def utr_derived_srna(args_srna, libs, texs, wig_fs, wig_rs):
inters = []
cdss, tas, tsss, pros, seq = read_data(args_srna)
out = open(args_srna.output_file, "w")
out.write("##gff-version 3\n")
out_t = open(args_srna.output_table, "w")
get_terminal(cdss, inters, seq, "start")
get_inter(cdss, inters)
get_terminal(cdss, inters, seq, "end")
inters = sorted(inters,
key=lambda k:
(k["strain"], k["start"], k["end"], k["strand"]))
args_srna = ArgsContainer().extend_utr_container(args_srna, cdss, tsss,
pros, out, out_t, texs)
for inter in inters:
for ta in tas:
if (inter["strain"] == ta.seq_id) and (inter["strand"]
== ta.strand):
class_utr(inter, ta, args_srna, wig_fs, wig_rs)
covers = get_utr_coverage(args_srna.utrs)
mediandict = set_cutoff(covers, args_srna)
print_median(args_srna.out_folder, mediandict)
detect_srna(mediandict, args_srna)
args_srna.out.close()
args_srna.out_t.close()
paras = [
args_srna.srnas, args_srna.utrs, seq, inters, tas, cdss, tas, tsss,
pros, covers
]
free_memory(paras)
def intergenic_srna(args_srna, libs, texs, wigs_f, wigs_r, tss_file):
'''get intergenic and antisense sRNA'''
inter_cutoff_coverage, inter_notex = get_intergenic_antisense_cutoff(
args_srna)
anti_cutoff_coverage, anti_notex = get_intergenic_antisense_cutoff(
args_srna)
nums, cdss, tas, pros, genes, ncs = read_data(args_srna)
tsss, num_tss = read_tss(tss_file)
detects = {"overlap": False, "uni_with_tss": False, "anti": False}
output = open(args_srna.output_file, "w")
out_table = open(args_srna.output_table, "w")
output.write("##gff-version 3\n")
for ta in tas:
detects["overlap"] = False
detects["anti"] = False
compare_ta_cds(cdss, ta, detects)
if (detects["overlap"]) and (not args_srna.in_cds):
continue
else:
if not detects["anti"]:
cutoff_coverage = inter_cutoff_coverage
notex = inter_notex
else:
cutoff_coverage = anti_cutoff_coverage
notex = anti_notex
args_srna = ArgsContainer().extend_inter_container(
args_srna, tsss, pros, nums, output, out_table, texs, detects,
cutoff_coverage, notex)
check_srna_condition(ta, args_srna, cdss, wigs_f, wigs_r)
file_name = args_srna.output_file.split(".")
file_name = file_name[0] + ".stat"
output.close()
out_table.close()
paras = [tsss, tas, pros, genes, cdss]
free_memory(paras)
def __init__(self, args):
"""Create an instance."""
self._args = args
if (len(args.__dict__) > 3):
if not os.path.exists(args.project_path):
print("Error: --project_path does not exists!")
sys.exit()
self._paths = Paths(args.project_path)
self.args_container = ArgsContainer()
self.helper = Helper()
def __init__(self, args_srna):
self.args_container = ArgsContainer()
self.helper = Helper()
self.multiparser = Multiparser()
self.gff_output = os.path.join(args_srna.out_folder, "gffs")
self.table_output = os.path.join(args_srna.out_folder, "tables")
self.stat_path = os.path.join(args_srna.out_folder, "statistics")
self.tss_path = self._check_folder_exist(args_srna.tss_folder)
self.pro_path = self._check_folder_exist(args_srna.pro_folder)
self.sorf_path = self._check_folder_exist(args_srna.sorf_file)
self.fasta_path = os.path.join(args_srna.fastas, "tmp")
self.tran_path = os.path.join(args_srna.trans, "tmp")
self.term_path = self._check_folder_exist(args_srna.terms)
self.merge_wigs = os.path.join(args_srna.out_folder, "merge_wigs")
self.prefixs = {
"merge": os.path.join(args_srna.out_folder, "tmp_merge"),
"utr": os.path.join(args_srna.out_folder, "tmp_utrsrna"),
"normal": os.path.join(args_srna.out_folder, "tmp_normal"),
"in_cds": os.path.join(args_srna.out_folder, "tmp_incds"),
"merge_table": os.path.join(args_srna.out_folder,
"tmp_merge_table"),
"utr_table": os.path.join(args_srna.out_folder,
"tmp_utrsrna_table"),
"normal_table": os.path.join(args_srna.out_folder,
"tmp_normal_table"),
"in_cds_table": os.path.join(args_srna.out_folder,
"tmp_incds_table"),
"basic": os.path.join(args_srna.out_folder, "tmp_basic"),
"energy": os.path.join(args_srna.out_folder, "tmp_energy")
}
self.tmps = {
"nr": os.path.join(args_srna.out_folder, "tmp_nr"),
"srna": os.path.join(args_srna.out_folder, "tmp_sRNA")
}
self.best_table = os.path.join(self.table_output, "best")
self.table_output = os.path.join(args_srna.out_folder, "tables")
self.stat_path = os.path.join(args_srna.out_folder, "statistics")
self.all_best = {
"all_gff": os.path.join(self.gff_output, "all_candidates"),
"best_gff": os.path.join(self.gff_output, "best"),
"all_table": os.path.join(self.table_output, "all_candidates"),
"best_table": os.path.join(self.table_output, "best")
}
def __init__(self, args):
"""Create an instance."""
self._args = args
self._paths = Paths(args.project_path)
self.args_container = ArgsContainer()
self.helper = Helper()