def main(gff, logger=None, noncanonical_gene=False):
function4gff.FIX_MISSING_ATTR(gff, logger=logger)
roots = []
for line in gff.lines:
try:
if line['line_type'] == 'feature' and not line[
'attributes'].has_key('Parent'):
roots.append(line)
except:
logger.warning(
'[Missing Attributes] Program failed.\n\t\t- Line {0:s}: {1:s}'
.format(str(line['line_index'] + 1), line['line_raw']))
#roots = [line for line in gff.lines if line['line_type']=='feature' and not line['attributes'].has_key('Parent')]
error_set = list()
for root in roots:
r = check_pseudo_child_type(gff, root)
if not r == None:
error_set.extend(r)
r = None
r = check_redundant_length(gff, root)
if not r == None:
error_set.extend(r)
r = None
if noncanonical_gene == False:
r = check_incomplete(gff, root)
if not r == None:
error_set.extend(r)
r = None
if noncanonical_gene == False:
r = check_internal_stop(gff, root)
if not r == None:
error_set.extend(r)
r = None
if noncanonical_gene == False:
r = check_distinct_isoform(gff, root)
if not r == None:
error_set.extend(r)
r = None
if noncanonical_gene == False:
r = check_merged_gene_parent(gff, root)
if not r == None:
error_set.extend(r)
r = None
# for e in error_set:
# print('{3:s}\t{0:s}\t{1:s}\t{2:s}\n'.format(e['ID'], e['eCode'], e['eTag'], e['line_num']))
if len(error_set):
return (error_set)
def main(gff, logger=None):
function4gff.FIX_MISSING_ATTR(gff, logger=logger)
FIX_PSEUDOGENE(gff)
features = [line for line in gff.lines if line['line_type'] == 'feature']
error_set = list()
for f in features:
r = check_pseudogene(gff, f)
if not r == None:
error_set.extend(r)
r = None
r = check_strand(gff, f)
if not r == None:
error_set.extend(r)
r = None
if len(error_set):
return (error_set)
def main(gff, gff_file, fasta_file, logger=None, noncanonical_gene=False):
function4gff.FIX_MISSING_ATTR(gff, logger=logger)
roots = []
for line in gff.lines:
try:
if line['line_type'] == 'feature' and 'Parent' not in line[
'attributes']:
roots.append(line)
except:
logger.warning(
'[Missing Attributes] Program failed.\n\t\t- Line {0:s}: {1:s}'
.format(str(line['line_index'] + 1), line['line_raw']))
#roots = [line for line in gff.lines if line['line_type']=='feature' and 'Parent' not in line['attributes']]
error_set = list()
trans_list = list()
for root in roots:
children = root['children']
for child in children:
trans_list.append(child)
r = None
if noncanonical_gene == False:
r = check_duplicate(gff, trans_list)
if r is not None:
error_set.extend(r)
r = None
if noncanonical_gene == False:
r = check_incorrectly_split_genes(gff, gff_file, fasta_file, logger)
if r is not None:
error_set.extend(r)
r = None
'''
for e in error_set:
tag = '[{0:s}]'.format(ERROR_INFO[e['eCode']])
print(e['ID'], e['eCode'], tag)
'''
if len(error_set):
return (error_set)
def script_main():
logger_stderr = logging.getLogger(__name__ + 'stderr')
logger_stderr.setLevel(logging.INFO)
stderr_handler = logging.StreamHandler()
stderr_handler.setFormatter(
logging.Formatter('%(levelname)-8s %(message)s'))
logger_stderr.addHandler(stderr_handler)
logger_null = logging.getLogger(__name__ + 'null')
null_handler = logging.NullHandler()
logger_null.addHandler(null_handler)
import argparse
from textwrap import dedent
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
description=dedent("""\
Testing environment:
1. Python 2.7
Inputs:
1. GFF3: Specify the file name with the -g or --gff argument; Please note that this program requires gene/pseudogene and mRNA/pseudogenic_transcript to have an ID attribute in column 9.
2. fasta file: Specify the file name with the -f or --fasta argument
Outputs:
1. Error report for the input GFF3 file
* Line_num: Line numbers of the found problematic models in the input GFF3 file.
* Error_code: Error codes for the found problematic models. Please refer to lib/ERROR/ERROR.py to see the full list of Error_code and the corresponding Error_tag.
* Error_tag: Detail of the found errors for the problematic models. Please refer to lib/ERROR/ERROR.py to see the full list of Error_code and the corresponding Error_tag.
Quick start:
gff3_QC -g example_file/example.gff3 -f example_file/reference.fa -o test
or
gff3_QC --gff example_file/example.gff3 --fasta example_file/reference.fa --output test
"""))
parser.add_argument('-g',
'--gff',
type=str,
help='Genome annotation file, gff3 format')
parser.add_argument('-f',
'--fasta',
type=str,
help='Genome sequences, fasta format')
parser.add_argument(
'-noncg',
'--noncanonical_gene',
action="store_true",
help='gff3 file is not formatted in the canonical gene model format.')
parser.add_argument(
'-i',
'--initial_phase',
action="store_true",
help='Check whether initial CDS phase is 0 (default: no check)')
parser.add_argument(
'-n',
'--allowed_num_of_n',
type=int,
default=0,
help=
'Max number of Ns allowed in a feature, anything more will be reported as an error (default: 0)'
)
parser.add_argument(
'-t',
'--check_n_feature_types',
nargs='*',
default=['CDS'],
help=
'Count the number of Ns in each feature with the type specified, multiple types may be specified, ex: -t CDS exon (default: "CDS")'
)
parser.add_argument('-o',
'--output',
type=str,
help='output file name (default: report.txt)')
parser.add_argument('-s',
'--statistic',
type=str,
help='statistic file name (default: statistic.txt)')
parser.add_argument('-v',
'--version',
action='version',
version='%(prog)s ' + __version__)
args = parser.parse_args()
if args.gff:
logger_stderr.info('Checking gff file (%s)...', args.gff)
elif not sys.stdin.isatty(): # if STDIN connected to pipe or file
args.gff = sys.stdin
logger_stderr.info('Reading from STDIN...')
else: # no input
parser.print_help()
sys.exit(1)
if args.fasta:
logger_stderr.info('Checking genome fasta (%s)...', args.fasta)
elif not sys.stdin.isatty(): # if STDIN connected to pipe or file
args.fasta = sys.stdin
logger_stderr.info('Reading from STDIN...')
else: # no input
parser.print_help()
sys.exit(1)
if args.allowed_num_of_n or args.check_n_feature_types:
check_n = True
else:
check_n = False
logger_stderr.info('Reading gff files: (%s)...\n', args.gff)
gff3 = Gff3(gff_file=args.gff,
fasta_external=args.fasta,
logger=logger_null)
logger_stderr.info('Checking errors in the gff files: (%s)...\n', args.gff)
if not gff3.check_parent_boundary():
sys.exit()
gff3.check_unresolved_parents()
if args.noncanonical_gene == False:
gff3.check_phase(args.initial_phase)
gff3.check_reference(fasta_external=args.fasta,
check_n=check_n,
allowed_num_of_n=args.allowed_num_of_n,
feature_types=args.check_n_feature_types)
logger_stderr.info('\t- Checking missing attributes: (%s)...\n',
'function4gff.FIX_MISSING_ATTR()')
function4gff.FIX_MISSING_ATTR(gff3, logger=logger_stderr)
error_set = list()
cmd = None
cmd = function4gff.extract_internal_detected_errors(gff3)
if cmd:
error_set.extend(cmd)
cmd = None
logger_stderr.info('\t- Checking intra-model errors: (%s)...\n', args.gff)
cmd = intra_model.main(gff3,
logger=logger_stderr,
noncanonical_gene=args.noncanonical_gene)
if cmd:
error_set.extend(cmd)
cmd = None
logger_stderr.info('\t- Checking inter-model errors: (%s)...\n', args.gff)
cmd = inter_model.main(gff3,
args.gff,
args.fasta,
logger=logger_stderr,
noncanonical_gene=args.noncanonical_gene)
if cmd:
error_set.extend(cmd)
cmd = None
logger_stderr.info('\t- Checking single-feature errors: (%s)...\n',
args.gff)
cmd = single_feature.main(gff3, logger=logger_stderr)
if cmd:
error_set.extend(cmd)
if args.output:
logger_stderr.info('Print QC report at {0:s}'.format(args.output))
report_fh = open(args.output, 'w')
else:
logger_stderr.info('Print QC report at {0:s}'.format('report.txt'))
report_fh = open('report.txt', 'w')
if args.statistic:
logger_stderr.info('Print QC statistic report at {0:s}'.format(
args.statistic))
statistic_fh = open(args.statistic, 'w')
else:
logger_stderr.info(
'Print QC statistic report at {0:s}'.format('statistic.txt'))
statistic_fh = open('statistic.txt', 'w')
report_fh.write('Line_num\tError_code\tError_tag\n')
for e in sorted(error_set, key=lambda x: sorted(x.keys())):
tag = '[{0:s}]'.format(e['eTag'])
report_fh.write('{0:s}\t{1:s}\t{2:s}\n'.format(str(e['line_num']),
str(e['eCode']),
str(tag)))
#statistic_file
error_counts = dict()
ERROR_INFO = ERROR.INFO
statistic_fh.write('Error_code\tNumber_of_problematic_models\tError_tag\n')
for s in sorted(error_set, key=lambda x: sorted(x.keys())):
if s['eCode'] not in error_counts:
error_counts[s['eCode']] = {
'count': 0,
'etag': ERROR_INFO[s['eCode']]
}
error_counts[s['eCode']]['count'] += 1
for a in error_counts:
statistic_fh.write('{0:s}\t{1:s}\t{2:s}\n'.format(
str(a), str(error_counts[a]['count']),
str(error_counts[a]['etag'])))