def main():
# setup logging
logging.basicConfig(level=logging.DEBUG,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
logging.info("AssemblyLine %s" % (assemblyline.__version__))
logging.info("----------------------------------")
# command line parsing
parser = argparse.ArgumentParser()
parser.add_argument("--mode", dest="mode", choices=['htseq', 'cufflinks'],
default='htseq')
parser.add_argument("--dryrun", dest="dryrun", action="store_true",
default=False)
parser.add_argument("--keep-tmp", dest="keep_tmp", action="store_true",
default=None)
parser.add_argument('-o', '--output-dir', dest="output_dir", default=None)
parser.add_argument("config_xml_file")
parser.add_argument('library_table')
parser.add_argument("gtf_file")
args = parser.parse_args()
if not os.path.exists(args.config_xml_file):
parser.error("config xml file '%s' not found" % (args.config_xml_file))
if not os.path.exists(args.library_table):
parser.error("library table file '%s' not found" % (args.library_table))
if not os.path.exists(args.gtf_file):
parser.error("gtf file '%s' not found" % (args.gtf_file))
gtf_file = os.path.abspath(args.gtf_file)
# read configuration
logging.info("Reading configuration file")
config = Config.from_xml(args.config_xml_file)
if args.output_dir is not None:
config.output_dir = os.path.abspath(args.output_dir)
else:
config.output_dir = os.getcwd()
config.keep_tmp = args.keep_tmp
config.dryrun = args.dryrun
# create output directory
if not os.path.exists(config.output_dir):
os.makedirs(config.output_dir)
# read library table
logging.info("Parsing library table")
num_libs = 0
for lib in Library.from_file(args.library_table):
if not os.path.exists(lib.bam_file):
logging.warning("\t[SKIPPED] Library %s BAM file not found" % (lib.library_id))
continue
# setup library dir
lib_dir = os.path.join(config.output_dir, lib.library_id)
if not os.path.exists(lib_dir):
os.makedirs(lib_dir)
if args.mode == 'htseq':
htseq_count(lib, gtf_file, config)
elif args.mode == 'cufflinks':
cufflinks(lib, gtf_file, config)
num_libs += 1
logging.info("Found %d libraries" % (num_libs))
logging.info("Done")
return 0
def main():
# setup logging
logging.basicConfig(
level=logging.DEBUG,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
logging.info("AssemblyLine %s" % (assemblyline.__version__))
logging.info("----------------------------------")
# command line parsing
parser = argparse.ArgumentParser()
parser.add_argument("--mode",
dest="mode",
choices=['htseq', 'cufflinks'],
default='htseq')
parser.add_argument("--dryrun",
dest="dryrun",
action="store_true",
default=False)
parser.add_argument("--keep-tmp",
dest="keep_tmp",
action="store_true",
default=None)
parser.add_argument('-o', '--output-dir', dest="output_dir", default=None)
parser.add_argument("config_xml_file")
parser.add_argument('library_table')
parser.add_argument("gtf_file")
args = parser.parse_args()
if not os.path.exists(args.config_xml_file):
parser.error("config xml file '%s' not found" % (args.config_xml_file))
if not os.path.exists(args.library_table):
parser.error("library table file '%s' not found" %
(args.library_table))
if not os.path.exists(args.gtf_file):
parser.error("gtf file '%s' not found" % (args.gtf_file))
gtf_file = os.path.abspath(args.gtf_file)
# read configuration
logging.info("Reading configuration file")
config = Config.from_xml(args.config_xml_file)
if args.output_dir is not None:
config.output_dir = os.path.abspath(args.output_dir)
else:
config.output_dir = os.getcwd()
config.keep_tmp = args.keep_tmp
config.dryrun = args.dryrun
# create output directory
if not os.path.exists(config.output_dir):
os.makedirs(config.output_dir)
# read library table
logging.info("Parsing library table")
num_libs = 0
for lib in Library.from_file(args.library_table):
if not os.path.exists(lib.bam_file):
logging.warning("\t[SKIPPED] Library %s BAM file not found" %
(lib.library_id))
continue
# setup library dir
lib_dir = os.path.join(config.output_dir, lib.library_id)
if not os.path.exists(lib_dir):
os.makedirs(lib_dir)
if args.mode == 'htseq':
htseq_count(lib, gtf_file, config)
elif args.mode == 'cufflinks':
cufflinks(lib, gtf_file, config)
num_libs += 1
logging.info("Found %d libraries" % (num_libs))
logging.info("Done")
return 0
def main():
# setup logging
logging.basicConfig(level=logging.DEBUG,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
logging.info("AssemblyLine %s" % (assemblyline.__version__))
logging.info("----------------------------------")
# parse command line
parser = argparse.ArgumentParser()
parser.add_argument('--min-transcript-length', type=int,
dest="min_transcript_length",
metavar="N",
default=config.MIN_TRANSCRIPT_LENGTH,
help="Skip ab initio transcripts equal to or below "
"this length [default=%(default)s]")
parser.add_argument("--gtf-score-attr", dest="gtf_score_attr",
default="FPKM", metavar="ATTR",
help="GTF attribute field containing transcript "
"expression [default='%(default)s']")
parser.add_argument('-o', '--output-dir', dest="output_dir",
default="assemblyline_out",
help="directory to store assemblyline results and "
"intermediate files [default=%(default)s]")
parser.add_argument("--random-test-frac", dest="random_test_frac",
default=0.1, metavar="FRAC", type=float,
help="if no user-defined tests are specified "
"using '--tests' randomly designate a fraction "
"of reference transcripts as test data for use "
"in classification [default=%(default)s]")
parser.add_argument("--tests", dest="test_file", default=None,
help="(optional) text file containing "
"reference 'gene_id' attributes "
"(one per line) that define test cases "
"to use for validation purposes")
parser.add_argument('ref_gtf_file')
parser.add_argument('library_table_file')
args = parser.parse_args()
# check command line parameters
if not os.path.exists(args.library_table_file):
parser.error("library table file %s not found" % (args.library_table_file))
if args.min_transcript_length < 0:
parser.error("min_transcript_length < 0")
if not os.path.exists(args.ref_gtf_file):
parser.error("reference GTF file %s not found" % (args.ref_gtf_file))
if (args.test_file is not None) and (not os.path.exists(args.test_file)):
parser.error("test file %s not found" % (args.test_file))
if (args.random_test_frac < 0):
parser.error("cannot set --random-test-frac < 0")
# show parameters
logging.info("Parameters:")
logging.info("min transcript length: %d" % (args.min_transcript_length))
logging.info("gtf score attr: %s" % (args.gtf_score_attr))
logging.info("output directory: %s" % (args.output_dir))
logging.info("reference GTF file: %s" % (args.ref_gtf_file))
logging.info("test file: %s" % (args.test_file))
logging.info("library table file: %s" % (args.library_table_file))
logging.info("----------------------------------")
# setup results
results = config.AssemblylineResults(args.output_dir)
# create output directory
if not os.path.exists(results.run_dir):
logging.debug("Creating output directory '%s'" % (results.run_dir))
os.makedirs(results.run_dir)
if not os.path.exists(results.tmp_dir):
logging.info("Creating tmp directory '%s'" % (results.tmp_dir))
os.makedirs(results.tmp_dir)
# parse sample table
logging.info("Parsing library table")
libraries = []
valid = True
library_num = 1
sample_num = 1
sample_id_map = {}
library_map_fileh = open(results.library_id_map, 'w')
sample_map_fileh = open(results.sample_id_map, 'w')
for library in Library.from_file(args.library_table_file):
# exclude samples
if not os.path.exists(library.gtf_file):
logging.warning("Library '%s' GTF file not found" % (library.library_id))
continue
# rename library id
new_library_id = "L%d" % (library_num)
print >>library_map_fileh, '\t'.join([new_library_id, library.library_id])
library_num += 1
library.library_id = new_library_id
# rename sample id
if library.sample_id not in sample_id_map:
new_sample_id = "S%d" % (sample_num)
print >>sample_map_fileh, '\t'.join([new_sample_id, library.sample_id])
sample_id_map[library.sample_id] = new_sample_id
sample_num += 1
else:
new_sample_id = sample_id_map[library.sample_id]
library.sample_id = new_sample_id
libraries.append(library)
if not valid:
logging.warning("Invalid libraries in table file")
library_map_fileh.close()
sample_map_fileh.close()
# setup output files
tmp_file = os.path.join(results.tmp_dir, "transcripts.unsorted.gtf")
tmpfileh = open(tmp_file, "w")
dropfileh = open(results.transcripts_dropped_gtf_file, "w")
statsfileh = open(results.transcript_stats_file, 'w')
header_fields = ['#library_id']
header_fields.extend(config.TRANSCRIPT_STATS_FIELDS)
header_fields.extend([("failed_q%d" % x) for x in config.TRANSCRIPT_SCORE_QUANTILES])
header_fields.extend([("passed_q%d" % x) for x in config.TRANSCRIPT_SCORE_QUANTILES])
print >>statsfileh, '\t'.join(header_fields)
# read test transcripts
test_gene_ids = set()
if args.test_file is not None:
fileh = open(args.test_file)
test_gene_ids.update(line.strip() for line in fileh)
fileh.close()
logging.info("Read %d test genes" % len(test_gene_ids))
# read reference GTF file and aggregate
logging.info("Adding reference GTF file")
add_reference_gtf_file(args.ref_gtf_file, test_gene_ids,
args.random_test_frac, tmpfileh)
# parse sample table
logging.info("Adding libraries")
for library in libraries:
t_dict = read_gtf_file(library, args.gtf_score_attr)
logging.debug("Read %s transcripts from file %s" % (len(t_dict),
library.gtf_file))
if len(t_dict) == 0:
logging.warning("Library %s has no transcripts" %
(library.library_id))
else:
filter_transcripts(library.library_id, t_dict,
tmpfileh, dropfileh, statsfileh,
args.min_transcript_length)
statsfileh.close()
tmpfileh.close()
logging.info("Sorting GTF")
retcode = sort_gtf(tmp_file, results.transcripts_gtf_file, tmp_dir=results.tmp_dir)
if retcode != 0:
logging.error("sort GTF failed")
if os.path.exists(results.transcripts_gtf_file):
os.remove(results.transcripts_gtf_file)
os.remove(tmp_file)
logging.info("Done")
return retcode