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from intervaltree import IntervalTree
from ragtag_utilities.utilities import log, get_ragtag_version
from ragtag_utilities.AGPFile import AGPFile
def sub_update(gff_file, agp_file):
# Make a dictionary associating each original sequence with an interval tree of component sequences
trans = defaultdict(IntervalTree)
agp = AGPFile(agp_file, mode="r")
for agp_line in agp.iterate_lines():
# Check that the agp file looks correct for this task
if agp_line.orientation == "-":
raise ValueError("The placement BED file is not formatted correctly. No sequences should be reverse complemented for misassembly correction.")
if not agp_line.comp_type == "W":
raise ValueError("The placement BED file is not formatted correctly. All lines should be WGS contig (W).")
if agp_line.is_gap:
raise ValueError("There should be no gaps in the correction AGP file.")
start, end = agp_line.obj_beg - 1, agp_line.obj_end
trans[agp_line.obj][start:end] = agp_line.comp
# Iterate through the gff intervals and update them according to trans
with open(gff_file, "r") as f:
for line in f:
line = line.rstrip()
if line.startswith("#"):
print(line) # Print this comment line
else:
fields = line.split("\t")
h, s, e = fields[0], int(fields[3]), int(fields[4])
s -= 1 # Keep everything zero-indexed
if h not in trans:
raise ValueError("Inconsistent input files.")
ovlps = trans[h][s:e]
if len(ovlps) > 1:
raise ValueError(
"%s:%d-%d in the gff file overlaps two sub sequences in the placement file. Make sure to run 'ragtag.py correct' with '--gff'" % (h, s, e)
)
if len(ovlps) < 1:
raise ValueError("The placement BED file is not formatted correctly.")
# Get the data from the overlapping interval and print the new line
o = list(ovlps)[0]
new_s = s - o.begin
new_e = e - o.begin
fields[0] = o.data
fields[3] = str(new_s + 1) # back to one-based indexing for gff format
fields[4] = str(new_e)
print("\t".join(fields))
def sup_update(gff_file, agp_file):
# Make a dictionary associating each original sequence with the destination sequence
trans = {}
strands = {}
seq_lens = {}
agp = AGPFile(agp_file, mode="r")
for agp_line in agp.iterate_lines():
if not agp_line.is_gap:
start, end = agp_line.obj_beg - 1, agp_line.obj_end
trans[agp_line.comp] = (start, end, agp_line.obj)
strands[agp_line.comp] = agp_line.orientation
seq_lens[agp_line.comp] = end - start
# Iterate through the gff intervals and update them according to trans
with open(gff_file, "r") as f:
for line in f:
line = line.rstrip()
if line.startswith("#"):
print(line) # Print this comment line
else:
fields = line.split("\t")
h, s, e, st = fields[0], int(fields[3]), int(fields[4]), fields[6]
s -= 1 # Keep everything zero-indexed
if h not in trans:
print()
print(line)
raise ValueError("Inconsistent input files.")
# Check if the original sequence has been reverse complemented
if strands[h] == "-":
l = seq_lens[h]
s, e = l-e, l-s
if st == "+":
st = "-"
else:
st = "+"
new_s = trans[h][0] + s
new_e = trans[h][0] + e
fields[0] = trans[h][2]
fields[3] = str(new_s + 1) # back to one-based indexing for gff format
fields[4] = str(new_e)
fields[6] = st
print("\t".join(fields))