def index(args):
if not os.path.exists(args.indexdir):
print "Index_dir %s does not exist!" % (args.indexdir)
sys.exit(1)
fasta_dir = args.fastadir
index_dir = os.path.join(args.indexdir, args.indexname)
g = GenomeIndex()
g.create_index(fasta_dir, index_dir)
# Create genome FASTA file for use with bedtools
with open(os.path.join(index_dir, "genome.fa"), 'w') as out:
for f in find_by_ext(fasta_dir, FASTA_EXT):
for line in open(f):
out.write(line)
test_chr = g.get_chromosomes()[0]
tmp = NamedTemporaryFile()
tmp.write("{}\t1\t2\n".format(test_chr))
tmp.flush()
b = pybedtools.BedTool(tmp.name)
try:
b.nucleotide_content(fi=os.path.join(index_dir, "genome.fa"))
except pybedtools.helpers.BEDToolsError as e:
if str(e).find("generating") == -1:
raise
def test_genome_index(index_dir, loc_and_seq):
from gimmemotifs.genome_index import GenomeIndex
g = GenomeIndex(index_dir)
loc, seq = loc_and_seq
assert seq == g.get_sequence(*loc)
def test_genome_index(index_dir, loc_and_seq):
from gimmemotifs.genome_index import GenomeIndex
g = GenomeIndex(index_dir)
loc, seq = loc_and_seq
assert seq == g.get_sequence(*loc)
def index_dir():
from gimmemotifs.genome_index import GenomeIndex
test_index_dir = 'tests/data/index/'
g = GenomeIndex()
g.create_index('tests/data/genome/', test_index_dir)
return test_index_dir
def index_dir():
from gimmemotifs.genome_index import GenomeIndex
test_index_dir = 'tests/data/index/'
g = GenomeIndex()
g.create_index('tests/data/genome/', test_index_dir)
return test_index_dir
def index(args):
if not os.path.exists(args.indexdir):
print "Index_dir %s does not exist!" % (args.indexdir)
sys.exit(1)
fasta_dir = args.fastadir
index_dir = os.path.join(args.indexdir, args.indexname)
g = GenomeIndex()
g.create_index(fasta_dir, index_dir)
create_bedtools_fa(index_dir, fasta_dir)
def __init__(self,
session=None,
conn='mysql://pita:@localhost/pita',
new=False,
index=None):
self.logger = logging.getLogger("pita")
# initialize db session
if session:
self.session = session
else:
self._init_session(conn, new)
# index to retrieve sequence
self.index = None
if index:
self.index = GenomeIndex(index)
self.cache_splice_stats = {}
self.cache_feature_stats = {}
def test2_as_fasta(self):
""" convert bed, regions, etc to Fasta """
tmpdir = mkdtemp()
g = GenomeIndex()
g.create_index(self.genome_dir, tmpdir)
fafile = os.path.join(self.datadir, "test.fa")
fa = Fasta(fafile)
bedfile = os.path.join(self.datadir, "test.bed")
regionfile = os.path.join(self.datadir, "test.txt")
regions = [l.strip() for l in open(regionfile)]
self.assertTrue(isinstance(as_fasta(fa), Fasta))
self.assertTrue(isinstance(as_fasta(fafile), Fasta))
self.assertTrue(isinstance(as_fasta(bedfile, tmpdir), Fasta))
self.assertTrue(isinstance(as_fasta(regionfile, tmpdir), Fasta))
self.assertTrue(isinstance(as_fasta(regions, tmpdir), Fasta))
with self.assertRaises(ValueError):
as_fasta(bedfile)
rmtree(tmpdir)
def test2_as_fasta(self):
""" convert bed, regions, etc to Fasta """
tmpdir = mkdtemp()
g = GenomeIndex()
g.create_index(self.genome_dir, tmpdir)
fafile = os.path.join(self.datadir, "test.fa")
fa = Fasta(fafile)
bedfile = os.path.join(self.datadir, "test.bed")
regionfile = os.path.join(self.datadir, "test.txt")
regions = [l.strip() for l in open(regionfile)]
self.assertTrue(isinstance(as_fasta(fa), Fasta))
self.assertTrue(isinstance(as_fasta(fafile), Fasta))
self.assertTrue(isinstance(as_fasta(bedfile, tmpdir), Fasta))
self.assertTrue(isinstance(as_fasta(regionfile, tmpdir), Fasta))
self.assertTrue(isinstance(as_fasta(regions, tmpdir), Fasta))
with self.assertRaises(ValueError):
as_fasta(bedfile)
rmtree(tmpdir)
def __init__(self, session=None, conn='mysql://pita:@localhost/pita', new=False, index=None):
self.logger = logging.getLogger("pita")
# initialize db session
if session:
self.session = session
else:
self._init_session(conn, new)
# index to retrieve sequence
self.index = None
if index:
self.index = GenomeIndex(index)
self.cache_splice_stats = {}
self.cache_feature_stats = {}
def _scan_regions(self, regions, nreport, scan_rc, cutoff=0.95):
index_dir = self.index_dir
motif_file = self.motifs
motif_digest = self.checksum.get(motif_file, None)
# determine which regions are not in the cache
scan_regions = regions
if self.use_cache:
scan_regions = []
for region in regions:
key = str((region, index_dir, motif_digest, nreport, scan_rc,
cutoff))
ret = self.cache.get(key)
if ret == NO_VALUE:
scan_regions.append(region)
# scan the regions that are not in the cache
if len(scan_regions) > 0:
n = 12
genome_index = GenomeIndex(index_dir)
motifs = load_motifs(motif_file, cutoff)
scan_func = partial(scan_region_mult,
genome_index=genome_index,
motifs=motifs,
nreport=nreport,
scan_rc=scan_rc)
jobs = []
chunksize = len(scan_regions) / n + 1
for i in range(n):
job = pool.apply_async(
scan_func,
(scan_regions[i * chunksize:(i + 1) * chunksize], ))
jobs.append(job)
# return values or store values in cache
i = 0
for job in jobs:
for ret in job.get():
if self.use_cache:
# store values in cache
region = scan_regions[i]
key = str((region, index_dir, motif_digest, nreport,
scan_rc, cutoff))
self.cache.set(key, ret)
else:
#return values
yield ret
i += 1
if self.use_cache:
# return results from cache
for region in regions:
key = str((region, index_dir, motif_digest, nreport, scan_rc,
cutoff))
ret = self.cache.get(key)
if ret == NO_VALUE or ret is None:
raise Exception("cache is not big enough to hold all "
"results, try increasing the cache size "
"or disable cache")
yield ret
def genome(args):
config = MotifConfig()
if not os.path.exists(args.indexdir):
print "Index_dir %s does not exist!" % (args.indexdir)
sys.exit(1)
if not os.path.exists(args.fastadir):
print "FASTA dir %s does not exist!" % (args.fastadir)
sys.exit(1)
pred_bin = "genePredToBed"
pred = find_executable(pred_bin)
if not pred:
sys.stderr.write("{} not found in path!\n".format(pred_bin))
sys.exit(1)
fastadir = args.fastadir
genomebuild = args.genomebuild
genome_dir = os.path.join(fastadir, genomebuild)
index_dir = os.path.join(args.indexdir, args.genomebuild)
# Check for rights to write to directory
if not os.path.exists(genome_dir):
try:
os.mkdir(genome_dir)
except:
sys.stderr.write("Could not create genome dir {}\n".format(genome_dir))
sys.exit(1)
# Download gene file based on URL + genomebuild
gene_file = os.path.join(config.get_gene_dir(), "%s.bed" % genomebuild)
tmp = NamedTemporaryFile(delete=False, suffix=".gz")
anno = []
f = urllib2.urlopen(UCSC_GENE_URL.format(genomebuild))
p = re.compile(r'\w+.Gene.txt.gz')
for line in f.readlines():
m = p.search(line)
if m:
anno.append(m.group(0))
sys.stderr.write("Retrieving gene annotation for {}\n".format(genomebuild))
url = ""
for a in ANNOS:
if a in anno:
url = UCSC_GENE_URL.format(genomebuild) + a
break
if url:
urllib.urlretrieve(
url,
tmp.name
)
sp.call("zcat {} | cut -f2-11 | {} /dev/stdin {}".format(tmp.name, pred, gene_file), shell=True)
else:
sys.stderr.write("No annotation found!")
# download genome based on URL + genomebuild
sys.stderr.write("Downloading {} genome\n".format(genomebuild))
for genome_url in [UCSC_GENOME_URL, ALT_UCSC_GENOME_URL]:
remote = genome_url.format(genomebuild)
genome_fa = os.path.join(
genome_dir,
os.path.split(remote)[-1]
)
sys.stderr.write("Trying to download {}\n".format(genome_url.format(genomebuild)))
urllib.urlretrieve(
genome_url.format(genomebuild),
genome_fa
)
if not check_genome_file(genome_fa):
continue
break
if not check_genome_file(genome_fa):
sys.stderr.write("Failed to download genome\n")
sys.exit(1)
sys.stderr.write("Unpacking\n")
if genome_fa.endswith("tar.gz"):
cmd = "tar -C {0} -xvzf {1} && rm {1}".format(genome_dir, genome_fa)
else:
cmd = "gunzip {0} && rm {0}".format(genome_fa)
sp.call(cmd, shell=True, cwd=genome_dir)
fa_files = glob("{}/*.fa".format(genome_dir))
if len(fa_files) == 1:
f = Fasta(fa_files[0])
for n,s in f.items():
with open("{}/{}.fa".format(n)) as f:
f.write("{}\n{}\n".format(n,s))
os.unlink(fa_files[0])
sys.stderr.write("Creating index\n")
g = GenomeIndex()
g = g.create_index(genome_dir, index_dir)
class AnnotationDb(object):
def __init__(self, session=None, conn='mysql://pita:@localhost/pita', new=False, index=None):
self.logger = logging.getLogger("pita")
# initialize db session
if session:
self.session = session
else:
self._init_session(conn, new)
# index to retrieve sequence
self.index = None
if index:
self.index = GenomeIndex(index)
self.cache_splice_stats = {}
self.cache_feature_stats = {}
def _init_session(self, conn, new=False):
self.engine = create_engine(conn)
self.engine.raw_connection().connection.text_factory = str
# recreate database
if new:
Base.metadata.drop_all(self.engine)
Base.metadata.create_all(self.engine)
Base.metadata.bind =self.engine
Session = scoped_session(sessionmaker(bind=self.engine))
self.session = Session()
def __enter__(self):
return self
def __exit__(self, _type, value, traceback):
self.session.close()
def dump_yaml(self):
dump_dict = {}
dump_dict['feature'] = [
[f.id,
f.chrom.encode('ascii','ignore'),
f.start,
f.end,
f.strand.encode('ascii','ignore'),
f.ftype.encode('ascii','ignore'),
f.seq.encode('ascii','ignore')]
for f in self.session.query(Feature)]
dump_dict['read_source'] = [
[r.id,
r.name.encode('ascii','ignore'),
r.source.encode('ascii','ignore'),
r.nreads]
for r in self.session.query(ReadSource)]
dump_dict['read_count'] = [
[r.read_source_id,
r.feature_id,
r.count,r.span.encode('ascii','ignore'),
r.extend_up,
r.extend_down]
for r in self.session.query(FeatureReadCount)]
dump_dict['evidence'] = [
[r.id, r.name.encode('ascii','ignore'),
r.source.encode('ascii','ignore')]
for r in self.session.query(Evidence)]
dump_dict['feature_evidence'] = [
[r.feature_id, r.evidence_id]
for r in self.session.query(FeatureEvidence)]
return yaml.dump(dump_dict)
def load_yaml(self, fname):
data = yaml.load(open(fname))
source_map = {}
if not data['feature']:
return
for old_id,name,fname,nreads in data['read_source']:
r = get_or_create(self.session, ReadSource,
name=name, source=fname, nreads=nreads)
self.session.commit()
source_map[old_id] = r.id
t = ["chrom","start","end","strand","ftype","seq"]
self.engine.execute(
Feature.__table__.insert(),
[dict(zip(t, row[1:])) for row in data['feature']]
)
self.session.commit()
first = self.fetch_feature(data['feature'][0][1:])
last = self.fetch_feature(data['feature'][-1][1:])
f_map = dict(zip([x[0] for x in data['feature']], range(first.id, last.id + 1)))
data['read_count'] = [
[source_map[row[0]]] + [f_map[row[1]]] + row[2:] for row in data['read_count']
]
t = ["read_source_id", "feature_id", "count", "span", "extend_up", "extend_down"]
self.engine.execute(
FeatureReadCount.__table__.insert(),
[dict(zip(t, row)) for row in data['read_count']]
)
if data['evidence']:
t = ["name","source"]
result = self.engine.execute(
Evidence.__table__.insert(),
[dict(zip(t, row[1:])) for row in data['evidence']]
)
self.session.commit()
first = self.fetch_evidence(data['evidence'][0][1:])
last = self.fetch_evidence(data['evidence'][-1][1:])
ev_map = dict(zip([x[0] for x in data['evidence']], range(first.id, last.id + 1)))
data['feature_evidence'] = [
[f_map[row[0]], ev_map[row[1]]] for row in data['feature_evidence']
]
t = ["feature_id", "evidence_id"]
self.engine.execute(
FeatureEvidence.__table__.insert(),
[dict(zip(t, row)) for row in data['feature_evidence']]
)
def add_transcript(self, name, source, exons):
"""
Add a transcript to the database
"""
# Sanity checks
for e1, e2 in zip(exons[:-1], exons[1:]):
if e1[0] != e2[0]:
sys.stderr.write("{0} - {1}\n".format(e1, e2))
raise ValueError("Different chromosomes!")
if e2[1] <= e1[2]:
sys.stderr.write("{0} - {1}\n".format(e1, e2))
raise ValueError("exons overlap, or in wrong order")
if e1[3] != e2[3]:
sys.stderr.write("{0} - {1}\n".format(e1, e2))
raise ValueError("strands don't match")
chrom = exons[0][0]
strand = exons[0][-1]
evidence = get_or_create(self.session, Evidence,
name = name,
source=source)
seqs = []
for exon in exons:
seq = ""
real_seq = ""
if self.index:
seq = ""
try:
seq = self.index.get_sequence(chrom, exon[1] - 20, exon[2] + 20, strand)
real_seq = seq[20:-20]
except Exception:
real_seq = self.index.get_sequence(chrom, exon[1], exon[2], strand)
seqs.append(seq)
exon = get_or_create(self.session, Feature,
chrom = chrom,
start = exon[1],
end = exon[2],
strand = strand,
ftype = "exon",
seq = real_seq
)
exon.evidences.append(evidence)
splice_donors = []
splice_acceptors = []
for i,(start,end) in enumerate([(e1[2], e2[1]) for e1, e2 in zip(exons[0:-1], exons[1:])]):
self.logger.debug("%s %s %s %s", chrom, start, end, strand)
sj = get_or_create(self.session, Feature,
chrom = chrom,
start = start,
end = end,
strand = strand,
ftype = "splice_junction"
)
sj.evidences.append(evidence)
if strand == "+":
if len(seqs) > (i + 1) and len(seqs[i]) > 46:
splice_donors.append(["{}_{}".format(name, i + 1), seqs[i][-23:-14]])
if len(seqs) > (i + 2) and len(seqs[i + 1]) > 46:
f = ["{}_{}".format(name, i + 1), seqs[i + 1][:23]]
splice_acceptors.append(f)
else:
if len(seqs) > (i + 2) and len(seqs[i + 1]) > 46:
f = ["{}_{}".format(name, i + 1), seqs[i + 1][-23:-14]]
splice_donors.append(f)
if len(seqs) > (i + 1) and len(seqs[i]) > 46:
f = ["{}_{}".format(name, i + 1), seqs[i][:23]]
splice_acceptors.append(f)
donor_score = get_splice_score(splice_donors, 5)
acceptor_score = get_splice_score(splice_acceptors, 3)
if donor_score + acceptor_score < 0:
self.logger.warning("Skipping %s, splicing not OK!", name)
self.session.rollback()
else:
self.session.commit()
def get_features(self, ftype=None, chrom=None, eager=False,
min_length=None, max_length=None, evidence=0):
query = self.session.query(Feature)
query = query.filter(Feature.flag.op("IS NOT")(True))
# pre-fetch associated read counts
if eager:
query = query.options(subqueryload('read_counts'))
if chrom:
query = query.filter(Feature.chrom == chrom)
if ftype:
query = query.filter(Feature.ftype == ftype)
features = [f for f in query]
# length filters
if max_length:
features = [f for f in features if
f.length <= max_length or len(f.evidences) >= evidence]
if min_length:
features = [f for f in features if
f.length >= min_length or len(f.evidences) >= evidence]
return features
def get_exons(self, chrom=None, eager=False, min_length=None,
max_length=None, evidence=0):
return self.get_features(ftype="exon", chrom=chrom, eager=eager,
min_length=min_length, max_length=max_length, evidence=evidence)
def get_splice_junctions(self, chrom=None, ev_count=None, read_count=None, max_reads=None, eager=False):
features = []
if ev_count and read_count:
# All splices with no read, but more than one evidence source
fs = self.session.query(Feature).\
filter(Feature.flag.op("IS NOT")(True)).\
filter(Feature.ftype == "splice_junction").\
filter(Feature.chrom == chrom).\
outerjoin(FeatureReadCount).\
group_by(Feature).\
having(func.sum(FeatureReadCount.count) < read_count)
for splice in fs:
self.logger.debug("Considering %s", splice)
for evidence in splice.evidences:
self.logger.debug(str(evidence))
if len(splice.evidences) >= ev_count:
features.append(splice)
else:
self.logger.debug("not enough evidence for {}".format(splice))
fs = self.session.query(Feature).\
filter(Feature.flag.op("IS NOT")(True)).\
filter(Feature.ftype == "splice_junction").\
filter(Feature.chrom == chrom).\
outerjoin(FeatureReadCount).\
group_by(Feature).\
having(func.sum(FeatureReadCount.count) == None)
for splice in fs:
self.logger.debug("Considering %s (no reads)", splice)
for evidence in splice.evidences:
self.logger.debug(str(evidence))
if len(splice.evidences) >= ev_count:
features.append(splice)
else:
self.logger.debug("not enough evidence for {}".format(splice))
# All splices with more than x reads
fs = self.session.query(Feature).\
filter(Feature.flag.op("IS NOT")(True)).\
filter(Feature.ftype == "splice_junction").\
filter(Feature.chrom == chrom).\
outerjoin(FeatureReadCount).\
group_by(Feature).\
having(func.sum(FeatureReadCount.count) >= read_count)
for f in fs:
self.logger.debug("Considering %s (reads)", f)
features.append(f)
#features += [f for f in fs]
elif max_reads:
fs = self.session.query(Feature).\
filter(Feature.flag.op("IS NOT")(True)).\
filter(Feature.ftype == "splice_junction").\
filter(Feature.chrom == chrom).\
outerjoin(FeatureReadCount).\
group_by(Feature).\
having(func.sum(FeatureReadCount.count) == None)
features += [f for f in fs if len(f.evidences) > 0]
fs = self.session.query(Feature).\
filter(Feature.flag.op("IS NOT")(True)).\
filter(Feature.ftype == "splice_junction").\
filter(Feature.chrom == chrom).\
outerjoin(FeatureReadCount).\
group_by(Feature).\
having(func.sum(FeatureReadCount.count) < max_reads)
features += [f for f in fs if len(f.evidences) > 0]
else:
features = self.get_features(ftype="splice_junction", chrom=chrom, eager=eager)
return features
def get_longest_3prime_exon(self, chrom, start5, strand):
if strand == "+":
q = self.session.query(Feature).\
filter(Feature.flag.op("IS NOT")(True)).\
filter(Feature.ftype == "exon").\
filter(Feature.chrom == chrom).\
filter(Feature.strand == strand).\
filter(Feature.start == start5).\
order_by(Feature.end)
return q.all()[-1]
else:
q = self.session.query(Feature).\
filter(Feature.ftype == "exon").\
filter(Feature.chrom == chrom).\
filter(Feature.strand == strand).\
filter(Feature.end == start5).\
order_by(Feature.end)
return q.all()[0]
def get_long_exons(self, chrom, l, evidence):
query = self.session.query(Feature)
query = query.filter(Feature.flag.op("IS NOT")(True))
query = query.filter(Feature.ftype == 'exon')
query = query.filter(Feature.chrom == chrom)
query = query.filter(Feature.end - Feature.start >= l)
return [e for e in query if len(e.evidences) <= evidence]
def filter_repeats(self, chrom, rep):
""" Flag all exons that overlap with a specified fraction
with a repeat track
"""
self.logger.warn("Filtering repeats: %s with fraction %s",
os.path.basename(rep["path"]), rep["fraction"])
exons = self.get_features("exon", chrom)
exon_tabix = exons_to_tabix_bed(exons)
overlap_it = tabix_overlap(exon_tabix, rep["tabix"], chrom, rep["fraction"])
exon_ids = [int(iv[3]) for iv in overlap_it]
chunk = 20
for i in range(0, len(exon_ids), chunk):
self.logger.warn("Filtering %s", exon_ids[i:i + chunk])
self.session.query(Feature).\
filter(Feature.id.in_(exon_ids[i:i + chunk])).\
update({Feature.flag:True}, synchronize_session=False)
self.session.commit()
#fobj = TabixIteratorAsFile(tabixfile.fetch(chrom))
#for line in fobj:
# print line
def filter_evidence(self, chrom, source, experimental):
self.logger.debug("Filtering %s", source)
#query = self.session.query(Feature).\
# update({Feature.flag:False}, synchronize_session=False)
#self.session.commit()
# Select all features that are supported by other evidence
n = self.session.query(Feature.id).\
join(FeatureEvidence).\
join(Evidence).\
filter(Evidence.source != source).\
filter(Evidence.source not in experimental).\
filter(Feature.chrom == chrom).\
subquery("n")
# Select the total number of transcript from this source
# per feature
s = self.session.query(Feature.id, func.count('*').label('total')).\
join(FeatureEvidence).\
join(Evidence).\
filter(Evidence.source == source).\
filter(Feature.chrom == chrom).\
group_by(Feature.id).\
subquery("s")
# Select all features where support from this source
# is only 1 transcript and which is not supported by any
# other sources
a = self.session.query(Feature.id).filter(and_(
Feature.id == s.c.id,
s.c.total == 1)).\
filter(Feature.id.notin_(n)).\
subquery("a")
#ids = [i[0] for i in query]
# Flag features
self.session.query(Feature).\
filter(Feature.id.in_(a)).\
update({Feature.flag:True}, synchronize_session=False)
self.session.commit()
def get_read_statistics(self, chrom, fnames, name, span="all", extend=(0,0), nreads=None):
if span not in ["all", "start", "end"]:
raise Exception("Incorrect span: {}".format(span))
tmp = NamedTemporaryFile(delete=False)
estore = {}
self.logger.debug("Writing exons to file %s", tmp.name)
exons = self.get_exons(chrom)
if len(exons) == 0:
return
for exon in exons:
start = exon.start
end = exon.end
if span == "start":
if exon.strand == "+":
end = start
elif exon.strand == "-":
start = end
if span == "end":
if exon.strand == "+":
start = end
elif exon.strand == "-":
end = start
if exon.strand == "-":
start -= extend[1]
end += extend[0]
else:
start -= extend[0]
end += extend[1]
if start < 0:
start = 0
estr = "{}:{}-{}".format(exon.chrom, start, end)
if estr in estore:
estore[estr].append(exon)
else:
estore[estr] = [exon]
tmp.write("{}\t{}\t{}\t{}\t{}\t{}\n".format(
exon.chrom,
start,
end,
str(exon),
0,
exon.strand
))
tmp.flush()
if type("") == type(fnames):
fnames = [fnames]
for i, fname in enumerate(fnames):
self.logger.debug("Creating read_source for %s %s", name, fname)
read_source = get_or_create(self.session, ReadSource, name=name, source=fname)
self.session.commit()
#rmrepeats = False
if fname.endswith("bam") and (not nreads or not nreads[i]):
#rmrepeats = True
self.logger.debug("Counting reads in %s", fname)
read_source.nreads = read_statistics(fname)
self.logger.debug("Getting overlap from %s", fname)
result = get_binned_stats(tmp.name, fname, 1, rpkm=False, rmdup=False, rmrepeats=False)
self.logger.debug("Reading results, save to exon stats")
insert_vals = []
for row in result:
try:
vals = row.strip().split("\t")
e = "%s:%s-%s" % (vals[0], vals[1], vals[2])
c = float(vals[3])
for exon in estore[e]:
insert_vals.append([read_source.id, exon.id, c, span, extend[0], extend[1]])
except:
self.logger.info("binned_stat line skipped: {}".format(row))
t = ["read_source_id", "feature_id", "count", "span", "extend_up", "extend_down"]
result = self.engine.execute(
FeatureReadCount.__table__.insert(),
[dict(zip(t,row)) for row in insert_vals]
)
tmp.close()
def get_splice_statistics(self, chrom, fnames, name):
if type("") == type(fnames):
fnames = [fnames]
for fname in fnames:
self.logger.debug("Getting splicing data from %s", fname)
read_source = get_or_create(self.session,
ReadSource, name=name, source=fname)
self.session.commit()
for line in open(fname):
vals = line.strip().split("\t")
if vals[0] == chrom:
start, end, c = [int(x) for x in vals[1:4]]
strand = vals[5]
splice = get_or_create(self.session, Feature,
chrom = chrom,
start = start,
end = end,
strand = strand,
ftype = "splice_junction"
)
self.session.commit()
count = get_or_create(self.session, FeatureReadCount,
feature_id = splice.id,
read_source_id = read_source.id)
if not count.count:
count.count = c
else:
count.count += c
self.session.commit()
def get_junction_exons(self, junction):
left = self.session.query(Feature).filter(and_(
Feature.chrom == junction.chrom,
Feature.strand == junction.strand,
Feature.end == junction.start,
Feature.ftype == "exon"
)).\
filter(Feature.flag.op("IS NOT")(True))
right = self.session.query(Feature).filter(and_(
Feature.chrom == junction.chrom,
Feature.strand == junction.strand,
Feature.start == junction.end,
Feature.ftype == "exon"
)).\
filter(Feature.flag.op("IS NOT")(True))
exon_pairs = []
for e1 in left:
for e2 in right:
exon_pairs.append((e1, e2))
return exon_pairs
def clear_stats_cache(self):
self.cache_feature_stats = {}
self.cache_splice_stats = {}
def feature_stats(self, feature, identifier):
if "{}{}".format(feature, identifier) not in self.cache_feature_stats:
q = self.session.query(FeatureReadCount, ReadSource).join(ReadSource)
q = q.filter(FeatureReadCount.feature_id == feature.id)
q = q.filter(ReadSource.name == identifier)
self.cache_feature_stats["{}{}".format(feature, identifier)] = sum([x[0].count for x in q.all()])
return self.cache_feature_stats["{}{}".format(feature, identifier)]
def splice_stats(self, exon1, exon2, identifier):
if "{}{}{}".format(self, exon1, exon2) not in self.cache_splice_stats:
q = self.session.query(Feature)
q = q.filter(Feature.ftype == "splice_junction")
q = q.filter(Feature.chrom == exon1.chrom)
q = q.filter(Feature.strand == exon1.strand)
q = q.filter(Feature.start == exon1.end)
q = q.filter(Feature.end == exon2.start)
splice = q.first()
self.cache_splice_stats["{}{}{}".format(self, exon1, exon2)] = self.feature_stats(splice, identifier)
return self.cache_splice_stats["{}{}{}".format(self, exon1, exon2)]
def intron_splice_stats(self, intron, identifier):
if "{}{}".format(self, intron) not in self.cache_splice_stats:
q = self.session.query(Feature)
q = q.filter(Feature.ftype == "splice_junction")
q = q.filter(Feature.chrom == intron.chrom)
q = q.filter(Feature.strand == intron.strand)
q = q.filter(Feature.start == intron.start)
q = q.filter(Feature.end == intron.end)
splice = q.first()
self.cache_splice_stats["{}{}".format(self, intron)] = self.feature_stats(splice, identifier)
return self.cache_splice_stats["{}{}".format(self, intron)]
def nreads(self, identifier):
q = self.session.query(ReadSource)
q = q.filter(ReadSource.name == identifier)
return sum([s.nreads for s in q.all()])
def get_splice_count(self, e1, e2):
counts = self.session.query(func.sum(FeatureReadCount.count)).\
join(Feature).\
filter(Feature.chrom == e1.chrom).\
filter(Feature.start == e1.end).\
filter(Feature.end == e2.start).\
filter(Feature.ftype == "splice_junction").\
group_by(Feature.id).all()
return sum([int(x[0]) for x in counts])
def fetch_feature(self, f):
""" Feature as list """
chrom, start, end, strand, ftype, seq = f
feature = self.session.query(Feature).\
filter(Feature.chrom == chrom).\
filter(Feature.start == start).\
filter(Feature.end == end).\
filter(Feature.strand == strand).\
filter(Feature.ftype == ftype)
if seq:
feature = feature.filter(Feature.seq == seq)
result = feature.first()
return result
def fetch_evidence(self, f):
""" Feature as list """
name, source = f
evidence = self.session.query(Evidence).\
filter(Evidence.name == name).\
filter(Evidence.source == source)
result = evidence.first()
return result
def get_transcript_statistics(self, exons):
stats = []
for exon in exons:
q = self.session.query(ReadSource,
func.sum(FeatureReadCount.count)).\
join(FeatureReadCount).\
join(Feature).\
filter(Feature.chrom == exon[0]).\
filter(Feature.start == exon[1]).\
filter(Feature.end == exon[2]).\
filter(Feature.strand == exon[3]).\
group_by(ReadSource.name)
stats.append(dict([(row[0].name, int(row[1])) for row in q.all()]))
return stats
class AnnotationDb(object):
def __init__(self,
session=None,
conn='mysql://pita:@localhost/pita',
new=False,
index=None):
self.logger = logging.getLogger("pita")
# initialize db session
if session:
self.session = session
else:
self._init_session(conn, new)
# index to retrieve sequence
self.index = None
if index:
self.index = GenomeIndex(index)
self.cache_splice_stats = {}
self.cache_feature_stats = {}
def _init_session(self, conn, new=False):
self.engine = create_engine(conn)
self.engine.raw_connection().connection.text_factory = str
# recreate database
if new:
Base.metadata.drop_all(self.engine)
Base.metadata.create_all(self.engine)
Base.metadata.bind = self.engine
Session = scoped_session(sessionmaker(bind=self.engine))
self.session = Session()
def __enter__(self):
return self
def __exit__(self, _type, value, traceback):
self.session.close()
def dump_yaml(self):
dump_dict = {}
dump_dict['feature'] = [[
f.id,
f.chrom.encode('ascii', 'ignore'), f.start, f.end,
f.strand.encode('ascii', 'ignore'),
f.ftype.encode('ascii', 'ignore'),
f.seq.encode('ascii', 'ignore')
] for f in self.session.query(Feature)]
dump_dict['read_source'] = [[
r.id,
r.name.encode('ascii', 'ignore'),
r.source.encode('ascii', 'ignore'), r.nreads
] for r in self.session.query(ReadSource)]
dump_dict['read_count'] = [[
r.read_source_id, r.feature_id, r.count,
r.span.encode('ascii', 'ignore'), r.extend_up, r.extend_down
] for r in self.session.query(FeatureReadCount)]
dump_dict['evidence'] = [[
r.id,
r.name.encode('ascii', 'ignore'),
r.source.encode('ascii', 'ignore')
] for r in self.session.query(Evidence)]
dump_dict['feature_evidence'] = [[
r.feature_id, r.evidence_id
] for r in self.session.query(FeatureEvidence)]
return yaml.dump(dump_dict)
def load_yaml(self, fname):
data = yaml.load(open(fname))
source_map = {}
if not data['feature']:
return
for old_id, name, fname, nreads in data['read_source']:
r = get_or_create(self.session,
ReadSource,
name=name,
source=fname,
nreads=nreads)
self.session.commit()
source_map[old_id] = r.id
t = ["chrom", "start", "end", "strand", "ftype", "seq"]
self.engine.execute(Feature.__table__.insert(),
[dict(zip(t, row[1:])) for row in data['feature']])
self.session.commit()
first = self.fetch_feature(data['feature'][0][1:])
last = self.fetch_feature(data['feature'][-1][1:])
f_map = dict(
zip([x[0] for x in data['feature']], range(first.id, last.id + 1)))
data['read_count'] = [[source_map[row[0]]] + [f_map[row[1]]] + row[2:]
for row in data['read_count']]
t = [
"read_source_id", "feature_id", "count", "span", "extend_up",
"extend_down"
]
self.engine.execute(FeatureReadCount.__table__.insert(),
[dict(zip(t, row)) for row in data['read_count']])
if data['evidence']:
t = ["name", "source"]
result = self.engine.execute(
Evidence.__table__.insert(),
[dict(zip(t, row[1:])) for row in data['evidence']])
self.session.commit()
first = self.fetch_evidence(data['evidence'][0][1:])
last = self.fetch_evidence(data['evidence'][-1][1:])
ev_map = dict(
zip([x[0] for x in data['evidence']],
range(first.id, last.id + 1)))
data['feature_evidence'] = [[f_map[row[0]], ev_map[row[1]]]
for row in data['feature_evidence']]
t = ["feature_id", "evidence_id"]
self.engine.execute(
FeatureEvidence.__table__.insert(),
[dict(zip(t, row)) for row in data['feature_evidence']])
def add_transcript(self, name, source, exons):
"""
Add a transcript to the database
"""
# Sanity checks
for e1, e2 in zip(exons[:-1], exons[1:]):
if e1[0] != e2[0]:
sys.stderr.write("{0} - {1}\n".format(e1, e2))
raise ValueError("Different chromosomes!")
if e2[1] <= e1[2]:
sys.stderr.write("{0} - {1}\n".format(e1, e2))
raise ValueError("exons overlap, or in wrong order")
if e1[3] != e2[3]:
sys.stderr.write("{0} - {1}\n".format(e1, e2))
raise ValueError("strands don't match")
chrom = exons[0][0]
strand = exons[0][-1]
evidence = get_or_create(self.session,
Evidence,
name=name,
source=source)
seqs = []
for exon in exons:
seq = ""
real_seq = ""
if self.index:
seq = ""
try:
seq = self.index.get_sequence(chrom, exon[1] - 20,
exon[2] + 20, strand)
real_seq = seq[20:-20]
except Exception:
real_seq = self.index.get_sequence(chrom, exon[1], exon[2],
strand)
seqs.append(seq)
exon = get_or_create(self.session,
Feature,
chrom=chrom,
start=exon[1],
end=exon[2],
strand=strand,
ftype="exon",
seq=real_seq)
exon.evidences.append(evidence)
splice_donors = []
splice_acceptors = []
for i, (start, end) in enumerate([
(e1[2], e2[1]) for e1, e2 in zip(exons[0:-1], exons[1:])
]):
self.logger.debug("%s %s %s %s", chrom, start, end, strand)
sj = get_or_create(self.session,
Feature,
chrom=chrom,
start=start,
end=end,
strand=strand,
ftype="splice_junction")
sj.evidences.append(evidence)
if strand == "+":
if len(seqs) > (i + 1) and len(seqs[i]) > 46:
splice_donors.append(
["{}_{}".format(name, i + 1), seqs[i][-23:-14]])
if len(seqs) > (i + 2) and len(seqs[i + 1]) > 46:
f = ["{}_{}".format(name, i + 1), seqs[i + 1][:23]]
splice_acceptors.append(f)
else:
if len(seqs) > (i + 2) and len(seqs[i + 1]) > 46:
f = ["{}_{}".format(name, i + 1), seqs[i + 1][-23:-14]]
splice_donors.append(f)
if len(seqs) > (i + 1) and len(seqs[i]) > 46:
f = ["{}_{}".format(name, i + 1), seqs[i][:23]]
splice_acceptors.append(f)
donor_score = get_splice_score(splice_donors, 5)
acceptor_score = get_splice_score(splice_acceptors, 3)
if donor_score + acceptor_score < 0:
self.logger.warning("Skipping %s, splicing not OK!", name)
self.session.rollback()
else:
self.session.commit()
def get_features(self,
ftype=None,
chrom=None,
eager=False,
min_length=None,
max_length=None,
evidence=0):
query = self.session.query(Feature)
query = query.filter(Feature.flag.op("IS NOT")(True))
# pre-fetch associated read counts
if eager:
query = query.options(subqueryload('read_counts'))
if chrom:
query = query.filter(Feature.chrom == chrom)
if ftype:
query = query.filter(Feature.ftype == ftype)
features = [f for f in query]
# length filters
if max_length:
features = [
f for f in features
if f.length <= max_length or len(f.evidences) >= evidence
]
if min_length:
features = [
f for f in features
if f.length >= min_length or len(f.evidences) >= evidence
]
return features
def get_exons(self,
chrom=None,
eager=False,
min_length=None,
max_length=None,
evidence=0):
return self.get_features(ftype="exon",
chrom=chrom,
eager=eager,
min_length=min_length,
max_length=max_length,
evidence=evidence)
def get_splice_junctions(self,
chrom=None,
ev_count=None,
read_count=None,
max_reads=None,
eager=False):
features = []
if ev_count and read_count:
# All splices with no read, but more than one evidence source
fs = self.session.query(Feature).\
filter(Feature.flag.op("IS NOT")(True)).\
filter(Feature.ftype == "splice_junction").\
filter(Feature.chrom == chrom).\
outerjoin(FeatureReadCount).\
group_by(Feature).\
having(func.sum(FeatureReadCount.count) < read_count)
for splice in fs:
self.logger.debug("Considering %s", splice)
for evidence in splice.evidences:
self.logger.debug(str(evidence))
if len(splice.evidences) >= ev_count:
features.append(splice)
else:
self.logger.debug(
"not enough evidence for {}".format(splice))
fs = self.session.query(Feature).\
filter(Feature.flag.op("IS NOT")(True)).\
filter(Feature.ftype == "splice_junction").\
filter(Feature.chrom == chrom).\
outerjoin(FeatureReadCount).\
group_by(Feature).\
having(func.sum(FeatureReadCount.count) == None)
for splice in fs:
self.logger.debug("Considering %s (no reads)", splice)
for evidence in splice.evidences:
self.logger.debug(str(evidence))
if len(splice.evidences) >= ev_count:
features.append(splice)
else:
self.logger.debug(
"not enough evidence for {}".format(splice))
# All splices with more than x reads
fs = self.session.query(Feature).\
filter(Feature.flag.op("IS NOT")(True)).\
filter(Feature.ftype == "splice_junction").\
filter(Feature.chrom == chrom).\
outerjoin(FeatureReadCount).\
group_by(Feature).\
having(func.sum(FeatureReadCount.count) >= read_count)
for f in fs:
self.logger.debug("Considering %s (reads)", f)
features.append(f)
#features += [f for f in fs]
elif max_reads:
fs = self.session.query(Feature).\
filter(Feature.flag.op("IS NOT")(True)).\
filter(Feature.ftype == "splice_junction").\
filter(Feature.chrom == chrom).\
outerjoin(FeatureReadCount).\
group_by(Feature).\
having(func.sum(FeatureReadCount.count) == None)
features += [f for f in fs if len(f.evidences) > 0]
fs = self.session.query(Feature).\
filter(Feature.flag.op("IS NOT")(True)).\
filter(Feature.ftype == "splice_junction").\
filter(Feature.chrom == chrom).\
outerjoin(FeatureReadCount).\
group_by(Feature).\
having(func.sum(FeatureReadCount.count) < max_reads)
features += [f for f in fs if len(f.evidences) > 0]
else:
features = self.get_features(ftype="splice_junction",
chrom=chrom,
eager=eager)
return features
def get_longest_3prime_exon(self, chrom, start5, strand):
if strand == "+":
q = self.session.query(Feature).\
filter(Feature.flag.op("IS NOT")(True)).\
filter(Feature.ftype == "exon").\
filter(Feature.chrom == chrom).\
filter(Feature.strand == strand).\
filter(Feature.start == start5).\
order_by(Feature.end)
return q.all()[-1]
else:
q = self.session.query(Feature).\
filter(Feature.ftype == "exon").\
filter(Feature.chrom == chrom).\
filter(Feature.strand == strand).\
filter(Feature.end == start5).\
order_by(Feature.end)
return q.all()[0]
def get_long_exons(self, chrom, l, evidence):
query = self.session.query(Feature)
query = query.filter(Feature.flag.op("IS NOT")(True))
query = query.filter(Feature.ftype == 'exon')
query = query.filter(Feature.chrom == chrom)
query = query.filter(Feature.end - Feature.start >= l)
return [e for e in query if len(e.evidences) <= evidence]
def filter_repeats(self, chrom, rep):
""" Flag all exons that overlap with a specified fraction
with a repeat track
"""
self.logger.warn("Filtering repeats: %s with fraction %s",
os.path.basename(rep["path"]), rep["fraction"])
exons = self.get_features("exon", chrom)
exon_tabix = exons_to_tabix_bed(exons)
overlap_it = tabix_overlap(exon_tabix, rep["tabix"], chrom,
rep["fraction"])
exon_ids = [int(iv[3]) for iv in overlap_it]
chunk = 20
for i in range(0, len(exon_ids), chunk):
self.logger.warn("Filtering %s", exon_ids[i:i + chunk])
self.session.query(Feature).\
filter(Feature.id.in_(exon_ids[i:i + chunk])).\
update({Feature.flag:True}, synchronize_session=False)
self.session.commit()
#fobj = TabixIteratorAsFile(tabixfile.fetch(chrom))
#for line in fobj:
# print line
def filter_evidence(self, chrom, source, experimental):
self.logger.debug("Filtering %s", source)
#query = self.session.query(Feature).\
# update({Feature.flag:False}, synchronize_session=False)
#self.session.commit()
# Select all features that are supported by other evidence
n = self.session.query(Feature.id).\
join(FeatureEvidence).\
join(Evidence).\
filter(Evidence.source != source).\
filter(Evidence.source not in experimental).\
filter(Feature.chrom == chrom).\
subquery("n")
# Select the total number of transcript from this source
# per feature
s = self.session.query(Feature.id, func.count('*').label('total')).\
join(FeatureEvidence).\
join(Evidence).\
filter(Evidence.source == source).\
filter(Feature.chrom == chrom).\
group_by(Feature.id).\
subquery("s")
# Select all features where support from this source
# is only 1 transcript and which is not supported by any
# other sources
a = self.session.query(Feature.id).filter(and_(
Feature.id == s.c.id,
s.c.total == 1)).\
filter(Feature.id.notin_(n)).\
subquery("a")
#ids = [i[0] for i in query]
# Flag features
self.session.query(Feature).\
filter(Feature.id.in_(a)).\
update({Feature.flag:True}, synchronize_session=False)
self.session.commit()
def get_read_statistics(self,
chrom,
fnames,
name,
span="all",
extend=(0, 0),
nreads=None):
if span not in ["all", "start", "end"]:
raise Exception("Incorrect span: {}".format(span))
tmp = NamedTemporaryFile(delete=False, suffix=".bed")
estore = {}
self.logger.debug("Writing exons to file %s", tmp.name)
exons = self.get_exons(chrom)
if len(exons) == 0:
return
for exon in exons:
start = exon.start
end = exon.end
if span == "start":
if exon.strand == "+":
end = start
elif exon.strand == "-":
start = end
if span == "end":
if exon.strand == "+":
start = end
elif exon.strand == "-":
end = start
if exon.strand == "-":
start -= extend[1]
end += extend[0]
else:
start -= extend[0]
end += extend[1]
if start < 0:
start = 0
estr = "{}:{}-{}".format(exon.chrom, start, end)
if estr in estore:
estore[estr].append(exon)
else:
estore[estr] = [exon]
tmp.write("{}\t{}\t{}\t{}\t{}\t{}\n".format(
exon.chrom, start, end, str(exon), 0, exon.strand))
tmp.flush()
if type("") == type(fnames):
fnames = [fnames]
for i, fname in enumerate(fnames):
self.logger.debug("Creating read_source for %s %s", name, fname)
read_source = get_or_create(self.session,
ReadSource,
name=name,
source=fname)
self.session.commit()
#rmrepeats = False
if fname.endswith("bam") and (not nreads or not nreads[i]):
#rmrepeats = True
self.logger.debug("Counting reads in %s", fname)
read_source.nreads = read_statistics(fname)
self.logger.debug("Getting overlap from %s", fname)
t = BamTrack(fname)
result = t.binned_stats(tmp.name,
1,
rpkm=False,
rmdup=False,
rmrepeats=False)
self.logger.debug("Reading results, save to exon stats")
insert_vals = []
for row in result:
try:
vals = row.strip().split("\t")
e = "%s:%s-%s" % (vals[0], vals[1], vals[2])
c = float(vals[3])
for exon in estore[e]:
insert_vals.append([
read_source.id, exon.id, c, span, extend[0],
extend[1]
])
except:
self.logger.info(
"binned_stat line skipped: {}".format(row))
t = [
"read_source_id", "feature_id", "count", "span", "extend_up",
"extend_down"
]
result = self.engine.execute(
FeatureReadCount.__table__.insert(),
[dict(zip(t, row)) for row in insert_vals])
tmp.close()
def get_splice_statistics(self, chrom, fnames, name):
if type("") == type(fnames):
fnames = [fnames]
for fname in fnames:
self.logger.debug("Getting splicing data from %s", fname)
read_source = get_or_create(self.session,
ReadSource,
name=name,
source=fname)
self.session.commit()
for line in open(fname):
vals = line.strip().split("\t")
if vals[0] == chrom:
start, end, c = [int(x) for x in vals[1:4]]
strand = vals[5]
splice = get_or_create(self.session,
Feature,
chrom=chrom,
start=start,
end=end,
strand=strand,
ftype="splice_junction")
self.session.commit()
count = get_or_create(self.session,
FeatureReadCount,
feature_id=splice.id,
read_source_id=read_source.id)
if not count.count:
count.count = c
else:
count.count += c
self.session.commit()
def get_junction_exons(self, junction):
left = self.session.query(Feature).filter(and_(
Feature.chrom == junction.chrom,
Feature.strand == junction.strand,
Feature.end == junction.start,
Feature.ftype == "exon"
)).\
filter(Feature.flag.op("IS NOT")(True))
right = self.session.query(Feature).filter(and_(
Feature.chrom == junction.chrom,
Feature.strand == junction.strand,
Feature.start == junction.end,
Feature.ftype == "exon"
)).\
filter(Feature.flag.op("IS NOT")(True))
exon_pairs = []
for e1 in left:
for e2 in right:
exon_pairs.append((e1, e2))
return exon_pairs
def clear_stats_cache(self):
self.cache_feature_stats = {}
self.cache_splice_stats = {}
def feature_stats(self, feature, identifier):
if "{}{}".format(feature, identifier) not in self.cache_feature_stats:
q = self.session.query(FeatureReadCount,
ReadSource).join(ReadSource)
q = q.filter(FeatureReadCount.feature_id == feature.id)
q = q.filter(ReadSource.name == identifier)
self.cache_feature_stats["{}{}".format(feature, identifier)] = sum(
[x[0].count for x in q.all()])
return self.cache_feature_stats["{}{}".format(feature, identifier)]
def splice_stats(self, exon1, exon2, identifier):
if "{}{}{}".format(self, exon1, exon2) not in self.cache_splice_stats:
q = self.session.query(Feature)
q = q.filter(Feature.ftype == "splice_junction")
q = q.filter(Feature.chrom == exon1.chrom)
q = q.filter(Feature.strand == exon1.strand)
q = q.filter(Feature.start == exon1.end)
q = q.filter(Feature.end == exon2.start)
splice = q.first()
self.cache_splice_stats["{}{}{}".format(
self, exon1, exon2)] = self.feature_stats(splice, identifier)
return self.cache_splice_stats["{}{}{}".format(self, exon1, exon2)]
def intron_splice_stats(self, intron, identifier):
if "{}{}".format(self, intron) not in self.cache_splice_stats:
q = self.session.query(Feature)
q = q.filter(Feature.ftype == "splice_junction")
q = q.filter(Feature.chrom == intron.chrom)
q = q.filter(Feature.strand == intron.strand)
q = q.filter(Feature.start == intron.start)
q = q.filter(Feature.end == intron.end)
splice = q.first()
self.cache_splice_stats["{}{}".format(
self, intron)] = self.feature_stats(splice, identifier)
return self.cache_splice_stats["{}{}".format(self, intron)]
def nreads(self, identifier):
q = self.session.query(ReadSource)
q = q.filter(ReadSource.name == identifier)
return sum([s.nreads for s in q.all()])
def get_splice_count(self, e1, e2):
counts = self.session.query(func.sum(FeatureReadCount.count)).\
join(Feature).\
filter(Feature.chrom == e1.chrom).\
filter(Feature.start == e1.end).\
filter(Feature.end == e2.start).\
filter(Feature.ftype == "splice_junction").\
group_by(Feature.id).all()
return sum([int(x[0]) for x in counts])
def fetch_feature(self, f):
""" Feature as list """
chrom, start, end, strand, ftype, seq = f
feature = self.session.query(Feature).\
filter(Feature.chrom == chrom).\
filter(Feature.start == start).\
filter(Feature.end == end).\
filter(Feature.strand == strand).\
filter(Feature.ftype == ftype)
if seq:
feature = feature.filter(Feature.seq == seq)
result = feature.first()
return result
def fetch_evidence(self, f):
""" Feature as list """
name, source = f
evidence = self.session.query(Evidence).\
filter(Evidence.name == name).\
filter(Evidence.source == source)
result = evidence.first()
return result
def get_transcript_statistics(self, exons):
stats = []
for exon in exons:
q = self.session.query(ReadSource,
func.sum(FeatureReadCount.count)).\
join(FeatureReadCount).\
join(Feature).\
filter(Feature.chrom == exon[0]).\
filter(Feature.start == exon[1]).\
filter(Feature.end == exon[2]).\
filter(Feature.strand == exon[3]).\
group_by(ReadSource.name)
stats.append(dict([(row[0].name, int(row[1])) for row in q.all()]))
return stats
