def read_insertions(telocate_out, sample_name, chromosomes, rp_threshold=0):
insertions = []
with open(telocate_out,"r") as raw:
for x, line in enumerate(raw):
if x > 1:
insert = mccutils.Insertion()
split_line = line.split("\t")
insert.chromosome = split_line[0]
insert.start = int(split_line[1])
te_name = split_line[3].split("/")[1]
if "old" in split_line[15]:
insert.type = "reference"
insert.end = insert.start+int(split_line[2])
insert.name = te_name+"_reference_"+sample_name+"_telocate_rp_"
else:
insert.type = "non-reference"
insert.end = insert.start
insert.name = te_name+"_non-reference_"+sample_name+"_telocate_rp_"
if split_line[12] == "parallel":
insert.strand = "+"
elif split_line[12] == "uncertain":
insert.strand = "."
else:
insert.strand = "-"
insert.telocate.read_pair_support = int(split_line[7])
if insert.telocate.read_pair_support >= rp_threshold and insert.chromosome in chromosomes:
insertions.append(insert)
return insertions
def read_insertions(bed,
te_to_family,
sample_name,
te_pos_to_family,
chromosomes,
reference=False):
inserts = []
with open(bed, "r") as b:
for line in b:
insert = mccutils.Insertion()
split_line = line.split("\t")
insert.chromosome = split_line[0]
if insert.chromosome in chromosomes:
insert.start = int(split_line[1])
insert.end = int(split_line[2])
if reference:
te_name = split_line[4].split(",")[0]
insert.family = te_to_family[te_name]
insert.strand = split_line[3]
insert.type = "reference"
insert.name = insert.family + "|reference|" + sample_name + "|tepid|nonab|"
else:
te_chrom = split_line[3]
te_start = split_line[4]
te_end = split_line[5]
insert.family = te_pos_to_family[te_chrom + "_" +
te_start + "_" + te_end]
insert.type = "non-reference"
insert.name = insert.family + "|non-reference|" + sample_name + "|tepid|"
insert.tepid.id = split_line[-1].replace("\n", "")
inserts.append(insert)
return inserts
def get_non_absent_ref_tes(te_gff, absence_bed, sample, out, log):
insertions = []
tmp_gff = out+"/tmp.ref_nonabs.gff"
command = ["bedtools", "subtract", "-A", "-a", te_gff, "-b", absence_bed]
mccutils.run_command_stdout(command, tmp_gff, log=log)
with open(tmp_gff,"r") as gff:
for line in gff:
if "#" not in line:
line = line.replace(";","\t")
split_line = line.split("\t")
insert = mccutils.Insertion()
insert.chromosome = split_line[0]
insert.start = int(split_line[3])
insert.end = int(split_line[4])
insert.temp.support = "!"
insert.name = split_line[9].split("=")[1]+"_reference_"+sample+"_temp_nonab_"
insert.strand = split_line[6]
insert.temp.classification = "!"
insert.temp.junction1Support = "!"
insert.temp.junction2Support = "!"
insert.temp.junction1 = '!'
insert.temp.junction2 = "!"
insert.temp.frequency = "!"
insert.type = "reference"
insertions.append(insert)
mccutils.remove(tmp_gff)
return insertions
def get_ref_tes(gff, taxon, chroms):
ref_inserts = []
te_family = {}
with open(taxon, "r") as t:
for line in t:
split_line = line.split("\t")
te_id = split_line[0]
family = split_line[1]
te_family[te_id] = family
with open(gff, "r") as g:
for line in g:
if "#" not in line:
split_line = line.split("\t")
insert = mccutils.Insertion()
insert.type = "reference"
insert.chromosome = split_line[0]
insert.start = int(split_line[3])
insert.end = int(split_line[4])
insert.strand = split_line[6]
insert.family = te_family[split_line[2]]
if insert.chromosome in chroms:
ref_inserts.append(insert)
return ref_inserts
def read_insertions(retroseq_vcf,
sample_name,
chromosomes,
support_threshold=0,
breakpoint_threshold=6):
insertions = []
with open(retroseq_vcf, "r") as vcf:
for line in vcf:
if "#" not in line:
insert = mccutils.Insertion()
line = line.replace(":", "\t")
line = line.replace("=", "\t")
line = line.replace(",", "\t")
split_line = line.split("\t")
insert.chromosome = split_line[0]
insert.start = int(split_line[10])
insert.end = int(split_line[11])
insert.retroseq.read_support = int(split_line[6])
insert.name = split_line[
9] + "_non-reference_" + sample_name + "_retroseq_rp_"
insert.retroseq.breakpoint_confidence = int(split_line[20])
if insert.retroseq.read_support >= support_threshold and insert.retroseq.breakpoint_confidence >= breakpoint_threshold and insert.chromosome in chromosomes:
insertions.append(insert)
return insertions
def get_insertions(gff,
sample_name,
chromosomes,
l_support_threshold=0,
r_support_threshold=0,
l_junction_threshold=0,
r_junction_threshold=0,
insert_type="ref"):
insertions = []
with open(gff, "r") as ingff:
for line in ingff:
if "#" not in line:
line = line.replace(";", "\t")
split_line = line.split("\t")
insert = mccutils.Insertion()
insert.chromosome = split_line[0]
insert.start = int(split_line[3])
insert.end = int(split_line[4])
insert.strand = split_line[6]
insert.type = insert_type
insert.name = split_line[8].split("=")[1]
te_name = ""
if insert_type == "ref":
insert.type = "reference"
insert.relocate2.right_junction = int(
split_line[11].split(":")[1])
insert.relocate2.left_junction = int(
split_line[12].split(":")[1])
insert.relocate2.right_support = int(
split_line[13].split(":")[1])
insert.relocate2.left_support = int(
split_line[14].split(":")[1])
else:
insert.type = "non-reference"
te_name = split_line[9].split("=")[1]
insert.name = te_name + "_non-reference_" + sample_name + "_relocate2_sr_"
insert.relocate2.right_junction = int(
split_line[12].split("=")[1])
insert.relocate2.left_junction = int(
split_line[13].split("=")[1])
insert.relocate2.right_support = int(
split_line[14].split("=")[1])
insert.relocate2.left_support = int(
split_line[15].split("=")[1])
if (insert.relocate2.right_junction >= r_junction_threshold and
insert.relocate2.left_junction >= l_junction_threshold
and
insert.relocate2.right_support >= r_support_threshold
and
insert.relocate2.left_support >= l_support_threshold
and insert.chromosome in chromosomes
and te_name != "repeat_name"):
insertions.append(insert)
return insertions
def read_insertion_summary(infile, sample):
insertions = []
with open(infile, "r") as inf:
for x, line in enumerate(inf):
if x > 0:
insert = mccutils.Insertion()
split_line = line.split("\t")
if len(split_line) == 14:
insert.chromosome = split_line[0]
insert.start = int(split_line[1]) - 1
insert.end = int(split_line[2])
insert.name = split_line[
3] + "_non-reference_" + split_line[
7] + "_" + sample + "_temp_"
if "antisense" in split_line[4]:
insert.strand = "-"
else:
insert.strand = "+"
insert.temp.classification = split_line[5]
insert.temp.support = float(split_line[6])
insert.temp.frequency = float(split_line[7])
insert.temp.junction1 = int(split_line[8])
insert.temp.junction1Support = int(split_line[9])
insert.temp.junction2 = int(split_line[10])
insert.temp.junction2Support = int(split_line[11])
insert.temp.fivePrimeSupport = float(split_line[12])
insert.temp.threePrimeSupport = float(
split_line[13].replace("\n", ""))
insert.type = "non-reference"
if insert.end >= insert.start and insert.end > 0 and insert.start > -1:
# if split read, use junction positions as start and end
if insert.temp.junction1Support > 0 and insert.temp.junction2Support > 0:
insert.start = insert.temp.junction1
insert.end = insert.temp.junction2
insert.name = insert.name + "sr_"
# read pair
else:
insert.name = insert.name + "rp_"
insertions.append(insert)
else:
print(
"<TEMP POST> Omitting malformed line from insertion summary results:",
line)
else:
print(
"<TEMP POST> Omitting malformed line from insertion summary results:",
line)
return insertions
def read_insertions(predictions,
ref_tes,
chroms,
sample,
both_end_support_needed=True,
support_threshold=0.1):
insertions = []
with open(predictions, "r") as tsv:
for line in tsv:
split_line = line.split("\t")
insert = mccutils.Insertion()
insert.chromosome = split_line[1]
insert.start = int(split_line[2])
insert.end = int(split_line[2])
insert.strand = split_line[3]
insert.family = split_line[4]
insert.popoolationte2.support_type = split_line[6]
insert.popoolationte2.frequency = float(split_line[8])
if (insert.popoolationte2.support_type == "FR"
or not both_end_support_needed
) and insert.popoolationte2.frequency > support_threshold:
# determine if insert is a ref insert
for x in range(0, len(ref_tes)):
if ref_tes[
x].start <= insert.start and insert.start <= ref_tes[
x].end:
insert.family = ref_tes[x].family
insert.popoolationte2.added = ref_tes[
x].popoolationte2.added
if not ref_tes[x].popoolationte2.added:
ref_tes[x].popoolationte2.added = True
insert.type = "reference"
insert.start = ref_tes[x].start
insert.end = ref_tes[x].end
insert.strand = ref_tes[x].strand
if insert.type == "reference":
insert.name = insert.family + "_reference_" + str(
insert.popoolationte2.frequency
) + "_" + sample + "_popoolationte2_rp_"
else:
insert.type = "non-reference"
insert.name = insert.family + "_non-reference_" + str(
insert.popoolationte2.frequency
) + "_" + sample + "_popoolationte2_rp_"
if not insert.popoolationte2.added:
insertions.append(insert)
return insertions
def get_insertions(gff, sample_name, chromosomes, ref_l_threshold=0, ref_r_threshold=0, nonref_l_threshold=0, nonref_r_threshold=0):
insertions = []
with open(gff, "r") as ingff:
for line in ingff:
if "#" not in line:
split_line = line.split("\t")
feats = split_line[8].split(";")
insert = mccutils.Insertion()
insert.chromosome = split_line[0]
insert.start = int(split_line[3])
insert.end = int(split_line[4])
insert.strand = split_line[6]
feat_id = ""
feat_te_name = ""
for feat in feats:
if "ID=" in feat:
feat_id = feat.split("=")[1]
elif "TE_Name=" in feat:
feat_te_name = feat.split("=")[1]
elif "Note=" in feat:
if "Shared" in feat:
insert.type = "reference"
elif "Non-reference" in feat:
insert.type = "non-reference"
else:
insert.type = "missing"
elif "left_flanking_read_count=" in feat:
insert.relocate.left_support = int(feat.split("=")[1])
elif "right_flanking_read_count=" in feat:
insert.relocate.right_support = int(feat.split("=")[1])
if insert.type == "reference":
insert.name = feat_te_name+"_reference_"+sample_name+"_relocate_sr_"
elif insert.type == "non-reference":
feat_te_name = feat_id.split(".")[0]
insert.name = feat_te_name+"_non-reference_"+sample_name+"_relocate_sr_"
if insert.type == "reference" and insert.relocate.left_support >= ref_l_threshold and insert.relocate.right_support >= ref_r_threshold and insert.chromosome in chromosomes:
insertions.append(insert)
elif insert.type == "non-reference" and insert.relocate.left_support >= nonref_l_threshold and insert.relocate.right_support >= nonref_r_threshold and insert.chromosome in chromosomes:
insertions.append(insert)
return insertions
def read_insertions(popoolationte, sample_name, chromosomes, require_both_end_support=True, percent_read_support_threshold=0.1):
insertions = []
with open(popoolationte, "r") as tsv:
for line in tsv:
insert = mccutils.Insertion()
split_line = line.split("\t")
insert.chromosome = split_line[0]
if "-" in split_line[8]:
insert.start = int(float(split_line[1]))
insert.end = int(float(split_line[15]))
elif "-" in split_line[15]:
insert.start = int(float(split_line[9]))
insert.end = int(float(split_line[1]))
else:
insert.start = int(float(split_line[9]))
insert.end = int(float(split_line[15]))
if "-" in split_line[6]:
insert.name = split_line[3]+"_non-reference_"+split_line[4]+"_"+sample_name+"_popoolationte_rp_"
else:
insert.name = split_line[3]+"_reference_"+split_line[4]+"_"+sample_name+"_popoolationte_rp_"
insert.popoolationte.support_type = split_line[2]
if "F" in insert.popoolationte.support_type:
insert.popoolationte.f_read_support = int(split_line[12])
insert.popoolationte.f_read_support_percent = float(split_line[10])
if "R" in insert.popoolationte.support_type:
insert.popoolationte.r_read_support = int(split_line[19])
insert.popoolationte.r_read_support_percent = float(split_line[17])
if not require_both_end_support:
if (insert.popoolationte.f_read_support_percent >= percent_read_support_threshold or insert.popoolationte.r_read_support_percent >= percent_read_support_threshold) and insert.chromosome in chromosomes:
insertions.append(insert)
else:
if "FR" in insert.popoolationte.support_type and (insert.popoolationte.f_read_support_percent >= percent_read_support_threshold or insert.popoolationte.r_read_support_percent >= percent_read_support_threshold) and insert.chromosome in chromosomes:
insertions.append(insert)
return insertions
def read_insertions(bed, chromosomes, sample_name, out_dir, min_read_cutoff=0):
insertions = []
with open(bed, "r") as inbed:
for line in inbed:
insert = mccutils.Insertion()
line = line.replace(";", "\t")
split_line = line.split("\t")
insert.chromosome = split_line[0]
insert.start = int(split_line[1]) + 1
insert.end = int(split_line[2])
insert.type = split_line[8].replace("\n", "")
insert.strand = split_line[4]
insert.family = split_line[5]
insert.name = insert.family + "_" + insert.type + "_" + sample_name + "_ngs_te_mapper_sr_"
insert.ngs_te_mapper.support = int(split_line[7])
if insert.ngs_te_mapper.support > min_read_cutoff and insert.chromosome in chromosomes:
insertions.append(insert)
return insertions
def get_non_absent_ref_tes(deletions, te_gff, te_to_family, sample_name):
ref_tes = []
with open(te_gff, "r") as gff:
for line in gff:
ref_te = mccutils.Insertion()
split_line = line.split("\t")
ref_te.chromosome = split_line[0]
ref_te.start = int(split_line[3])
ref_te.end = int(split_line[4])
ref_te.strand = split_line[6]
feats = split_line[8]
split_feats = feats.split(";")
te_id = ""
for f in split_feats:
if "ID=" in f:
te_id = f.split("=")[1]
ref_te.family = te_to_family[te_id]
ref_te.type = "reference"
ref_te.name = ref_te.family + "|reference|" + sample_name + "|tepid|nonab|"
ref_tes.append(ref_te)
absent = []
for deletion in deletions:
key = "_".join([
deletion.chromosome,
str(deletion.start),
str(deletion.end), deletion.strand, deletion.family
])
absent.append(key)
non_absent = []
for te in ref_tes:
key = "_".join(
[te.chromosome,
str(te.start),
str(te.end), te.strand, te.family])
if key not in absent:
non_absent.append(te)
return non_absent
def read_insertions(jitterbug_gff,
taxonomy,
chroms,
sample_name,
min_fwd_read_support=0,
min_rev_read_support=0,
min_sr_support=0,
min_zygosity=0.0):
insertions = []
te_family = {}
with open(taxonomy, "r") as tsv:
for line in tsv:
line = line.replace("\n", "")
split_line = line.split("\t")
te_family[split_line[0]] = split_line[1]
with open(jitterbug_gff, "r") as gff:
for line in gff:
line = line.replace("\n", "")
split_line = line.split("\t")
if len(split_line) == 9:
insert = mccutils.Insertion()
insert.chromosome = split_line[0]
if insert.chromosome in chroms:
insert.start = int(split_line[3])
insert.end = int(split_line[4])
insert.type = "non-reference"
feats = split_line[8]
feats = feats.replace(" ", "")
feats = feats.split(";")
supporting_families = []
sr = False
family = "NONE"
for feat in feats:
if "softclipped_pos" in feat:
pos = feat.split("=")[1]
pos = pos.replace("(", "")
pos = pos.replace(")", "")
pos = pos.split(",")
start = int(pos[0]) - 1
end = int(pos[1])
if start > -1 and end > -1:
insert.start = start
insert.end = end
sr = True
if "predicted_superfam" in feat:
te = feat.split("=")[1]
family = te_family[te]
if "supporting_fwd_reads" in feat:
insert.jitterbug.supporting_fwd_reads = int(
feat.split("=")[1])
if "supporting_rev_reads" in feat:
insert.jitterbug.supporting_rev_reads = int(
feat.split("=")[1])
if "softclipped_support" in feat:
insert.jitterbug.split_read_support = int(
feat.split("=")[1])
if "zygosity" in feat:
insert.jitterbug.zygosity = float(
feat.split("=")[1])
insert.name = family + "|non-reference|" + sample_name + "|jitterbug|"
if sr:
insert.name += "sr|"
else:
insert.name = "rp|"
if ((insert.jitterbug.supporting_fwd_reads >=
min_fwd_read_support)
and (insert.jitterbug.supporting_rev_reads >=
min_rev_read_support) and
(insert.jitterbug.split_read_support >= min_sr_support)
and (insert.jitterbug.zygosity >= min_zygosity)):
insertions.append(insert)
return insertions
