def agp(args):
"""
%prog agp <fastafile|sizesfile>
Convert the sizes file to a trivial AGP file.
"""
from jcvi.formats.agp import OO
p = OptionParser(agp.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
(sizesfile, ) = args
sizes = Sizes(sizesfile)
agpfile = sizes.filename.rsplit(".", 1)[0] + ".agp"
fw = open(agpfile, "w")
o = OO() # Without a filename
for ctg, size in sizes.iter_sizes():
o.add(ctg, ctg, size)
o.write_AGP(fw)
fw.close()
logging.debug("AGP file written to `{0}`.".format(agpfile))
return agpfile
def agp(args):
"""
%prog agp <fastafile|sizesfile>
Convert the sizes file to a trivial AGP file.
"""
from jcvi.formats.agp import OO
p = OptionParser(agp.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
sizesfile, = args
sizes = Sizes(sizesfile)
agpfile = sizes.filename.rsplit(".", 1)[0] + ".agp"
fw = open(agpfile, "w")
o = OO() # Without a filename
for ctg, size in sizes.iter_sizes():
o.add(ctg, ctg, size)
o.write_AGP(fw)
fw.close()
logging.debug("AGP file written to `{0}`.".format(agpfile))
return agpfile
def fasta(args):
"""
%prog fasta bedfile scf.fasta pseudomolecules.fasta
Use OM bed to scaffold and create pseudomolecules. bedfile can be generated
by running jcvi.assembly.opticalmap bed --blockonly
"""
from jcvi.formats.sizes import Sizes
from jcvi.formats.agp import OO, build
p = OptionParser(fasta.__doc__)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
bedfile, scffasta, pmolfasta = args
pf = bedfile.rsplit(".", 1)[0]
bed = Bed(bedfile)
selected = select_bed(bed)
oo = OO()
seen = set()
sizes = Sizes(scffasta).mapping
agpfile = pf + ".agp"
agp = open(agpfile, "w")
for b in selected:
scf = range_parse(b.accn).seqid
chr = b.seqid
cs = (chr, scf)
if cs not in seen:
oo.add(chr, scf, sizes[scf], b.strand)
seen.add(cs)
else:
logging.debug("Seen {0}, ignored.".format(cs))
oo.write_AGP(agp, gaptype="contig")
agp.close()
build([agpfile, scffasta, pmolfasta])
def fasta(args):
"""
%prog fasta bedfile scf.fasta pseudomolecules.fasta
Use OM bed to scaffold and create pseudomolecules. bedfile can be generated
by running jcvi.assembly.opticalmap bed --blockonly
"""
from jcvi.formats.sizes import Sizes
from jcvi.formats.agp import OO, build
p = OptionParser(fasta.__doc__)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
bedfile, scffasta, pmolfasta = args
pf = bedfile.rsplit(".", 1)[0]
bed = Bed(bedfile)
selected = select_bed(bed)
oo = OO()
seen = set()
sizes = Sizes(scffasta).mapping
agpfile = pf + ".agp"
agp = open(agpfile, "w")
for b in selected:
scf = range_parse(b.accn).seqid
chr = b.seqid
cs = (chr, scf)
if cs not in seen:
oo.add(chr, scf, sizes[scf], b.strand)
seen.add(cs)
else:
logging.debug("Seen {0}, ignored.".format(cs))
oo.write_AGP(agp, gaptype="contig")
agp.close()
build([agpfile, scffasta, pmolfasta])