def test_code_convert(self):
"""testing code correction function"""
from mirtop.mirna.realign import make_id
from mirtop.gff.update import read_uid_10
if not make_id(read_uid_10("@#%$")) == "iso-12-B1NY4":
raise ValueError("Update ID is not working.")
if not make_id(read_uid_10("@#%$@2")) == "iso-13-B1NYDX":
raise ValueError("Update ID is not working.")
def read(fn, args):
"""Read GTF/GFF file and load into annotate, chrom counts, sample, line"""
samples = read_samples(fn)
lines = defaultdict(dict)
sep = " " if args.out_format == "gtf" else "="
corrupted_uid = 0
with open(fn) as inh:
for line in inh:
if line.startswith("#"):
continue
line = paste_columns(feature(line), sep=sep)
gff = feature(line)
cols = gff.columns
attr = gff.attributes
if attr['UID'] and not read_id(attr['UID']):
corrupted_uid += 1
continue
if 'UID' not in attr:
msg = "UID not found."
if 'Read' not in attr:
if not is_sequence(attr['Read']):
msg = msg + " Sequence not valid in Read attribute."
else:
attr['UID'] = make_id(attr['Read'])
if 'sequence' not in attr:
msg = msg + " Sequence not found in sequence attribute."
if not is_sequence(attr['sequence']):
msg = msg + " Sequence not valid in sequence attribute."
else:
attr['UID'] = make_id(attr['Read'])
if 'UID' not in attr:
logger.warning("Line is not a valid GFF3 line: %s" %
line.strip())
logger.warning(msg)
if cols['start'] not in lines[cols['chrom']]:
lines[cols['chrom']][cols['start']] = []
uid = "%s-%s-%s" % (attr['UID'],
attr['Variant'],
attr['Name'])
if args.keep_name:
uid = "%s-%s" % (uid, attr['Read'])
lines[cols['chrom']][cols['start']].append(
[uid,
cols['chrom'],
attr['Expression'].strip().split(","),
samples,
line.strip()])
logger.info("Lines skipped due to corrupted UID: %s" % corrupted_uid)
return lines
def _get_hits(fn):
hits = Counter()
with open(fn) as handle:
for line in handle:
attr = read_attributes(line, "=")
query_sequence = attr['TS'].replace("U", "T")
if query_sequence and query_sequence.find("N") > -1:
continue
idu = make_id(query_sequence)
hits[idu] += 1
return hits
def _get_hits(fn):
hits = Counter()
with open(fn) as handle:
for line in handle:
attr = read_attributes(line, "=")
query_sequence = attr['TS'].replace("U", "T")
if query_sequence and query_sequence.find("N") > -1:
continue
idu = make_id(query_sequence)
hits[idu] += 1
return hits
def to10to11(gff_line):
gff_line = gff_line.replace("_snp", "_snv")
gff_line = gff_line.replace("_add", "_add3p")
features = feature(gff_line)
if "iso_5p" in features.attributes["Variant"]:
variants = features.attributes["Variant"].split(",")
iso_5p = [v.split(":") for v in variants if v.startswith("iso_5p")]
iso_5p = -1 * int(iso_5p[0][1])
if iso_5p > 0:
iso_5p = "+%s" % iso_5p
variants = [
"iso_5p:%s" % iso_5p if v.startswith("iso_5p") else v
for v in variants
]
features.attributes["Variant"] = ",".join(variants)
features.attributes["UID"] = make_id(
read_uid_10(features.attributes["UID"]))
return features.paste_columns()
def read_file(fn, args):
"""
Read isomiR-SEA file and convert to mirtop GFF format.
Args:
*fn(str)*: file name with isomiR-SEA output information.
*database(str)*: database name.
*args(namedtuple)*: arguments from command line.
See *mirtop.libs.parse.add_subparser_gff()*.
Returns:
*reads (nested dicts)*:gff_list has the format as
defined in *mirtop.gff.body.read()*.
"""
database = args.database
gtf = args.gtf
sep = " " if args.out_format == "gtf" else "="
map_mir = mapper.read_gtf_to_mirna(gtf)
reads = defaultdict(dict)
reads_in = 0
sample = os.path.splitext(os.path.basename(fn))[0]
hits = _get_hits(fn)
logger.debug("ISOMIRSEA::SAMPLE::%s" % sample)
with open(fn) as handle:
for line in handle:
cols = line.strip().split("\t")
attr = read_attributes(line, "=")
query_name = attr['TS']
query_sequence = attr['TS'].replace("U", "T")
start = int(cols[3])
end = int(cols[4])
isomirseq_iso = attr['ISO']
if query_name not in reads and query_sequence == None:
continue
if query_sequence and query_sequence.find("N") > -1:
continue
counts = attr["TC"]
chrom = cols[0]
# logger.debug("SEQBUSTER:: cigar {cigar}".format(**locals()))
cigar = attr['CI'].replace("U", "T")
idu = make_id(query_sequence)
isoformat = cigar2variants(cigar, query_sequence, attr['ISO'])
logger.debug("\nISOMIRSEA::NEW::query: {query_sequence}\n"
" precursor {chrom}\n"
" name: {query_name}\n"
" idu: {idu}\n"
" start: {start}\n"
" cigar: {cigar}\n"
" iso: {isoformat}\n"
" variant: {isoformat}".format(**locals()))
source = "isomiR" if isoformat != "NA" else "ref_miRNA"
strand = "+"
database = cols[1]
mirName = attr['MIN'].split()[0]
preName = attr['PIN'].split()[0]
score = "."
Filter = attr['FILTER']
isotag = attr['ISO']
tchrom, tstart = _genomic2transcript(map_mir[mirName], chrom,
start)
start = start if not tstart else tstart
chrom = chrom if not tstart else tchrom
end = start + len(query_sequence)
hit = hits[idu]
fields = {
'seq_name': query_sequence,
'idseq': idu,
'name': mirName,
'parent': preName,
'variant': isoformat,
'cigar': cigar,
'counts': counts,
'filter': Filter,
'hits': hit,
'chrom': chrom,
'start': start,
'end': end,
'database': database,
'source': source,
'score': score,
'strand': strand
}
# TODO: convert to genomic if args.out_genomic
line = feature(fields).line
if args.add_extra:
extra = variant_with_nt(line, args.precursors, args.matures)
line = "%s Changes %s;" % (line, extra)
line = paste_columns(feature(line), sep=sep)
if start not in reads[chrom]:
reads[chrom][start] = []
if Filter == "Pass":
reads_in += 1
reads[chrom][start].append([idu, chrom, counts, sample, line])
logger.info("Hits: %s" % reads_in)
return reads
def read_file(fn, precursors, database, mirna_gtf):
"""
read bam file and perform realignment of hits
"""
reads = defaultdict(dict)
sample = os.path.splitext(os.path.basename(fn))[0]
map_mir = mapper.read_gtf_to_mirna(mirna_gtf)
non_mirna = 0
non_chromosome_mirna = 0
outside_mirna = 0
lines_read = 0
with open(fn) as handle:
handle.readline()
for line in handle:
lines_read += 1
cols = line.strip().split("\t")
query_name = cols[0]
query_sequence = cols[0]
if len(cols) < 12:
non_mirna += 1
continue
miRNA = cols[11]
if not miRNA:
if cols[13]:
miRNA = cols[13]
elif cols[15]:
miRNA = cols[15]
else:
continue
if query_name not in reads and query_sequence == None:
continue
if query_sequence and query_sequence.find("N") > -1:
continue
for loc in cols[5].split(";")[:1]:
if loc.find("-") < 0:
non_chromosome_mirna += 1
continue
chrom = loc.split(":")[0]
start, end = loc.split(":")[1].split("-")
preName, reference_start = genomic2transcript(map_mir[miRNA], chrom, int(start))
if not chrom:
non_chromosome_mirna += 1
continue
# reference_start = int(cols[4]) - 1
logger.debug("\nPROST::NEW::query: {query_sequence}\n"
" precursor {chrom}\n"
" name: {query_name}\n"
" start: {start}\n"
" reference_start: {reference_start}\n"
" mirna: {miRNA}".format(**locals()))
Filter = "PASS"
hit = "NA"
isoformat = _make_variant(cols[19:])
idu = make_id(query_sequence)
strand = "."
counts = cols[9]
cigar = "NA"
score = "."
source = "isomiR" if isoformat != "NA" else "ref_miRNA"
attrb = ("Read {query_sequence}; UID {idu}; Name {miRNA}; Parent {preName}; Variant {isoformat}; Cigar {cigar}; Expression {counts}; Filter {Filter}; Hits {hit};").format(**locals())
res = ("{chrom}\t{database}\t{source}\t{start}\t{end}\t{score}\t{strand}\t.\t{attrb}").format(**locals())
if start not in reads[chrom]:
reads[chrom][start] = []
reads[chrom][start].append([idu, chrom, counts, sample, res])
logger.info("Lines loaded: %s" % lines_read)
logger.info("Skipped lines because non miRNA in line: %s" % non_mirna)
logger.info("Skipped lines because non chromosome in GTF: %s" % non_chromosome_mirna)
logger.info("Skipped lines because outside precursor: %s" % outside_mirna)
logger.info("Hits: %s" % len(reads))
return reads
def test_code(self):
"""testing code correction function"""
from mirtop.mirna.realign import make_id
print make_id("AAACCCTTTGGG")
print make_id("AAACCCTTTGGGA")
print make_id("AAACCCTTTGGGAT")
def _convert(s, test, reverse=False):
code = read_id(s) if reverse else make_id(s)
if code != test:
raise ValueError("%s didn't result on %s but in %s" %
(s, test, code))
def read_file(fn, database, gtf):
"""
read bam file and perform realignment of hits
"""
map_mir = mapper.read_gtf_to_mirna(gtf)
reads = defaultdict(dict)
reads_in = 0
sample = os.path.splitext(os.path.basename(gtf))[0]
hits = _get_hits(fn)
with open(fn) as handle:
for line in handle:
cols = line.strip().split("\t")
attr = read_attributes(line, "=")
query_name = attr['TS']
query_sequence = attr['TS'].replace("U", "T")
start = int(cols[3])
end = int(cols[4])
isomirseq_iso = attr['ISO']
if query_name not in reads and query_sequence == None:
continue
if query_sequence and query_sequence.find("N") > -1:
continue
counts = attr["TC"]
chrom = cols[0]
# logger.debug("SEQBUSTER:: cigar {cigar}".format(**locals()))
cigar = attr['CI'].replace("U", "T")
idu = make_id(query_sequence)
isoformat = cigar2variants(cigar, query_sequence, attr['ISO'])
logger.debug("\nSOMIRSEA::NEW::query: {query_sequence}\n"
" precursor {chrom}\n"
" name: {query_name}\n"
" idu: {idu}\n"
" start: {start}\n"
" cigar: {cigar}\n"
" iso: {isoformat}\n"
" variant: {isoformat}".format(**locals()))
source = "isomiR" if isoformat != "NA" else "ref_miRNA"
strand = "+"
database = cols[1]
mirName = attr['MIN'].split()[0]
preName = attr['PIN'].split()[0]
score = "."
Filter = attr['FILTER']
isotag = attr['ISO']
tchrom, tstart = genomic2transcript(map_mir[mirName], chrom, start)
start = start if not tstart else tstart
chrom = chrom if not tstart else tchrom
end = start + len(query_sequence)
hit = hits[idu]
attrb = (
"Read {query_sequence}; UID {idu}; Name {mirName}; Parent {preName}; Variant {isoformat}; Isocode {isotag}; Cigar {cigar}; Expression {counts}; Filter {Filter}; Hits {hit};"
).format(**locals())
res = (
"{chrom}\t{database}\t{source}\t{start}\t{end}\t{score}\t{strand}\t.\t{attrb}"
).format(**locals())
if start not in reads[chrom]:
reads[chrom][start] = []
if Filter == "Pass":
reads_in += 1
reads[chrom][start].append([idu, chrom, counts, sample, res])
logger.info("Hits: %s" % reads_in)
return reads
def read_file(folder, args):
"""
Read sRNAbench file and convert to mirtop GFF format.
Args:
*fn(str)*: file name with sRNAbench output information.
*database(str)*: database name.
*args(namedtuple)*: arguments from command line.
See *mirtop.libs.parse.add_subparser_gff()*.
Returns:
*reads (nested dicts)*:gff_list has the format as
defined in *mirtop.gff.body.read()*.
"""
reads_anno = os.path.join(folder, "reads.annotation")
reads_iso = os.path.join(folder, "microRNAannotation.txt")
sep = " " if args.out_format == "gtf" else "="
sample = os.path.basename(folder)
database = args.database
precursors = args.precursors
matures = args.matures
n_out = 0
n_in = 0
n_ns = 0
n_notassign = 0
n_notindb = 0
reads = defaultdict(dict)
seen = set()
source_iso = _read_iso(reads_iso)
logger.info("Reads with isomiR information %s" % len(source_iso))
with open(reads_anno) as handle:
for sequence in handle:
cols = sequence.strip().split("\t")
query_name = cols[0]
query_sequence = cols[0]
if query_name not in reads and not query_sequence:
continue
if query_sequence and query_sequence.find("N") > -1:
n_ns += 1
continue
if cols[3].find("mature") == -1:
n_in += 1
continue
counts = int(cols[1])
hits = len(
set([mirna.split("#")[1] for mirna in cols[4].split("$")]))
for nhit in cols[4].split("$"):
logger.debug("SRNABENCH::line hit: %s" % nhit)
hit_info = nhit.split("#")
pos_info = hit_info[3].split(",")
start = int(pos_info[1]) - 1
end = start + len(query_sequence) # int(pos_info[2]) - 1
chrom = pos_info[0]
mirName = hit_info[1]
if chrom not in precursors or chrom not in matures:
n_notindb += 1
if mirName not in matures[chrom]:
n_notindb += 1
if (query_sequence, mirName) in seen:
continue
seen.add((query_sequence, mirName))
if (query_sequence, mirName) not in source_iso:
continue
isoformat = source_iso[(query_sequence, mirName)]
if isoformat == "mv":
n_notassign += 1
continue
source = "isomiR" if isoformat != "NA" else "ref_miRNA"
logger.debug("SRNABENCH::query: {query_sequence}\n"
" precursor {chrom}\n"
" name: {query_name}\n"
" start: {start}\n"
" external: {isoformat}\n"
" hit: {hits}".format(**locals()))
logger.debug("SRNABENCH:: start %s end %s" % (start, end))
if len(precursors[chrom]) < start + len(query_sequence):
n_out += 1
continue
Filter = "Pass"
cigar = make_cigar(query_sequence,
precursors[chrom][start:end])
preName = chrom
score = "."
strand = "+"
idu = make_id(query_sequence)
# attrb = ("Read {query_sequence}; UID {idu}; Name {mirName};"
# " Parent {preName}; Variant {isoformat};"
# " Cigar {cigar}; Expression {counts};"
# " Filter {Filter}; Hits {hits};").format(**locals())
# line = ("{chrom}\t{database}\t{source}\t{start}\t{end}\t"
# "{score}\t{strand}\t.\t{attrb}").format(**locals())
fields = {
'seq_name': query_sequence,
'idseq': idu,
'name': mirName,
'parent': preName,
'variant': isoformat,
'cigar': cigar,
'counts': counts,
'filter': Filter,
'hits': hits,
'chrom': chrom,
'start': start,
'end': end,
'database': database,
'source': source,
'score': score,
'strand': strand
}
# TODO: convert to genomic if args.out_genomic
line = feature(fields).line
if args.add_extra:
extra = variant_with_nt(line, args.precursors,
args.matures)
line = "%s Changes %s;" % (line, extra)
line = paste_columns(feature(line), sep=sep)
if start not in reads[chrom]:
reads[chrom][start] = []
if Filter == "Pass":
n_in += 1
reads[chrom][start].append(
[idu, chrom, counts, sample, line])
logger.info("Loaded %s reads with %s hits" % (len(reads), n_in))
logger.info("Reads without precursor information: %s" % n_notindb)
logger.info("Reads with MV as variant definition,"
" not supported by GFF: %s" % n_notassign)
logger.info("Hit Filtered by having > 3 changes: %s" % n_out)
return reads
def _analyze_line(line, precursors, database, sample, sep, args):
start_idx = 10
end_idx = 11
attr_idx = 15
query_name = line[3]
sequence = line[4]
if str(line).find(get_primary_transcript(guess_database(args))) < 0: # only working with mirbase
return None
logger.debug(("READ::line name:{0}").format(line))
if sequence and sequence.find("N") > -1:
return None
chrom = line[attr_idx].strip().split("Name=")[-1]
start = line[1]
end = line[2]
strand = line[5]
counts = float(line[6])
Filter = "Pass"
reads = dict()
if not start:
return None
if strand == "+":
start = int(start) - int(line[start_idx]) + 1
else:
start = int(line[end_idx]) - int(end)
iso = isomir()
iso.align = line
iso.set_pos(start, len(sequence))
logger.debug("READ::From BAM start %s end %s at chrom %s" % (iso.start, iso.end, chrom))
if len(precursors[chrom]) < start + len(sequence):
logger.debug("READ::%s start + %s sequence size are bigger than"
" size precursor %s" % (
chrom,
len(sequence),
len(precursors[chrom])))
iso.subs, iso.add, iso.cigar = filter.tune(
sequence, precursors[chrom],
start, None)
logger.debug("READ::After tune start %s end %s" % (iso.start, iso.end))
logger.debug("READ::iso add %s iso subs %s" % (iso.add, iso.subs))
idu = make_id(sequence)
reads[query_name] = hits()
reads[query_name].set_sequence(sequence)
reads[query_name].counts = counts
reads[query_name].sequence = sequence
reads[query_name].set_precursor(chrom, iso)
reads = annotate(reads, args.matures, args.precursors, quiet=True)
gff_line = body.create(reads, args.database, sample, args, quiet=True)
if start not in gff_line[chrom]:
return None
line = gff_line[chrom][start][0][4]
logger.debug("READ::line:%s" % line)
if args.add_extra:
extra = variant_with_nt(line, args.precursors,
args.matures)
line = "%s Changes %s;" % (line, extra)
line = paste_columns(feature(line), sep=sep)
return {'chrom': chrom,
'start': start,
'name': query_name,
'mirna': reads[query_name].precursors[chrom].mirna,
'line': [idu, chrom, counts, sample, line]}
def read_file(fn, args):
"""
Read isomiR-SEA file and convert to mirtop GFF format.
Args:
*fn(str)*: file name with isomiR-SEA output information.
*database(str)*: database name.
*args(namedtuple)*: arguments from command line.
See *mirtop.libs.parse.add_subparser_gff()*.
Returns:
*reads (nested dicts)*:gff_list has the format as
defined in *mirtop.gff.body.read()*.
"""
database = args.database
gtf = args.gtf
sep = " " if args.out_format == "gtf" else "="
map_mir = mapper.read_gtf_to_mirna(gtf)
reads = defaultdict(dict)
reads_in = 0
sample = os.path.splitext(os.path.basename(fn))[0]
hits = _get_hits(fn)
logger.debug("ISOMIRSEA::SAMPLE::%s" % sample)
with open(fn) as handle:
for line in handle:
cols = line.strip().split("\t")
attr = read_attributes(line, "=")
query_name = attr['TS']
query_sequence = attr['TS'].replace("U", "T")
start = int(cols[3])
end = int(cols[4])
isomirseq_iso = attr['ISO']
if query_name not in reads and query_sequence == None:
continue
if query_sequence and query_sequence.find("N") > -1:
continue
counts = attr["TC"]
chrom = cols[0]
# logger.debug("SEQBUSTER:: cigar {cigar}".format(**locals()))
cigar = attr['CI'].replace("U", "T")
idu = make_id(query_sequence)
isoformat = cigar2variants(cigar, query_sequence, attr['ISO'])
logger.debug("\nISOMIRSEA::NEW::query: {query_sequence}\n"
" precursor {chrom}\n"
" name: {query_name}\n"
" idu: {idu}\n"
" start: {start}\n"
" cigar: {cigar}\n"
" iso: {isoformat}\n"
" variant: {isoformat}".format(**locals()))
source = "isomiR" if isoformat != "NA" else "ref_miRNA"
strand = "+"
database = cols[1]
mirName = attr['MIN'].split()[0]
preName = attr['PIN'].split()[0]
score = "."
Filter = attr['FILTER']
isotag = attr['ISO']
tchrom, tstart = _genomic2transcript(map_mir[mirName],
chrom, start)
start = start if not tstart else tstart
chrom = chrom if not tstart else tchrom
end = start + len(query_sequence)
hit = hits[idu]
attrb = ("Read {query_sequence}; UID {idu}; Name {mirName};"
" Parent {preName}; Variant {isoformat};"
" Isocode {isotag}; Cigar {cigar}; Expression {counts};"
" Filter {Filter}; Hits {hit};").format(**locals())
line = ("{chrom}\t{database}\t{source}\t{start}\t{end}\t"
"{score}\t{strand}\t.\t{attrb}").format(**locals())
if args.add_extra:
extra = variant_with_nt(line, args.precursors, args.matures)
line = "%s Changes %s;" % (line, extra)
line = paste_columns(read_gff_line(line), sep=sep)
if start not in reads[chrom]:
reads[chrom][start] = []
if Filter == "Pass":
reads_in += 1
reads[chrom][start].append([idu, chrom, counts, sample, line])
logger.info("Hits: %s" % reads_in)
return reads
def _convert(s, test, reverse=False):
code = read_id(s) if reverse else make_id(s)
if code != test:
raise ValueError("%s didn't result on %s but in %s" %
(s, test, code))
def read_file(folder, args):
"""
Read sRNAbench file and convert to mirtop GFF format.
Args:
*fn(str)*: file name with sRNAbench output information.
*database(str)*: database name.
*args(namedtuple)*: arguments from command line.
See *mirtop.libs.parse.add_subparser_gff()*.
Returns:
*reads (nested dicts)*:gff_list has the format as
defined in *mirtop.gff.body.read()*.
"""
reads_anno = os.path.join(folder, "reads.annotation")
reads_iso = os.path.join(folder, "microRNAannotation.txt")
sep = " " if args.out_format == "gtf" else "="
sample = os.path.basename(folder)
database = args.database
precursors = args.precursors
matures = args.matures
n_out = 0
n_in = 0
n_ns = 0
n_notassign = 0
n_notindb = 0
reads = defaultdict(dict)
seen = set()
source_iso = _read_iso(reads_iso)
logger.info("Reads with isomiR information %s" % len(source_iso))
with open(reads_anno) as handle:
for sequence in handle:
cols = sequence.strip().split("\t")
query_name = cols[0]
query_sequence = cols[0]
if query_name not in reads and not query_sequence:
continue
if query_sequence and query_sequence.find("N") > -1:
n_ns += 1
continue
if cols[3].find("mature") == -1:
n_in += 1
continue
counts = int(cols[1])
hit = len(set([mirna.split("#")[1] for mirna in cols[4].split("$")]))
for nhit in cols[4].split("$"):
logger.debug("SRNABENCH::line hit: %s" % nhit)
hit_info = nhit.split("#")
pos_info = hit_info[3].split(",")
start = int(pos_info[1]) - 1
end = start + len(query_sequence) # int(pos_info[2]) - 1
chrom = pos_info[0]
mirName = hit_info[1]
if chrom not in precursors or chrom not in matures:
n_notindb += 1
if mirName not in matures[chrom]:
n_notindb += 1
if (query_sequence, mirName) in seen:
continue
seen.add((query_sequence, mirName))
if (query_sequence, mirName) not in source_iso:
continue
isoformat = source_iso[(query_sequence, mirName)]
if isoformat == "mv":
n_notassign += 1
continue
source = "isomiR" if isoformat != "NA" else "ref_miRNA"
logger.debug("SRNABENCH::query: {query_sequence}\n"
" precursor {chrom}\n"
" name: {query_name}\n"
" start: {start}\n"
" external: {isoformat}\n"
" hit: {hit}".format(**locals()))
logger.debug("SRNABENCH:: start %s end %s" % (start, end))
if len(precursors[chrom]) < start + len(query_sequence):
n_out += 1
continue
Filter = "Pass"
cigar = make_cigar(query_sequence,
precursors[chrom][start:end])
preName = chrom
score = "."
strand = "+"
idu = make_id(query_sequence)
attrb = ("Read {query_sequence}; UID {idu}; Name {mirName};"
" Parent {preName}; Variant {isoformat};"
" Cigar {cigar}; Expression {counts};"
" Filter {Filter}; Hits {hit};").format(**locals())
line = ("{chrom}\t{database}\t{source}\t{start}\t{end}\t"
"{score}\t{strand}\t.\t{attrb}").format(**locals())
if args.add_extra:
extra = variant_with_nt(line, args.precursors,
args.matures)
line = "%s Changes %s;" % (line, extra)
line = paste_columns(read_gff_line(line), sep=sep)
if start not in reads[chrom]:
reads[chrom][start] = []
if Filter == "Pass":
n_in += 1
reads[chrom][start].append([idu, chrom, counts,
sample, line])
logger.info("Loaded %s reads with %s hits" % (len(reads), n_in))
logger.info("Reads without precursor information: %s" % n_notindb)
logger.info("Reads with MV as variant definition,"
" not supported by GFF: %s" % n_notassign)
logger.info("Hit Filtered by having > 3 changes: %s" % n_out)
return reads