def annotate_gene_and_tss_ids(path_info_list, strand,
gene_id_value_obj,
tss_id_value_obj):
# cluster paths to determine gene ids
cluster_tree = ClusterTree(0,1)
# map tss positions to unique ids
tss_pos_id_map = {}
for i,path_info in enumerate(path_info_list):
start = path_info.path[0].start
end = path_info.path[-1].end
# cluster transcript coordinates
cluster_tree.insert(start, end, i)
# map TSS positions to IDs
tss_pos = end if strand == NEG_STRAND else start
if tss_pos not in tss_pos_id_map:
tss_id = tss_id_value_obj.next()
tss_pos_id_map[tss_pos] = tss_id
else:
tss_id = tss_pos_id_map[tss_pos]
path_info.tss_id = tss_id
# retrieve transcript clusters and assign gene ids
for start, end, indexes in cluster_tree.getregions():
gene_id = gene_id_value_obj.next()
for i in indexes:
path_info_list[i].gene_id = gene_id
def annotate_gene_and_tss_ids(path_info_list, strand,
gene_id_value_obj,
tss_id_value_obj):
# cluster paths to determine gene ids
cluster_tree = ClusterTree(0,1)
# map tss positions to unique ids
tss_pos_id_map = {}
for i,path_info in enumerate(path_info_list):
start = path_info.path[0].start
end = path_info.path[-1].end
# cluster transcript coordinates
cluster_tree.insert(start, end, i)
# map TSS positions to IDs
tss_pos = end if strand == NEG_STRAND else start
if tss_pos not in tss_pos_id_map:
tss_id = tss_id_value_obj.next()
tss_pos_id_map[tss_pos] = tss_id
else:
tss_id = tss_pos_id_map[tss_pos]
path_info.tss_id = tss_id
# retrieve transcript clusters and assign gene ids
for start, end, indexes in cluster_tree.getregions():
gene_id = gene_id_value_obj.next()
for i in indexes:
path_info_list[i].gene_id = gene_id
def cluster_gtf_features(gtf_files, source=None):
# read all features
chrom_feature_dict = collections.defaultdict(
lambda: collections.defaultdict(lambda: []))
for gtf_file in gtf_files:
logging.debug('Parsing gtf file: %s' % (gtf_file))
for f in Feature.parse_gtf(gtf_file):
# bin by chromosome and strand
chrom_feature_dict[f.chrom][f.strand].append(f)
# cluster transcripts into genes
if source is None:
source = 'merge'
logging.debug('Clustering transcripts into genes')
cur_gene_id = 1
for strand_feature_dict in chrom_feature_dict.itervalues():
for strand_features in strand_feature_dict.itervalues():
# initialize each transcript to be in a 'gene' by itself
cluster_map = {}
cluster_tree = ClusterTree(0, 1)
for i, f in enumerate(strand_features):
cluster_map[i] = set((i, ))
for start, end in f.exons:
cluster_tree.insert(start, end, i)
for start, end, indexes in cluster_tree.getregions():
# group transcripts into larger clusters
new_cluster = set()
for i in indexes:
new_cluster.update(cluster_map[i])
# reassign transcript clusters to new cluster
for i in new_cluster:
cluster_map[i] = new_cluster
del cluster_tree
# now all transcripts are assigned to a gene cluster
# enumerate all gene clusters
clusters = set()
for clust in cluster_map.itervalues():
clusters.add(frozenset(clust))
del cluster_map
# now assign gene ids to each cluster
for clust in clusters:
new_gene_id = '%s%011d' % (source, cur_gene_id)
for i in clust:
f = strand_features[i]
f.attrs['orig_gene_id'] = f.attrs['gene_id']
f.attrs['gene_id'] = new_gene_id
cur_gene_id += 1
# output genes
logging.debug('Writing transcripts')
for chrom in sorted(chrom_feature_dict):
strand_feature_dict = chrom_feature_dict[chrom]
features = []
for strand_features in strand_feature_dict.itervalues():
features.extend(strand_features)
features.sort(key=operator.attrgetter('start'))
for f in features:
for gtf_feature in f.to_gtf_features(source=source):
yield str(gtf_feature)
def cluster_gtf_features(gtf_files, source=None):
# read all features
chrom_feature_dict = collections.defaultdict(lambda: collections.defaultdict(lambda: []))
for gtf_file in gtf_files:
logging.debug('Parsing gtf file: %s' % (gtf_file))
for f in Feature.parse_gtf(gtf_file):
# bin by chromosome and strand
chrom_feature_dict[f.chrom][f.strand].append(f)
# cluster transcripts into genes
if source is None:
source = 'merge'
logging.debug('Clustering transcripts into genes')
cur_gene_id = 1
for strand_feature_dict in chrom_feature_dict.itervalues():
for strand_features in strand_feature_dict.itervalues():
# initialize each transcript to be in a 'gene' by itself
cluster_map = {}
cluster_tree = ClusterTree(0,1)
for i,f in enumerate(strand_features):
cluster_map[i] = set((i,))
for start,end in f.exons:
cluster_tree.insert(start, end, i)
for start, end, indexes in cluster_tree.getregions():
# group transcripts into larger clusters
new_cluster = set()
for i in indexes:
new_cluster.update(cluster_map[i])
# reassign transcript clusters to new cluster
for i in new_cluster:
cluster_map[i] = new_cluster
del cluster_tree
# now all transcripts are assigned to a gene cluster
# enumerate all gene clusters
clusters = set()
for clust in cluster_map.itervalues():
clusters.add(frozenset(clust))
del cluster_map
# now assign gene ids to each cluster
for clust in clusters:
new_gene_id = '%s%011d' % (source, cur_gene_id)
for i in clust:
f = strand_features[i]
f.attrs['orig_gene_id'] = f.attrs['gene_id']
f.attrs['gene_id'] = new_gene_id
cur_gene_id += 1
# output genes
logging.debug('Writing transcripts')
for chrom in sorted(chrom_feature_dict):
strand_feature_dict = chrom_feature_dict[chrom]
features = []
for strand_features in strand_feature_dict.itervalues():
features.extend(strand_features)
features.sort(key=operator.attrgetter('start'))
for f in features:
for gtf_feature in f.to_gtf_features(source=source):
yield str(gtf_feature)
def read_reference_gtf(ref_gtf_file):
gene_map = {}
for f in GTFFeature.parse(open(ref_gtf_file)):
# get gene by id
gene_id = f.attrs["gene_id"]
if gene_id not in gene_map:
g = Gene()
g.gene_id = gene_id
g.chrom = f.seqid
g.strand = f.strand
g.gene_start = f.start
g.gene_end = f.end
gene_map[gene_id] = g
else:
g = gene_map[gene_id]
# update gene
g.gene_start = min(g.gene_start, f.start)
g.gene_end = max(g.gene_end, f.end)
if f.feature_type == "exon":
g.exons.add((f.start, f.end))
elif f.feature_type == "CDS":
g.is_coding = True
if "gene_name" in f.attrs:
g.gene_names.add(f.attrs["gene_name"])
g.annotation_sources.add(f.source)
logging.info("Sorting genes")
genes = sorted(gene_map.values(), key=operator.attrgetter('chrom', 'gene_start'))
del gene_map
# cluster loci
logging.debug("Building interval index")
locus_cluster_trees = collections.defaultdict(lambda: ClusterTree(0,1))
for i,g in enumerate(genes):
locus_cluster_trees[g.chrom].insert(g.gene_start, g.gene_end, i)
locus_trees = collections.defaultdict(lambda: IntervalTree())
for chrom, cluster_tree in locus_cluster_trees.iteritems():
for locus_start,locus_end,indexes in cluster_tree.getregions():
# cluster gene exons and add to interval tree
exon_tree = IntervalTree()
for i in indexes:
g = genes[i]
cluster_tree = ClusterTree(0,1)
for start,end in g.exons:
cluster_tree.insert(start, end, 1)
# update exons
exon_clusters = []
for start,end,indexes in cluster_tree.getregions():
exon_clusters.append((start,end))
g.exons = exon_clusters
del cluster_tree
for start,end in g.exons:
exon_tree.insert_interval(Interval(start, end, value=g))
# add to locus interval tree
locus_trees[chrom].insert_interval(Interval(locus_start, locus_end, value=exon_tree))
logging.debug("Done indexing reference GTF file")
return locus_trees
def cluster_isoforms(transcripts):
# cluster exons
cluster_tree = ClusterTree(0,1)
for t in transcripts:
for e in t.exons:
cluster_tree.insert(e.start, e.end, 1)
exons = []
for start,end,indexes in cluster_tree.getregions():
exons.append((start,end))
del cluster_tree
return exons
def main():
logging.basicConfig(
level=logging.DEBUG,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
parser = argparse.ArgumentParser()
parser.add_argument('gtf_file')
parser.add_argument('chrom_sizes')
parser.add_argument("output_prefix")
args = parser.parse_args()
# read one locus at a time
locus_file = args.output_prefix + '.locus.bed'
intergenic_file = args.output_prefix + '.intergenic.bed'
intron_file = args.output_prefix + '.intron.bed'
locus_fileh = open(locus_file, 'w')
introns = set()
logging.info('Parsing transcripts by locus')
for locus_transcripts in parse_gtf(open(args.gtf_file)):
# find borders of locus
locus_chrom = locus_transcripts[0].chrom
locus_start = min(t.start for t in locus_transcripts)
locus_end = max(t.end for t in locus_transcripts)
print >> locus_fileh, '\t'.join(
[locus_chrom, str(locus_start),
str(locus_end)])
logging.debug(
"[LOCUS] %s:%d-%d %d transcripts" %
(locus_chrom, locus_start, locus_end, len(locus_transcripts)))
# cluster locus exons
cluster_tree = ClusterTree(0, 1)
for t in locus_transcripts:
# update locus
for e in t.exons:
cluster_tree.insert(e.start, e.end, 1)
exon_clusters = []
for start, end, indexes in cluster_tree.getregions():
exon_clusters.append((start, end))
# get intronic regions
e1 = exon_clusters[0]
for j in xrange(1, len(exon_clusters)):
e2 = exon_clusters[j]
introns.add((locus_chrom, e1[1], e2[0]))
e1 = e2
locus_fileh.close()
# write introns
logging.info('Writing introns')
intron_fileh = open(intron_file, 'w')
for chrom, start, end in sorted(introns):
print >> intron_fileh, '\t'.join([chrom, str(start), str(end)])
intron_fileh.close()
# take complement of locus file to find intergenic regions
logging.info('Complementing locus intervals to find intergenic regions')
args = ['bedtools', 'complement', '-i', locus_file, '-g', args.chrom_sizes]
with open(intergenic_file, 'w') as f:
subprocess.call(args, stdout=f)
def main():
logging.basicConfig(level=logging.DEBUG,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
parser = argparse.ArgumentParser()
parser.add_argument('gtf_file')
parser.add_argument('chrom_sizes')
parser.add_argument("output_prefix")
args = parser.parse_args()
# read one locus at a time
locus_file = args.output_prefix + '.locus.bed'
intergenic_file = args.output_prefix + '.intergenic.bed'
intron_file = args.output_prefix + '.intron.bed'
locus_fileh = open(locus_file, 'w')
introns = set()
logging.info('Parsing transcripts by locus')
for locus_transcripts in parse_gtf(open(args.gtf_file)):
# find borders of locus
locus_chrom = locus_transcripts[0].chrom
locus_start = min(t.start for t in locus_transcripts)
locus_end = max(t.end for t in locus_transcripts)
print >>locus_fileh, '\t'.join([locus_chrom, str(locus_start), str(locus_end)])
logging.debug("[LOCUS] %s:%d-%d %d transcripts" %
(locus_chrom, locus_start, locus_end,
len(locus_transcripts)))
# cluster locus exons
cluster_tree = ClusterTree(0,1)
for t in locus_transcripts:
# update locus
for e in t.exons:
cluster_tree.insert(e.start, e.end, 1)
exon_clusters = []
for start,end,indexes in cluster_tree.getregions():
exon_clusters.append((start,end))
# get intronic regions
e1 = exon_clusters[0]
for j in xrange(1, len(exon_clusters)):
e2 = exon_clusters[j]
introns.add((locus_chrom, e1[1], e2[0]))
e1 = e2
locus_fileh.close()
# write introns
logging.info('Writing introns')
intron_fileh = open(intron_file, 'w')
for chrom, start,end in sorted(introns):
print >>intron_fileh, '\t'.join([chrom, str(start), str(end)])
intron_fileh.close()
# take complement of locus file to find intergenic regions
logging.info('Complementing locus intervals to find intergenic regions')
args = ['bedtools', 'complement',
'-i', locus_file,
'-g', args.chrom_sizes]
with open(intergenic_file, 'w') as f:
subprocess.call(args, stdout=f)
def get_gtf_metadata(gtf_file,
omit_attrs=None,
group_by="gene_id",
feature_type="exon"):
if omit_attrs is None:
omit_attrs = []
# read gtf file and group by gene
gene_feature_map = collections.defaultdict(lambda: [])
gene_attrs_set = set()
for feature in GTFFeature.parse(open(gtf_file)):
if feature.feature_type != feature_type:
continue
feature_id = feature.attrs[group_by]
gene_feature_map[feature_id].append(feature)
gene_attrs_set.update(feature.attrs.keys())
gene_attrs_set.difference_update(omit_attrs)
gene_attrs_list = sorted(gene_attrs_set)
metadata_fields = ["tracking_id", "locus", "strand", "num_exons", "transcript_length"] + gene_attrs_list
metadata_inds = dict((x,i) for i,x in enumerate(metadata_fields))
metadata_dict = {}
# output metadata sorted by gene id
for feature_id,features in gene_feature_map.iteritems():
# collect attributes for this gene
attrdict = collections.defaultdict(lambda: set())
# cluster exons together for each gene
cluster_tree = ClusterTree(0,1)
for i,f in enumerate(features):
cluster_tree.insert(f.start, f.end, i)
for k,v in f.attrs.iteritems():
if k in gene_attrs_set:
# some attributes have multiple values separated by a comma
attrdict[k].update(v.split(','))
# determine larger exon clusters
transcript_length = 0
exon_clusters = []
for start, end, indexes in cluster_tree.getregions():
exon_clusters.append((start,end))
transcript_length += (end - start)
del cluster_tree
chrom = features[0].seqid
locus_start = min(e[0] for e in exon_clusters)
locus_end = max(e[1] for e in exon_clusters)
locus_string = "%s:%d-%d" % (chrom, locus_start, locus_end)
strand = features[0].strand
num_exons = len(exon_clusters)
# make metadata row
metadata = [feature_id, locus_string, strand, num_exons, transcript_length] + ['NA'] * len(gene_attrs_list)
# get all attributes
for k,vals in attrdict.iteritems():
ind = metadata_inds[k]
metadata[ind] = ','.join(map(str, sorted(vals)))
metadata_dict[metadata[0]] = metadata
return metadata_fields, metadata_dict
def cluster_tss(tss_dict, chrom_sizes, upstream=0, downstream=0):
trees = collections.defaultdict(lambda: ClusterTree(0,1))
tss_ids = sorted(tss_dict)
for i,tss_id in enumerate(tss_ids):
chrom, strand, tstart, tend = tss_dict[tss_id]
if strand == NEG_STRAND:
pstart = tend - 1 - downstream
pstart = max(tstart, pstart)
pend = tend - 1 + upstream
pend = min(pend, chrom_sizes[chrom])
else:
pstart = tstart - upstream
pstart = max(0, pstart)
pend = tstart + downstream
pend = min(tend, pend)
trees[chrom].insert(pstart, pend, i)
# get clusters
cur_p_id = 1
for chrom in sorted(trees):
tree = trees[chrom]
for start, end, indexes in tree.getregions():
p_id = 'P%07d' % (cur_p_id)
for i in indexes:
tss_id = tss_ids[i]
yield tss_id, p_id, chrom, start, end
cur_p_id += 1
def read_reference_gtf(ref_gtf_file):
gene_map = {}
for f in GTFFeature.parse(open(ref_gtf_file)):
# get gene by id
gene_id = f.attrs["gene_id"]
if gene_id not in gene_map:
g = Gene()
g.gene_id = gene_id
g.chrom = f.seqid
g.strand = f.strand
g.gene_start = f.start
g.gene_end = f.end
gene_map[gene_id] = g
else:
g = gene_map[gene_id]
# update gene
g.gene_start = min(g.gene_start, f.start)
g.gene_end = max(g.gene_end, f.end)
if f.feature_type == "exon":
g.exons.add((f.start, f.end))
elif f.feature_type == "CDS":
g.is_coding = True
if "gene_name" in f.attrs:
g.gene_names.add(f.attrs["gene_name"])
g.annotation_sources.add(f.source)
logging.info("Sorting genes")
genes = sorted(gene_map.values(),
key=operator.attrgetter('chrom', 'gene_start'))
del gene_map
# cluster loci
logging.debug("Building interval index")
locus_cluster_trees = collections.defaultdict(lambda: ClusterTree(0, 1))
locus_trees = collections.defaultdict(lambda: IntervalTree())
for i, g in enumerate(genes):
locus_cluster_trees[g.chrom].insert(g.gene_start, g.gene_end, i)
for chrom, cluster_tree in locus_cluster_trees.iteritems():
for locus_start, locus_end, indexes in cluster_tree.getregions():
# cluster gene exons and add to interval tree
exon_tree = IntervalTree()
for i in indexes:
g = genes[i]
cluster_tree = ClusterTree(0, 1)
for start, end in g.exons:
cluster_tree.insert(start, end, 1)
# update exons
exon_clusters = []
for start, end, indexes in cluster_tree.getregions():
exon_clusters.append((start, end))
g.exons = exon_clusters
del cluster_tree
for start, end in g.exons:
exon_tree.insert_interval(Interval(start, end, value=g))
# add to locus interval tree
locus_trees[chrom].insert_interval(
Interval(locus_start, locus_end, value=exon_tree))
logging.debug("Done indexing reference GTF file")
return locus_trees
def get_locus_genes(features):
gene_map = collections.defaultdict(lambda: Gene())
for f in features:
# get gene by id
gene_id = f.attrs["gene_id"]
if gene_id not in gene_map:
g = Gene()
g.gene_id = gene_id
g.strand = f.strand
g.gene_start = f.start
g.gene_end = f.end
gene_map[gene_id] = g
else:
g = gene_map[gene_id]
# update gene
g.gene_start = min(g.gene_start, f.start)
g.gene_end = max(g.gene_end, f.end)
if f.feature_type == "exon":
g.exons.add((f.start, f.end))
elif f.feature_type == "CDS":
g.is_coding = True
if "gene_name" in f.attrs:
g.gene_names.add(f.attrs["gene_name"])
g.annotation_sources.add(f.source)
for g in gene_map.itervalues():
# cluster gene exons
cluster_tree = ClusterTree(0,1)
for start,end in g.exons:
cluster_tree.insert(start, end, 1)
# update exons
exon_clusters = []
for start,end,indexes in cluster_tree.getregions():
exon_clusters.append((start,end))
g.exons = exon_clusters
del cluster_tree
return sorted(gene_map.values(), key=operator.attrgetter('gene_start'))
def build_locus_trees(gtf_file):
transcripts = []
locus_cluster_trees = collections.defaultdict(lambda: ClusterTree(0,1))
for locus_transcripts in parse_gtf(open(gtf_file)):
for t in locus_transcripts:
is_ref = bool(int(t.attrs[GTFAttr.REF]))
if not is_ref:
continue
i = len(transcripts)
transcripts.append(t)
locus_cluster_trees[t.chrom].insert(t.start, t.end, i)
# build interval trees of loci
locus_trees = collections.defaultdict(lambda: IntervalTree())
for chrom, cluster_tree in locus_cluster_trees.iteritems():
for locus_start, locus_end, indexes in cluster_tree.getregions():
for i in indexes:
locus_transcripts = [transcripts[i] for i in indexes]
locus_trees[chrom].insert_interval(Interval(locus_start, locus_end, value=locus_transcripts))
return locus_trees
def main():
logging.basicConfig(
level=logging.DEBUG,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
parser = argparse.ArgumentParser()
parser.add_argument('bed_file')
args = parser.parse_args()
trees = collections.defaultdict(lambda: ClusterTree(0, 1))
for f in BEDFeature.parse(open(args.bed_file)):
tree = trees[f.chrom]
for start, end in f.exons:
tree.insert(start, end, 1)
footprint = 0
for chrom in sorted(trees):
chromprint = 0
tree = trees[chrom]
for start, end, indexes in tree.getregions():
chromprint += (end - start)
#print chrom, chromprint
footprint += chromprint
print 'total', footprint
def partition_transcripts_by_strand(transcripts):
"""
uses information from stranded transcripts to infer strand for
unstranded transcripts
"""
def add_transcript(t, nodes_iter, transcript_maps, node_data):
for n in nodes_iter:
node_data[n]['scores'][t.strand] += t.score
t_id = t.attrs[GTFAttr.TRANSCRIPT_ID]
transcript_maps[t.strand][t_id] = t
# divide transcripts into independent regions of
# transcription with a single entry and exit point
boundaries = find_exon_boundaries(transcripts)
node_data_func = lambda: {'ref_strands': [False, False],
'scores': [0.0, 0.0, 0.0]}
node_data = collections.defaultdict(node_data_func)
strand_transcript_maps = [{}, {}, {}]
strand_ref_transcripts = [[], []]
unresolved_transcripts = []
for t in transcripts:
is_ref = bool(int(t.attrs.get(GTFAttr.REF, "0")))
if is_ref:
# label nodes by ref strand
for n in split_exons(t,boundaries):
node_data[n]['ref_strands'][t.strand] = True
strand_ref_transcripts[t.strand].append(t)
elif t.strand != NO_STRAND:
add_transcript(t, split_exons(t, boundaries),
strand_transcript_maps, node_data)
else:
unresolved_transcripts.append(t)
# resolve unstranded transcripts
logging.debug("\t\t%d unstranded transcripts" %
(len(unresolved_transcripts)))
# keep track of remaining unresolved nodes
unresolved_nodes = set()
if len(unresolved_transcripts) > 0:
resolved = []
still_unresolved_transcripts = []
for t in unresolved_transcripts:
nodes = list(split_exons(t,boundaries))
t.strand = resolve_strand(nodes, node_data)
if t.strand != NO_STRAND:
resolved.append(t)
else:
unresolved_nodes.update(nodes)
still_unresolved_transcripts.append(t)
for t in resolved:
add_transcript(t, split_exons(t, boundaries),
strand_transcript_maps, node_data)
unresolved_transcripts = still_unresolved_transcripts
if len(unresolved_transcripts) > 0:
logging.debug("\t\t%d unresolved transcripts" %
(len(unresolved_transcripts)))
# if there are still unresolved transcripts then we can try to
# extrapolate and assign strand to clusters of nodes at once, as
# long as some of the nodes have a strand assigned
# cluster unresolved nodes
unresolved_nodes = sorted(unresolved_nodes)
cluster_tree = ClusterTree(0,1)
for i,n in enumerate(unresolved_nodes):
cluster_tree.insert(n[0], n[1], i)
# try to assign strand to clusters of nodes
node_strand_map = {}
for start, end, indexes in cluster_tree.getregions():
nodes = [unresolved_nodes[i] for i in indexes]
strand = resolve_strand(nodes, node_data)
for n in nodes:
node_strand_map[n] = strand
# for each transcript assign strand to the cluster with
# the best overlap
unresolved_count = 0
for t in unresolved_transcripts:
strand_bp = [0,0]
nodes = list(split_exons(t, boundaries))
for n in nodes:
strand = node_strand_map[n]
if strand != NO_STRAND:
strand_bp[strand] += (n[1] - n[0])
total_strand_bp = sum(strand_bp)
if total_strand_bp > 0:
if strand_bp[POS_STRAND] >= strand_bp[NEG_STRAND]:
t.strand = POS_STRAND
else:
t.strand = NEG_STRAND
else:
unresolved_count += 1
add_transcript(t, nodes, strand_transcript_maps, node_data)
logging.debug("\t\tCould not resolve %d transcripts" %
(unresolved_count))
del cluster_tree
return strand_transcript_maps, strand_ref_transcripts
def partition_transcripts_by_strand(transcripts):
"""
uses information from stranded transcripts to infer strand for
unstranded transcripts
"""
def add_transcript(t, nodes_iter, transcript_lists, node_data):
for n in nodes_iter:
node_data[n]['scores'][t.strand] += t.score
t_id = t.attrs[GTFAttr.TRANSCRIPT_ID]
transcript_lists[t.strand].append(t)
# divide transcripts into independent regions of
# transcription with a single entry and exit point
boundaries = find_exon_boundaries(transcripts)
node_data_func = lambda: {
'ref_strands': [False, False],
'scores': [0.0, 0.0, 0.0]
}
node_data = collections.defaultdict(node_data_func)
strand_transcript_lists = [[], [], []]
strand_ref_transcripts = [[], []]
unresolved_transcripts = []
for t in transcripts:
is_ref = bool(int(t.attrs.get(GTFAttr.REF, "0")))
if is_ref:
# label nodes by ref strand
for n in split_exons(t, boundaries):
node_data[n]['ref_strands'][t.strand] = True
strand_ref_transcripts[t.strand].append(t)
elif t.strand != NO_STRAND:
add_transcript(t, split_exons(t, boundaries),
strand_transcript_lists, node_data)
else:
unresolved_transcripts.append(t)
# resolve unstranded transcripts
logging.debug("\t\t%d unstranded transcripts" %
(len(unresolved_transcripts)))
# keep track of remaining unresolved nodes
unresolved_nodes = set()
if len(unresolved_transcripts) > 0:
resolved = []
still_unresolved_transcripts = []
for t in unresolved_transcripts:
nodes = list(split_exons(t, boundaries))
t.strand = resolve_strand(nodes, node_data)
if t.strand != NO_STRAND:
resolved.append(t)
else:
unresolved_nodes.update(nodes)
still_unresolved_transcripts.append(t)
for t in resolved:
add_transcript(t, split_exons(t, boundaries),
strand_transcript_lists, node_data)
unresolved_transcripts = still_unresolved_transcripts
if len(unresolved_transcripts) > 0:
logging.debug("\t\t%d unresolved transcripts" %
(len(unresolved_transcripts)))
# if there are still unresolved transcripts then we can try to
# extrapolate and assign strand to clusters of nodes at once, as
# long as some of the nodes have a strand assigned
# cluster unresolved nodes
unresolved_nodes = sorted(unresolved_nodes)
cluster_tree = ClusterTree(0, 1)
for i, n in enumerate(unresolved_nodes):
cluster_tree.insert(n[0], n[1], i)
# try to assign strand to clusters of nodes
node_strand_map = {}
for start, end, indexes in cluster_tree.getregions():
nodes = [unresolved_nodes[i] for i in indexes]
strand = resolve_strand(nodes, node_data)
for n in nodes:
node_strand_map[n] = strand
# for each transcript assign strand to the cluster with
# the best overlap
unresolved_count = 0
for t in unresolved_transcripts:
strand_bp = [0, 0]
nodes = list(split_exons(t, boundaries))
for n in nodes:
strand = node_strand_map[n]
if strand != NO_STRAND:
strand_bp[strand] += (n[1] - n[0])
total_strand_bp = sum(strand_bp)
if total_strand_bp > 0:
if strand_bp[POS_STRAND] >= strand_bp[NEG_STRAND]:
t.strand = POS_STRAND
else:
t.strand = NEG_STRAND
else:
unresolved_count += 1
add_transcript(t, nodes, strand_transcript_lists, node_data)
logging.debug("\t\tCould not resolve %d transcripts" %
(unresolved_count))
del cluster_tree
return strand_transcript_lists, strand_ref_transcripts