def annotate_chr(chr, chrbed, g, scores, nbedline, abedline, opts, splits):
current_chr = number(chr)
for line in chrbed:
accn = line.accn
if accn not in g or (opts.atg_name and "chr" not in chr):
abedline[accn] = line
continue
gaccns = g[accn]
new = [a for a in gaccns if re.search(new_id_pat, a)]
newgrp = ";".join(sorted(new))
if accn in scores:
scores[accn] = sorted(scores[accn], key=lambda x: x[1])
scores[accn] = sorted(scores[accn], key=lambda x: float(x[3]), reverse=True)
accns = []
print >> sys.stderr, accn
for elem in scores[accn]:
print >> sys.stderr, "\t" + ", ".join([str(x)\
for x in elem[1:]])
if opts.atg_name:
achr, arank = atg_name(elem[1])
if not achr or achr != current_chr:
continue
accns.append(elem[1])
if len(new) > 1:
if newgrp not in scores: scores[newgrp] = []
scores[newgrp].append(elem)
else:
accns[0:0] = [accn]
line.accn = ";".join([str(x) for x in accns])
if len(scores[accn]) > 1: break
if len(new) > 1:
splits.add(newgrp)
else:
abedline[line.accn] = line
return abedline, splits
def atg_name(name, retval="chr,rank", trimpad0=True):
atg_name_pat = re.compile(r"""
^(?P<locus>
(?P<prefix>\D+)(?P<chr>[\d+CM])(?P<sep>\D+)(?P<rank>\d+)
)
\.?(?P<iso>\d+)?
""", re.VERBOSE)
seps = ["g", "te", "trna", "s"]
pad0s = ["chr", "rank"]
if name is not None:
m = re.match(atg_name_pat, name)
if m is not None and m.group('sep').lower() in seps:
retvals = []
for grp in retval.split(","):
val = number(m.group(grp)) \
if trimpad0 and grp in pad0s \
else m.group(grp)
retvals.append(val)
return (x for x in retvals)
else:
return (None for x in retval.split(","))
def allocate(self, info, chr, start_id, end_id, id_table):
start_bp = info[0].start
end_bp = info[-1].end
current_chr = number(chr)
needed = info
assert end_id > start_id, \
"end ({0}) > start ({1})".format(end_id, start_id)
spots = end_id - start_id - 1
available = [x for x in xrange(start_id + 1, end_id) if
(current_chr, x) not in self.black]
message = "chr{0} need {1} ids, has {2} spots ({3} available)".\
format(current_chr, len(needed), spots, len(available))
start_gene = gene_name(current_chr, start_id)
end_gene = gene_name(current_chr, end_id)
message += " between {0} - {1}\n".format(start_gene, end_gene)
assert end_bp > start_bp
b = "\t".join(str(x) for x in (chr, start_bp - 1, end_bp))
cmd = "echo '{0}' |".format(b)
cmd += " intersectBed -a {0} -b stdin".format(self.gapfile)
gaps = list(BedLine(x) for x in popen(cmd, debug=False))
ngaps = len(gaps)
gapsexpanded = []
GeneDensity = 10000. # assume 10Kb per gene
for gap in gaps:
gap_bp = int(gap.score)
gap_ids = int(round(gap_bp / GeneDensity))
gapsexpanded += [gap] * gap_ids
lines = sorted(info + gapsexpanded, key=lambda x: x.start)
message += "between bp: {0} - {1}, there are {2} gaps (total {3} ids)".\
format(start_bp, end_bp, ngaps, len(lines))
needed = lines
stride = Stride(needed, available)
conf = stride.conf
message += " stride: {0}".format(conf)
print >> sys.stderr, message
nneeded = len(needed)
if conf is None: # prefix rule - prepend version number for spills
magic = 400000 # version 4
firstdigit = 100000
step = 10 # stride for the prefixed ids
rank = start_id + magic
if rank > magic + firstdigit:
rank -= firstdigit
available = []
while len(available) != nneeded:
rank += step
if (current_chr, rank) in self.black: # avoid blacklisted ids
continue
available.append(rank)
else: # follow the best stride
available = stride.available
if start_id == 0: # follow right flank at start of chr
available = available[- nneeded:]
else: # follow left flank otherwise
available = available[:nneeded]
# Finally assign the ids
assert len(needed) == len(available)
for b, rank in zip(needed, available):
name = gene_name(current_chr, rank)
print >> sys.stderr, "\t".join((str(b), name))
id_table[b.accn] = name
self.black.add((current_chr, rank))
print >> sys.stderr
def renumber(args):
"""
%prog renumber Mt35.consolidated.bed > tagged.bed
Renumber genes for annotation updates.
"""
from jcvi.algorithms.lis import longest_increasing_subsequence
from jcvi.utils.grouper import Grouper
p = OptionParser(renumber.__doc__)
p.add_option("--pad0", default=6, type="int",
help="Pad gene identifiers with 0 [default: %default]")
p.add_option("--prefix", default="Medtr",
help="Genome prefix [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
bedfile, = args
pf = bedfile.rsplit(".", 1)[0]
abedfile = pf + ".a.bed"
bbedfile = pf + ".b.bed"
if need_update(bedfile, (abedfile, bbedfile)):
prepare(bedfile)
mbed = Bed(bbedfile)
g = Grouper()
for s in mbed:
accn = s.accn
g.join(*accn.split(";"))
bed = Bed(abedfile)
for chr, sbed in bed.sub_beds():
if "chr" not in chr:
continue
current_chr = number(chr)
ranks = []
gg = set()
for s in sbed:
accn = s.accn
achr, arank = atg_name(accn)
if achr != current_chr:
continue
ranks.append(arank)
gg.add(accn)
lranks = longest_increasing_subsequence(ranks)
print >> sys.stderr, current_chr, len(sbed), "==>", len(ranks), \
"==>", len(lranks)
granks = set(gene_name(current_chr, x) for x in lranks) | \
set(gene_name(current_chr, x, sep="te") for x in lranks)
tagstore = {}
for s in sbed:
achr, arank = atg_name(s.accn)
accn = s.accn
if accn in granks:
tag = (accn, FRAME)
elif accn in gg:
tag = (accn, RETAIN)
else:
tag = (".", NEW)
tagstore[accn] = tag
# Find cases where genes overlap
for s in sbed:
accn = s.accn
gaccn = g[accn]
tags = [((tagstore[x][-1] if x in tagstore else NEW), x) for x in gaccn]
group = [(PRIORITY.index(tag), x) for tag, x in tags]
best = min(group)[-1]
if accn != best:
tag = (best, OVERLAP)
else:
tag = tagstore[accn]
print "\t".join((str(s), "|".join(tag)))
