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.set_annot_reformat_opts()
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():
current_chr = chr_number(chr)
if not current_chr:
continue
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, prefix=opts.prefix, \
pad0=opts.pad0, uc=opts.uc) for x in lranks) | \
set(gene_name(current_chr, x, prefix=opts.prefix, \
pad0=opts.pad0, sep="te", uc=opts.uc) 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)))
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.set_annot_reformat_opts()
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():
current_chr = chr_number(chr)
if not current_chr:
continue
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, prefix=opts.prefix, \
pad0=opts.pad0, uc=opts.uc) for x in lranks) | \
set(gene_name(current_chr, x, prefix=opts.prefix, \
pad0=opts.pad0, sep="te", uc=opts.uc) 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)))
def instantiate(args):
"""
%prog instantiate tagged.bed blacklist.ids big_gaps.bed
instantiate NEW genes tagged by renumber.
"""
p = OptionParser(instantiate.__doc__)
p.set_annot_reformat_opts()
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
taggedbed, blacklist, gapsbed = args
r = NameRegister(prefix=opts.prefix, pad0=opts.pad0, uc=opts.uc)
r.get_blacklist(blacklist)
r.get_gaps(gapsbed)
# Run through the bed, identify stretch of NEW ids to instantiate,
# identify the flanking FRAMEs, interpolate!
bed = Bed(taggedbed)
outputbed = taggedbed.rsplit(".", 1)[0] + ".new.bed"
fw = open(outputbed, "w")
tagkey = lambda x: x.rsplit("|", 1)[-1]
for chr, sbed in bed.sub_beds():
current_chr = chr_number(chr)
if not current_chr:
continue
sbed = list(sbed)
ranks = []
for i, s in enumerate(sbed):
nametag = s.extra[0]
tag = tagkey(nametag)
if tag in (NEW, FRAME):
ranks.append((i, nametag))
blocks = []
for tag, names in groupby(ranks, key=lambda x: tagkey(x[-1])):
names = list(names)
if tag == NEW:
blocks.append((tag, [sbed[x[0]] for x in names]))
else:
start, end = names[0][-1], names[-1][-1]
start, end = atg_name(start,
retval="rank"), atg_name(end,
retval="rank")
blocks.append((tag, [start, end]))
id_table = {} # old to new name conversion
for i, (tag, info) in enumerate(blocks):
if tag != NEW:
continue
start_id = 0 if i == 0 else blocks[i - 1][1][-1]
end_id = start_id + 10000 if i == len(blocks) -1 \
else blocks[i + 1][1][0]
r.allocate(info, chr, start_id, end_id, id_table)
# Output new names
for i, s in enumerate(sbed):
nametag = s.extra[0]
name, tag = nametag.split("|")
if tag == NEW:
assert name == '.'
name = id_table[s.accn]
elif tag == OVERLAP:
if name in id_table:
name = id_table[name]
s.extra[0] = "|".join((name, tag))
print >> fw, s
fw.close()
def instantiate(args):
"""
%prog instantiate tagged.bed blacklist.ids big_gaps.bed
instantiate NEW genes tagged by renumber.
"""
p = OptionParser(instantiate.__doc__)
p.set_annot_reformat_opts()
p.add_option("--extended_stride", default=False, action="store_true",
help="Toggle extended strides for gene numbering")
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
taggedbed, blacklist, gapsbed = args
r = NameRegister(prefix=opts.prefix, pad0=opts.pad0, uc=opts.uc)
r.get_blacklist(blacklist)
r.get_gaps(gapsbed)
# Run through the bed, identify stretch of NEW ids to instantiate,
# identify the flanking FRAMEs, interpolate!
bed = Bed(taggedbed)
outputbed = taggedbed.rsplit(".", 1)[0] + ".new.bed"
fw = open(outputbed, "w")
tagkey = lambda x: x.rsplit("|", 1)[-1]
for chr, sbed in bed.sub_beds():
current_chr = chr_number(chr)
if not current_chr:
continue
sbed = list(sbed)
ranks = []
for i, s in enumerate(sbed):
nametag = s.extra[0]
tag = tagkey(nametag)
if tag in (NEW, FRAME):
ranks.append((i, nametag))
blocks = []
for tag, names in groupby(ranks, key=lambda x: tagkey(x[-1])):
names = list(names)
if tag == NEW:
blocks.append((tag, [sbed[x[0]] for x in names]))
else:
start, end = names[0][-1], names[-1][-1]
start, end = atg_name(start, retval="rank"), atg_name(end, retval="rank")
blocks.append((tag, [start, end]))
id_table = {} # old to new name conversion
for i, (tag, info) in enumerate(blocks):
if tag != NEW:
continue
start_id = 0 if i == 0 else blocks[i - 1][1][-1]
end_id = start_id + 10000 if i == len(blocks) -1 \
else blocks[i + 1][1][0]
r.allocate(info, chr, start_id, end_id, id_table, extended_stride=opts.extended_stride)
# Output new names
for i, s in enumerate(sbed):
nametag = s.extra[0]
name, tag = nametag.split("|")
if tag == NEW:
assert name == '.'
name = id_table[s.accn]
elif tag == OVERLAP:
if name in id_table:
name = id_table[name]
s.extra[0] = "|".join((name, tag))
print >> fw, s
fw.close()
