSample: %s" % (_INDENTATION * 2, sample.name))
makefile_handle.write('%s"%s":\n' % (_INDENTATION * 1,
sample.name))
for library in sample.libraries:
print("%sLibrary: %s" % (_INDENTATION * 3,
library.name))
makefile_handle.write('%s"%s":\n'
% (_INDENTATION * 2,
library.name))
sink_cache = {}
destination = os.path.join(target_name,
"reads",
sample.name,
library.name)
for lane in library.lanes:
convert_reads(config, destination, lane, sink_cache)
ReadSink.close_all_sinks()
for lane_name in sorted(sink_cache):
makefile_handle.write('%s"%s":\n' % (_INDENTATION * 3, lane_name))
for (reads_type, sink) in sorted(sink_cache[lane_name].items()):
makefile_handle.write('%s%s "%s"\n'
% (_INDENTATION * 4,
("%s:" % (reads_type,)).ljust(20),
sink.filename))
makefile_handle.write("\n")
print("\tDone ...")
print()
return 0
