def setTranscriptsAnnotByOverlap(queries, transcripts):
"""
Annotate each query by the information coming from the transcripts overlapping them.
:param region: Regions to annotate.
:type region: anacore.region.Region
:param transcripts: The list of transcripts where overlapped transcripts will be searched.
:type transcripts: anacore.region.RegionList
"""
transcripts_by_chr = splittedByRef(transcripts)
queries_by_chr = splittedByRef(queries)
for chrom, curr_query, overlapped_subjects in iterOverlappedByRegion(queries_by_chr, transcripts_by_chr):
curr_query.annot["ANN"] = getTranscriptsAnnot(curr_query, overlapped_subjects)
def setVariantsByOverlap(queries, variants):
"""
Annotate each query by the list of variants overlapping them.
:param queries: Regions to annotate.
:type queries: anacore.region.Region
:param variants: The list of variants where overlapped variants will be searched.
:type variants: anacore.region.RegionList
"""
variants_by_chr = splittedByRef(variants)
queries_by_chr = splittedByRef(queries)
for chrom, curr_query, overlapped_subjects in iterOverlappedByRegion(queries_by_chr, variants_by_chr):
curr_query.annot["VAR"] = []
for sbjct in overlapped_subjects:
curr_query.annot["VAR"].append(sbjct)
def testSplittedByRef(self):
reg_list = RegionList([
Region(10, 30, "-", "chr1", "region1"),
Region(40, 70, "-", "chr1", "region2"),
Region(80, 100, "-", "chr2", "region3")
])
reg_by_chr = splittedByRef(reg_list)
expected = ["chr1:region1", "chr1:region2", "chr2:region3"]
observed = []
for chrom, regions in sorted(reg_by_chr.items()):
named_regions = []
for curr_region in regions:
named_regions.append("{}:{}".format(chrom, curr_region.name))
observed.extend(named_regions)
self.assertEqual(expected, observed)
)
group_output = parser.add_argument_group('Outputs') # Outputs
group_output.add_argument(
'-o',
'--output-regions',
default="renamed.bed",
help=
'Path to the file containing the renamed regions (format: BED). [Default: %(default)s]'
)
args = parser.parse_args()
# Get transcripts
gene_by_tr = getGeneByRefTr(args.input_reference_tr)
selected_transcripts = getTranscriptAnnot(args.input_annotation,
gene_by_tr)
tr_by_chr = splittedByRef(selected_transcripts)
# Write renamed regions
out_nb_col = BEDIO.getMaxNbCol(args.input_regions)
if out_nb_col == 3:
out_nb_col = 4
with BEDIO(args.input_regions) as FH_regions:
with BEDIO(args.output_regions, "w", out_nb_col) as FH_out:
for record_idx, record in enumerate(FH_regions):
target = Region(record.start, record.end, record.strand,
record.chrom)
if args.is_thick_based and record.thickStart is not None and record.thickEnd is not None:
target.start = record.thickStart
target.end = record.thickEnd
overlapped_tr = list()
if record.chrom in tr_by_chr:
overlapped_tr = tr_by_chr[record.chrom].getOverlapped(
help='Path to the annotated file. (format: VCF).')
args = parser.parse_args()
# Logger
logging.basicConfig(
format=
'%(asctime)s -- [%(filename)s][pid:%(process)d][%(levelname)s] -- %(message)s'
)
log = logging.getLogger(os.path.basename(__file__))
log.setLevel(logging.INFO)
log.info("Command: " + " ".join(sys.argv))
# Load annotations
log.info("Load model from {}.".format(args.input_annotations))
genes = loadModel(args.input_annotations, "genes")
genes_by_chr = splittedByRef(genes)
# Annot variants
log.info("Annot variants in {}.".format(args.input_variants))
with BreakendVCFIO(args.output_variants, "w",
args.annotation_field) as writer:
with BreakendVCFIO(args.input_variants) as reader:
# Header
writer.copyHeader(reader)
writer.ANN_titles = [
"SYMBOL", "Gene", "Feature", "Feature_type", "Protein",
"STRAND", "RNA_ELT_TYPE", "RNA_ELT_POS", "CDS_position",
"Protein_position", "GENE_SHARD", "IN_FRAME"
]
writer.info[args.annotation_field] = HeaderInfoAttr(
id=args.annotation_field,