def compute_tss_type(args_srna, cdss, genes, wigs_f, wigs_r):
tsss, num_tss = read_tss(args_srna.tss_file)
if "TSS_class" not in os.listdir(args_srna.out_folder):
os.mkdir(os.path.join(args_srna.out_folder, "TSS_class"))
new_tss_file = os.path.join(args_srna.out_folder, "TSS_class",
"_".join([args_srna.prefix, "TSS.gff"]))
new_tss_fh = open(new_tss_file, "w")
num_tss = 0
for tss in tsss:
tss_type = compare_tss_cds(tss, cdss, genes)
tss.attributes = tss_type[1]
tss.attributes["ID"] = "tss" + str(num_tss)
tss.attribute_string = "".join([tss_type[0], ";ID=tss", str(num_tss)])
num_tss += 1
wigs_fm = modify_wigs_for_tss_type(wigs_f, "+")
wigs_rm = modify_wigs_for_tss_type(wigs_r, "-")
final_tsss = fix_primary_type(tsss, wigs_fm, wigs_rm)
for tss in final_tsss:
tss.attribute_string = ";".join(
["=".join(items) for items in tss.attributes.items()])
new_tss_fh.write("\t".join([
str(field) for field in [
tss.seq_id, tss.source, tss.feature, tss.start, tss.end,
tss.score, tss.strand, tss.phase, tss.attribute_string
]
]) + "\n")
new_tss_fh.close()
wigs_fm = {}
wigs_rm = {}
def compute_tss_type(args_srna, cdss, genes, wigs_f, wigs_r):
tsss, num_tss = read_tss(args_srna.tss_file)
if "TSS_class" not in os.listdir(args_srna.out_folder):
os.mkdir(os.path.join(args_srna.out_folder, "TSS_class"))
new_tss_file = os.path.join(args_srna.out_folder, "TSS_class",
"_".join([args_srna.prefix, "TSS.gff"]))
new_tss_fh = open(new_tss_file, "w")
num_tss = 0
for tss in tsss:
tss_type = compare_tss_cds(tss, cdss, genes)
tss.attributes = tss_type[1]
tss.attributes["ID"] = "tss" + str(num_tss)
tss.attribute_string = "".join([tss_type[0], ";ID=tss", str(num_tss)])
num_tss += 1
wigs_fm = modify_wigs_for_tss_type(wigs_f, "+")
wigs_rm = modify_wigs_for_tss_type(wigs_r, "-")
final_tsss = fix_primary_type(tsss, wigs_fm, wigs_rm)
for tss in final_tsss:
tss.attribute_string = ";".join(
["=".join(items) for items in tss.attributes.items()])
new_tss_fh.write("\t".join([str(field) for field in [
tss.seq_id, tss.source, tss.feature, tss.start,
tss.end, tss.score, tss.strand, tss.phase,
tss.attribute_string]]) + "\n")
new_tss_fh.close()
wigs_fm = {}
wigs_rm = {}
def upstream(tss_file, fasta_file, gff_file, out_class, args_pro, prefix):
'''get the upstream sequence of TSS'''
if fasta_file is not None:
files = {
"pri": open("tmp/primary.fa", "w"),
"sec": open("tmp/secondary.fa", "w"),
"inter": open("tmp/internal.fa", "w"),
"anti": open("tmp/antisense.fa", "w"),
"orph": open("tmp/orphan.fa", "w")
}
tsss, seq = read_data(tss_file, fasta_file)
num_tss = 0
if not args_pro.source:
out = open(out_class, "w")
out.write("##gff-version 3\n")
cdss, genes = read_gff(gff_file)
for tss in tsss:
if ("type" not in tss.attributes.keys()) and (args_pro.source):
print("Error: The TSS gff file may not generated from ANNOgesic."
"Please run with --tss_source!")
sys.exit()
if args_pro.source:
name = ">" + "_".join([str(tss.start), tss.strand, tss.seq_id])
print_fasta(seq, tss, files, name, args_pro.nt_before)
else:
tss_type = compare_tss_cds(tss, cdss, genes)
tss.attributes = tss_type[1]
tss.attributes["ID"] = tss.seq_id + "_tss" + str(num_tss)
tss.attribute_string = "".join(
[tss_type[0], ";ID=", tss.seq_id, "_tss",
str(num_tss)])
num_tss += 1
if not args_pro.source:
if args_pro.tex_wigs is not None:
libs, texs = read_libs(args_pro.input_libs, args_pro.tex_wigs)
wigs_f = read_wig(
os.path.join(args_pro.wig_path, prefix + "_forward.wig"), "+",
libs)
wigs_r = read_wig(
os.path.join(args_pro.wig_path, prefix + "_reverse.wig"), "+",
libs)
else:
wigs_f = None
wigs_r = None
sort_tsss = sorted(tsss,
key=lambda k: (k.seq_id, k.start, k.end, k.strand))
final_tsss = fix_primary_type(sort_tsss, wigs_f, wigs_r)
for tss in final_tsss:
name = ">" + "_".join([str(tss.start), tss.strand, tss.seq_id])
tss.attribute_string = ";".join(
["=".join(items) for items in tss.attributes.items()])
out.write("\t".join([
str(field) for field in [
tss.seq_id, tss.source, tss.feature, tss.start, tss.end,
tss.score, tss.strand, tss.phase, tss.attribute_string
]
]) + "\n")
if fasta_file is not None:
print_fasta(seq, tss, files, name, args_pro.nt_before)
def upstream(tss_file, fasta_file, gff_file, out_class, args_pro, prefix):
'''get the upstream sequence of TSS'''
if fasta_file is not None:
files = {"pri": open("tmp/primary.fa", "w"),
"sec": open("tmp/secondary.fa", "w"),
"inter": open("tmp/internal.fa", "w"),
"anti": open("tmp/antisense.fa", "w"),
"orph": open("tmp/orphan.fa", "w")}
tsss, seq = read_data(tss_file, fasta_file)
num_tss = 0
if not args_pro.source:
out = open(out_class, "w")
out.write("##gff-version 3\n")
cdss, genes = read_gff(gff_file)
for tss in tsss:
if ("type" not in tss.attributes.keys()) and (args_pro.source):
print("Error: The TSS gff file may not generated from ANNOgesic."
"Please run with --tss_source!")
sys.exit()
if args_pro.source:
name = ">" + "_".join([str(tss.start), tss.strand, tss.seq_id])
print_fasta(seq, tss, files, name, args_pro.nt_before)
else:
tss_type = compare_tss_cds(tss, cdss, genes)
tss.attributes = tss_type[1]
tss.attributes["ID"] = tss.seq_id + "_tss" + str(num_tss)
tss.attribute_string = "".join([
tss_type[0], ";ID=", tss.seq_id, "_tss", str(num_tss)])
num_tss += 1
if not args_pro.source:
if args_pro.tex_wigs is not None:
libs, texs = read_libs(args_pro.input_libs, args_pro.tex_wigs)
wigs_f = read_wig(os.path.join(
args_pro.wig_path, prefix + "_forward.wig"), "+", libs)
wigs_r = read_wig(os.path.join(
args_pro.wig_path, prefix + "_reverse.wig"), "+", libs)
else:
wigs_f = None
wigs_r = None
sort_tsss = sorted(tsss, key=lambda k: (k.seq_id, k.start,
k.end, k.strand))
final_tsss = fix_primary_type(sort_tsss, wigs_f, wigs_r)
for tss in final_tsss:
name = ">" + "_".join([str(tss.start), tss.strand, tss.seq_id])
tss.attribute_string = ";".join(
["=".join(items) for items in tss.attributes.items()])
out.write("\t".join([str(field) for field in [
tss.seq_id, tss.source, tss.feature, tss.start,
tss.end, tss.score, tss.strand, tss.phase,
tss.attribute_string]]) + "\n")
if fasta_file is not None:
print_fasta(seq, tss, files, name, args_pro.nt_before)
def upstream(tss_file, fasta_file, gff_file, out_class, args_pro):
files = {
"pri": open("tmp/primary.fa", "w"),
"sec": open("tmp/secondary.fa", "w"),
"inter": open("tmp/internal.fa", "w"),
"anti": open("tmp/antisense.fa", "w"),
"orph": open("tmp/orphan.fa", "w")
}
tsss, seq = read_data(tss_file, fasta_file)
num_tss = 0
if not args_pro.source:
out = open(out_class, "w")
out.write("##gff-version 3\n")
cdss, genes = read_gff(gff_file)
for tss in tsss:
if args_pro.source is True:
name = ">" + "_".join([str(tss.start), tss.strand, tss.seq_id])
print_fasta(seq, tss, files, name, args_pro.nt_before)
else:
tss_type = compare_tss_cds(tss, cdss, genes)
tss.attributes = tss_type[1]
tss.attributes["ID"] = "tss" + str(num_tss)
tss.attribute_string = "".join(
[tss_type[0], ";ID=tss", str(num_tss)])
num_tss += 1
if not args_pro.source:
wigs_f = read_wig("tmp/merge_forward.wig", "+")
wigs_r = read_wig("tmp/merge_reverse.wig", "-")
sort_tsss = sorted(tsss,
key=lambda k: (k.seq_id, k.start, k.end, k.strand))
final_tsss = fix_primary_type(sort_tsss, wigs_f, wigs_r)
for tss in final_tsss:
name = ">" + "_".join([str(tss.start), tss.strand, tss.seq_id])
tss.attribute_string = ";".join(
["=".join(items) for items in tss.attributes.items()])
out.write("\t".join([
str(field) for field in [
tss.seq_id, tss.source, tss.feature, tss.start, tss.end,
tss.score, tss.strand, tss.phase, tss.attribute_string
]
]) + "\n")
print_fasta(seq, tss, files, name, args_pro.nt_before)