def read_matrix_file_and_add_as_features(self):
"""Read the HiC matrix file and add each bin as further feature in the
annotation.
"""
print("- Reading HiC matrix file")
self.hic_matrix = hicsuntdracones.hicmatrix.HiCMatrix(
self._matrix_file)
self.hic_matrix.hic_matrix_df.set_index(
self.hic_matrix.hic_matrix_df["Regions"], inplace=True)
self.hic_matrix.normalize_by_columns_sum()
for genome_bin in self.hic_matrix.bins():
chrom = hicsuntdracones.hicmatrix.remove_position_information(
genome_bin)
# As the bin counting starts with 0 but the gff starts a 1
# we have to add 1 here to the position.
pos = hicsuntdracones.hicmatrix.bin_number(genome_bin)
pos_adjusted = pos + 1
self._features.update([gffutils.Feature(
seqid=chrom,
source='-',
featuretype='HiC_bin',
start=pos_adjusted,
end=pos_adjusted+self._bin_size,
strand="+",
attributes=f"ID={genome_bin}")])
def create_parents(orphans, parent_dict, feature_list, intermediate_dict,
gene):
added_parent_ids = []
new_orphans = []
top_feature = None
for orphan, parent in orphans:
if parent not in added_parent_ids:
children = [
feature for feature in feature_list
if "Parent" in feature.attributes
and feature.attributes["Parent"][0] == parent
]
starts = [child.start for child in children]
ends = [child.end for child in children]
if parent in parent_dict:
original_parent = parent_dict[parent]
else:
original_parent = intermediate_dict[parent]
parent_feature = gffutils.Feature(
seqid=children[0].seqid,
source="Liftoff",
featuretype=original_parent.featuretype,
start=min(starts),
end=max(ends),
strand=children[0].strand,
id=original_parent.id,
attributes=original_parent.attributes)
feature_list.append(parent_feature)
if parent_feature.id != gene.id:
new_orphans.append(
(parent_feature, parent_feature["Parent"][0]))
else:
top_feature = parent_feature
added_parent_ids.append(parent)
return new_orphans, top_feature
def location_to_feature(db, chrom, start, stop, strand, source, featuretype):
if strand not in STRANDS:
strand = '.'
overlapping_genes = db.region(seqid=chrom,
start=start,
end=stop,
strand=strand,
featuretype='gene')
exon_id = 'exon:{chrom}:{start}-{stop}:{strand}'.format(chrom=chrom,
start=start,
stop=stop,
strand=strand)
attributes = {}
for g in overlapping_genes:
attributes = merge_attributes(attributes, g.attributes)
exon = gffutils.Feature(chrom,
source=source,
featuretype=featuretype,
start=start,
end=stop,
strand=strand,
id=exon_id,
attributes=attributes)
return exon
def test_pr_144():
# previously this would fail with:
# UnboundLocalError: local variable 'part' referenced before assignment
f = gffutils.Feature(attributes={'a': ['']})
# Make sure everything got converted correctly
assert f.attributes['a'] == ['']
assert str(f) == ". . . . . . . . a"
g = gffutils.feature.feature_from_line(str(f))
assert g == f
def top_level_features(db):
"""Generator that returns top level features from db
:db: gffutils.FeatureDB
:returns: Iterator of top-level features (having no parent)
"""
# Get all top level features
top_level_features = db.execute(
"select * "
"from features "
"where id not in (select distinct(child) from relations)")
for row in top_level_features:
yield (gffutils.Feature(**row))
def convert_all_children_coords(shortest_path_nodes, children, parent):
shortest_path_nodes.sort(key=lambda x: x.query_block_start)
mapped_children = {}
for child in children:
lifted_start = convert_coord(child.start, parent, shortest_path_nodes)
lifted_end = convert_coord(child.end, parent, shortest_path_nodes)
if (lifted_start != lifted_end
or child.start == child.end) and lifted_start != 0:
strand = get_strand(shortest_path_nodes[1], parent)
mapped_children[child.id] = gffutils.Feature(
id=child.id,
seqid=shortest_path_nodes[1].reference_name,
start=min(lifted_start, lifted_end) + 1,
end=max(lifted_start, lifted_end) + 1,
featuretype=child.featuretype,
source="Liftoff",
attributes=child.attributes,
strand=strand)
return mapped_children
def add_matrix_bins_as_features(self, matrix_file, features):
hic_matrix = hicsuntdracones.hicmatrix.HiCMatrix(matrix_file)
hic_matrix.normalize_by_columns_sum()
interaction_matrix = hic_matrix.hic_matrix_df
interaction_matrix.set_index(interaction_matrix["Regions"],
inplace=True)
for genome_bin in interaction_matrix["Regions"]:
chrom_part = "-".join(genome_bin.split("-")[:-1])
# As the bin counting starts with 0 but the gff starts at 1
# we have to add 1 here to the position.
# pos = int(genome_bin.split("-")[-1]) + 1
pos = int(genome_bin.split("-")[-1])
pos_adjusted = pos + 1
features.update([
gffutils.Feature(seqid=chrom_part,
source='-',
featuretype='HiC_bin',
start=pos_adjusted,
end=pos_adjusted + self._bin_size,
strand="+",
attributes=f"ID={genome_bin}")
])
return interaction_matrix
def output_RI(gff_out, donor, acceptor, intron_len, source="RI"):
"""
Output a retained intron event.
"""
chrom = donor.chrom
strand = donor.strand
donor_start = donor.start_coord
donor_end = donor.end_coord
acceptor_start = acceptor.start_coord
acceptor_end = acceptor.end_coord
ri_name = "%s@%s" % (donor.coords_str, acceptor.coords_str)
gene_start = donor_start
gene_end = acceptor_end
# For GFF record purposes, ensure start < end always
if gene_start > gene_end:
gene_start, gene_end = gene_end, gene_start
gene_rec = gffutils.Feature(seqid=chrom,
source=source,
featuretype="gene",
start=gene_start,
end=gene_end,
strand=strand,
attributes={
"ID": [ri_name],
"Name": [ri_name]
})
# Output mRNA containing the retained intron and then output its exons
# First output retained intron using "withRI" suffix
long_mRNA_name = "%s.A" % (ri_name)
# Long mRNA record has same start/end as gene record
long_mRNA_rec = gffutils.Feature(seqid=chrom,
source=source,
featuretype="mRNA",
start=gene_start,
end=gene_end,
strand=strand,
attributes={
"ID": [long_mRNA_name],
"Parent": [ri_name]
})
# Retained intron belongs to long mRNA
ri_exon_name = "%s.withRI" % (long_mRNA_name)
# Retained intron record has same start/end as gene record as well
ri_exon_rec = gffutils.Feature(seqid=chrom,
source=source,
featuretype="exon",
start=gene_start,
end=gene_end,
strand=strand,
attributes={
"ID": [ri_exon_name],
"Parent": [long_mRNA_name]
})
# Output mRNA splicing out the intron and then output its exons
short_mRNA_name = "%s.B" % (ri_name)
# Short mRNA has same start/end as gene record
short_mRNA_rec = gffutils.Feature(seqid=chrom,
source=source,
featuretype="mRNA",
start=gene_start,
end=gene_end,
strand=strand,
attributes={
"ID": [short_mRNA_name],
"Parent": [ri_name]
})
up_exon_name = "%s.up" % (short_mRNA_name)
up_exon_rec = gffutils.Feature(seqid=chrom,
source=source,
featuretype="exon",
start=donor.gff_start,
end=donor.gff_end,
strand=strand,
attributes={
"ID": [up_exon_name],
"Parent": [short_mRNA_name]
})
dn_exon_name = "%s.dn" % (short_mRNA_name)
dn_exon_rec = gffutils.Feature(seqid=chrom,
source=source,
featuretype="exon",
start=acceptor.gff_start,
end=acceptor.gff_end,
strand=strand,
attributes={
"ID": [dn_exon_name],
"Parent": [short_mRNA_name]
})
# Serialize records to GFF
# gene
gff_out.write_rec(gene_rec)
# long mRNA
gff_out.write_rec(long_mRNA_rec)
# retained intron
gff_out.write_rec(ri_exon_rec)
# short mRNA
gff_out.write_rec(short_mRNA_rec)
gff_out.write_rec(up_exon_rec)
gff_out.write_rec(dn_exon_rec)
assert len(parent_gene) < 2
if feature.featuretype == 'gene':
feature.attributes[args.geneid] = feature.attributes['ID']
elif len(parent_gene) == 1:
parent_gene = parent_gene[0]
gene_id = parent_gene.attributes['ID']
assert len(gene_id) == 1
feature.attributes[args.geneid] = gene_id
if args.add_tss != '' and feature.featuretype == args.add_tss:
if feature.strand == '+':
start = feature.start
elif feature.strand == '-':
start = feature.end
else:
raise Exception('Invalid strand: %s' % feature.strand)
tss = gffutils.Feature(seqid=feature.seqid,
source=feature.source,
featuretype='TSS',
start=start,
end=start,
strand=feature.strand,
attributes={
'ID': ['TSS_%s' % tss_id],
'Parent': feature['ID'],
args.geneid: feature.attributes[args.geneid]
})
tss_id = tss_id + 1
print(tss)
print(feature)