def agp(args):
"""
%prog agp main_results/ contigs.fasta
Generate AGP file based on LACHESIS output.
"""
p = OptionParser(agp.__doc__)
p.set_outfile()
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
odir, contigsfasta = args
fwagp = must_open(opts.outfile, 'w')
orderingfiles = natsorted(iglob(odir, "*.ordering"))
sizes = Sizes(contigsfasta).mapping
contigs = set(sizes.keys())
anchored = set()
for ofile in orderingfiles:
co = ContigOrdering(ofile)
anchored |= set([x.contig_name for x in co])
obj = op.basename(ofile).split('.')[0]
co.write_agp(obj, sizes, fwagp)
singletons = contigs - anchored
logging.debug('Anchored: {}, Singletons: {}'.
format(len(anchored), len(singletons)))
for s in natsorted(singletons):
order_to_agp(s, [(s, "?")], sizes, fwagp)
def agp(args):
"""
%prog agp main_results/ contigs.fasta
Generate AGP file based on LACHESIS output.
"""
p = OptionParser(agp.__doc__)
p.set_outfile()
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
odir, contigsfasta = args
fwagp = must_open(opts.outfile, 'w')
orderingfiles = natsorted(iglob(odir, "*.ordering"))
sizes = Sizes(contigsfasta).mapping
contigs = set(sizes.keys())
anchored = set()
for ofile in orderingfiles:
co = ContigOrdering(ofile)
anchored |= set([x.contig_name for x in co])
obj = op.basename(ofile).split('.')[0]
co.write_agp(obj, sizes, fwagp)
singletons = contigs - anchored
logging.debug('Anchored: {}, Singletons: {}'.\
format(len(anchored), len(singletons)))
for s in natsorted(singletons):
order_to_agp(s, [(s, "?")], sizes, fwagp)
def write_unplaced_agp(agpfile, scaffolds, unplaced_agp):
agp = AGP(agpfile)
scaffolds_seen = set(x.component_id for x in agp)
sizes = Sizes(scaffolds).mapping
fwagp = must_open(unplaced_agp, "w")
for s in sorted(sizes.keys()):
if s in scaffolds_seen:
continue
order_to_agp(s, [(s, "?")], sizes, fwagp)
logging.debug("Write unplaced AGP to `{0}`.".format(unplaced_agp))
def write_unplaced_agp(agpfile, scaffolds, unplaced_agp):
agp = AGP(agpfile)
scaffolds_seen = set(x.component_id for x in agp)
sizes = Sizes(scaffolds).mapping
fwagp = must_open(unplaced_agp, "w")
for s in sorted(sizes.keys()):
if s in scaffolds_seen:
continue
order_to_agp(s, [(s, "?")], sizes, fwagp)
logging.debug("Write unplaced AGP to `{0}`.".format(unplaced_agp))
def main(args):
"""
%prog deltafile
Plot one query. Extract the references that have major matches to this
query. Control "major" by option --refcov.
"""
p = OptionParser(main.__doc__)
p.add_option("--refids", help="Use subset of contigs in the ref")
p.add_option("--refcov", default=.01, type="float",
help="Minimum reference coverage [default: %default]")
p.add_option("--all", default=False, action="store_true",
help="Plot one pdf file per ref in refidsfile [default: %default]")
p.add_option("--color", default="similarity",
choices=("similarity", "direction", "none"),
help="Color the dots based on")
p.add_option("--nolayout", default=False, action="store_true",
help="Do not rearrange contigs")
p.set_align(pctid=0, hitlen=0)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
deltafile, = args
reffasta, queryfasta = open(deltafile).readline().split()
color = opts.color
layout = not opts.nolayout
prefix = op.basename(deltafile).split(".")[0]
qsizes = Sizes(queryfasta).mapping
rsizes = Sizes(reffasta).mapping
refs = SetFile(opts.refids) if opts.refids else set(rsizes.keys())
refcov = opts.refcov
pctid = opts.pctid
hitlen = opts.hitlen
deltafile = filter([deltafile, "--pctid={0}".format(pctid),
"--hitlen={0}".format(hitlen)])
if opts.all:
for r in refs:
pdffile = plot_some_queries([r], qsizes, rsizes, deltafile, refcov,
prefix=prefix, color=color,
layout=layout)
if pdffile:
sh("mv {0} {1}.pdf".format(pdffile, r))
else:
plot_some_queries(refs, qsizes, rsizes,
deltafile, refcov,
prefix=prefix, color=color, layout=layout)
def main(args):
"""
%prog deltafile
Plot one query. Extract the references that have major matches to this
query. Control "major" by option --refcov.
"""
p = OptionParser(main.__doc__)
p.add_option("--refids", help="Use subset of contigs in the ref")
p.add_option("--refcov", default=.01, type="float",
help="Minimum reference coverage [default: %default]")
p.add_option("--all", default=False, action="store_true",
help="Plot one pdf file per ref in refidsfile [default: %default]")
p.add_option("--color", default="similarity",
choices=("similarity", "direction", "none"),
help="Color the dots based on")
p.add_option("--nolayout", default=False, action="store_true",
help="Do not rearrange contigs")
p.set_align(pctid=0, hitlen=0)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
deltafile, = args
reffasta, queryfasta = open(deltafile).readline().split()
color = opts.color
layout = not opts.nolayout
prefix = op.basename(deltafile).split(".")[0]
qsizes = Sizes(queryfasta).mapping
rsizes = Sizes(reffasta).mapping
refs = SetFile(opts.refids) if opts.refids else set(rsizes.keys())
refcov = opts.refcov
pctid = opts.pctid
hitlen = opts.hitlen
deltafile = filter([deltafile, "--pctid={0}".format(pctid),
"--hitlen={0}".format(hitlen)])
if opts.all:
for r in refs:
pdffile = plot_some_queries([r], qsizes, rsizes, deltafile, refcov,
prefix=prefix, color=color,
layout=layout)
if pdffile:
sh("mv {0} {1}.pdf".format(pdffile, r))
else:
plot_some_queries(refs, qsizes, rsizes,
deltafile, refcov,
prefix=prefix, color=color, layout=layout)
def covfilter(args):
"""
%prog covfilter blastfile fastafile
Fastafile is used to get the sizes of the queries. Two filters can be
applied, the id% and cov%.
"""
p = OptionParser(covfilter.__doc__)
p.add_option("--pctid", dest="pctid", default=90, type="int",
help="Percentage identity cutoff [default: %default]")
p.add_option("--pctcov", dest="pctcov", default=50, type="int",
help="Percentage identity cutoff [default: %default]")
p.add_option("--ids", dest="ids", default=None,
help="Print out the ids that satisfy [default: %default]")
p.add_option("--list", dest="list", default=False, action="store_true",
help="List the id% and cov% per gene [default: %default]")
set_outfile(p, outfile=None)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
from jcvi.algorithms.supermap import supermap
blastfile, fastafile = args
sizes = Sizes(fastafile).mapping
querysupermap = blastfile + ".query.supermap"
if not op.exists(querysupermap):
supermap(blastfile, filter="query")
blastfile = querysupermap
assert op.exists(blastfile)
covered = 0
mismatches = 0
gaps = 0
alignlen = 0
queries = set()
valid = set()
blast = BlastSlow(querysupermap)
for query, blines in blast.iter_hits():
blines = list(blines)
queries.add(query)
# per gene report
this_covered = 0
this_alignlen = 0
this_mismatches = 0
this_gaps = 0
for b in blines:
this_covered += abs(b.qstart - b.qstop + 1)
this_alignlen += b.hitlen
this_mismatches += b.nmismatch
this_gaps += b.ngaps
this_identity = 100. - (this_mismatches + this_gaps) * 100. / this_alignlen
this_coverage = this_covered * 100. / sizes[query]
if opts.list:
print "{0}\t{1:.1f}\t{2:.1f}".format(query, this_identity, this_coverage)
if this_identity >= opts.pctid and this_coverage >= opts.pctcov:
valid.add(query)
covered += this_covered
mismatches += this_mismatches
gaps += this_gaps
alignlen += this_alignlen
mapped_count = len(queries)
valid_count = len(valid)
cutoff_message = "(id={0.pctid}% cov={0.pctcov}%)".format(opts)
print >> sys.stderr, "Identity: {0} mismatches, {1} gaps, {2} alignlen".\
format(mismatches, gaps, alignlen)
total = len(sizes.keys())
print >> sys.stderr, "Total mapped: {0} ({1:.1f}% of {2})".\
format(mapped_count, mapped_count * 100. / total, total)
print >> sys.stderr, "Total valid {0}: {1} ({2:.1f}% of {3})".\
format(cutoff_message, valid_count, valid_count * 100. / total, total)
print >> sys.stderr, "Average id = {0:.2f}%".\
format(100 - (mismatches + gaps) * 100. / alignlen)
queries_combined = sum(sizes[x] for x in queries)
print >> sys.stderr, "Coverage: {0} covered, {1} total".\
format(covered, queries_combined)
print >> sys.stderr, "Average coverage = {0:.2f}%".\
format(covered * 100. / queries_combined)
if opts.ids:
filename = opts.ids
fw = must_open(filename, "w")
for id in valid:
print >> fw, id
logging.debug("Queries beyond cutoffs {0} written to `{1}`.".\
format(cutoff_message, filename))
outfile = opts.outfile
if not outfile:
return
fp = open(blastfile)
fw = must_open(outfile, "w")
blast = Blast(blastfile)
for b in blast.iter_line():
if b.query in valid:
print >> fw, b
def draw_chromosomes(
root,
bedfile,
sizes,
iopts,
mergedist,
winsize,
imagemap,
mappingfile=None,
gauge=False,
legend=True,
empty=False,
title=None,
):
bed = Bed(bedfile)
prefix = bedfile.rsplit(".", 1)[0]
if imagemap:
imgmapfile = prefix + ".map"
mapfh = open(imgmapfile, "w")
print('<map id="' + prefix + '">', file=mapfh)
if mappingfile:
mappings = DictFile(mappingfile, delimiter="\t")
classes = sorted(set(mappings.values()))
preset_colors = (DictFile(
mappingfile, keypos=1, valuepos=2, delimiter="\t")
if DictFile.num_columns(mappingfile) >= 3 else {})
else:
classes = sorted(set(x.accn for x in bed))
mappings = dict((x, x) for x in classes)
preset_colors = {}
logging.debug("A total of {} classes found: {}".format(
len(classes), ",".join(classes)))
# Assign colors to classes
ncolors = max(3, min(len(classes), 12))
palette = set1_n if ncolors <= 8 else set3_n
colorset = palette(number=ncolors)
colorset = sample_N(colorset, len(classes))
class_colors = dict(zip(classes, colorset))
class_colors.update(preset_colors)
logging.debug("Assigned colors: {}".format(class_colors))
chr_lens = {}
centromeres = {}
if sizes:
chr_lens = Sizes(sizes).sizes_mapping
else:
for b, blines in groupby(bed, key=(lambda x: x.seqid)):
blines = list(blines)
maxlen = max(x.end for x in blines)
chr_lens[b] = maxlen
for b in bed:
accn = b.accn
if accn == "centromere":
centromeres[b.seqid] = b.start
if accn in mappings:
b.accn = mappings[accn]
else:
b.accn = "-"
chr_number = len(chr_lens)
if centromeres:
assert chr_number == len(
centromeres), "chr_number = {}, centromeres = {}".format(
chr_number, centromeres)
r = 0.7 # width and height of the whole chromosome set
xstart, ystart = 0.15, 0.85
xinterval = r / chr_number
xwidth = xinterval * 0.5 # chromosome width
max_chr_len = max(chr_lens.values())
ratio = r / max_chr_len # canvas / base
# first the chromosomes
for a, (chr, clen) in enumerate(sorted(chr_lens.items())):
xx = xstart + a * xinterval + 0.5 * xwidth
root.text(xx, ystart + 0.01, str(get_number(chr)), ha="center")
if centromeres:
yy = ystart - centromeres[chr] * ratio
ChromosomeWithCentromere(root,
xx,
ystart,
yy,
ystart - clen * ratio,
width=xwidth)
else:
Chromosome(root, xx, ystart, ystart - clen * ratio, width=xwidth)
chr_idxs = dict((a, i) for i, a in enumerate(sorted(chr_lens.keys())))
alpha = 1
# color the regions
for chr in sorted(chr_lens.keys()):
segment_size, excess = 0, 0
bac_list = []
prev_end, prev_klass = 0, None
for b in bed.sub_bed(chr):
clen = chr_lens[chr]
idx = chr_idxs[chr]
klass = b.accn
if klass == "centromere":
continue
start = b.start
end = b.end
if start < prev_end + mergedist and klass == prev_klass:
start = prev_end
xx = xstart + idx * xinterval
yystart = ystart - end * ratio
yyend = ystart - start * ratio
root.add_patch(
Rectangle(
(xx, yystart),
xwidth,
yyend - yystart,
fc=class_colors.get(klass, "lightslategray"),
lw=0,
alpha=alpha,
))
prev_end, prev_klass = b.end, klass
if imagemap:
"""
`segment` : size of current BAC being investigated + `excess`
`excess` : left-over bases from the previous BAC, as a result of
iterating over `winsize` regions of `segment`
"""
if excess == 0:
segment_start = start
segment = (end - start + 1) + excess
while True:
if segment < winsize:
bac_list.append(b.accn)
excess = segment
break
segment_end = segment_start + winsize - 1
tlx, tly, brx, bry = (
xx,
(1 - ystart) + segment_start * ratio,
xx + xwidth,
(1 - ystart) + segment_end * ratio,
)
print(
"\t" + write_ImageMapLine(
tlx,
tly,
brx,
bry,
iopts.w,
iopts.h,
iopts.dpi,
chr + ":" + ",".join(bac_list),
segment_start,
segment_end,
),
file=mapfh,
)
segment_start += winsize
segment -= winsize
bac_list = []
if imagemap and excess > 0:
bac_list.append(b.accn)
segment_end = end
tlx, tly, brx, bry = (
xx,
(1 - ystart) + segment_start * ratio,
xx + xwidth,
(1 - ystart) + segment_end * ratio,
)
print(
"\t" + write_ImageMapLine(
tlx,
tly,
brx,
bry,
iopts.w,
iopts.h,
iopts.dpi,
chr + ":" + ",".join(bac_list),
segment_start,
segment_end,
),
file=mapfh,
)
if imagemap:
print("</map>", file=mapfh)
mapfh.close()
logging.debug("Image map written to `{0}`".format(mapfh.name))
if gauge:
xstart, ystart = 0.9, 0.85
Gauge(root, xstart, ystart - r, ystart, max_chr_len)
if "centromere" in class_colors:
del class_colors["centromere"]
# class legends, four in a row
if legend:
xstart = 0.1
xinterval = 0.8 / len(class_colors)
xwidth = 0.04
yy = 0.08
for klass, cc in sorted(class_colors.items()):
if klass == "-":
continue
root.add_patch(
Rectangle((xstart, yy),
xwidth,
xwidth,
fc=cc,
lw=0,
alpha=alpha))
root.text(xstart + xwidth + 0.01, yy, latex(klass), fontsize=10)
xstart += xinterval
if empty:
root.add_patch(
Rectangle((xstart, yy), xwidth, xwidth, fill=False, lw=1))
root.text(xstart + xwidth + 0.01, yy, empty, fontsize=10)
if title:
root.text(0.5, 0.95, markup(title), ha="center", va="center")
def scaffold(args):
"""
%prog scaffold ctgfasta linksfile
Use the linksfile to build scaffolds. The linksfile can be
generated by calling assembly.bundle.link() or assembly.bundle.bundle().
Use --prefix to place the sequences with same prefix together. The final
product is an AGP file.
"""
from jcvi.algorithms.graph import nx
from jcvi.formats.agp import order_to_agp
p = OptionParser(scaffold.__doc__)
p.add_option("--prefix", default=False, action="store_true",
help="Keep IDs with same prefix together [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
ctgfasta, linksfile = args
sizes = Sizes(ctgfasta).mapping
logfile = "scaffold.log"
fwlog = open(logfile, "w")
pf = ctgfasta.rsplit(".", 1)[0]
agpfile = pf + ".agp"
fwagp = open(agpfile, "w")
clinks = []
g = nx.MultiGraph() # use this to get connected components
fp = open(linksfile)
for row in fp:
c = LinkLine(row)
distance = max(c.distance, 50)
g.add_edge(c.aseqid, c.bseqid,
orientation=c.orientation, distance=distance)
def get_bname(sname, prefix=False):
return sname.rsplit("_", 1)[0] if prefix else "chr0"
scaffoldbuckets = defaultdict(list)
seqnames = sorted(sizes.keys())
for h in nx.connected_component_subgraphs(g):
partialorder = solve_component(h, sizes, fwlog)
name = partialorder[0][0]
bname = get_bname(name, prefix=opts.prefix)
scaffoldbuckets[bname].append(partialorder)
ctgbuckets = defaultdict(set)
for name in seqnames:
bname = get_bname(name, prefix=opts.prefix)
ctgbuckets[bname].add(name)
# Now the buckets contain a mixture of singletons and partially resolved
# scaffolds. Print the scaffolds first then remaining singletons.
scafname = "{0}.scf_{1:04d}"
for bname, ctgs in sorted(ctgbuckets.items()):
scaffolds = scaffoldbuckets[bname]
scaffolded = set()
ctgorder = []
for scafID, scaf in enumerate(scaffolds):
ctgorder = []
for node, start, end, orientation in scaf:
ctgorder.append((node, orientation))
scaffolded.add(node)
scaf = scafname.format(bname, scafID)
order_to_agp(scaf, ctgorder, sizes, fwagp)
singletons = sorted(ctgbuckets[bname] - scaffolded)
nscaffolds = len(scaffolds)
nsingletons = len(singletons)
msg = "{0}: Scaffolds={1} Singletons={2}".\
format(bname, nscaffolds, nsingletons)
print >> sys.stderr, msg
for singleton in singletons:
ctgorder = [(singleton, "+")]
order_to_agp(singleton, ctgorder, sizes, fwagp)
fwagp.close()
logging.debug("AGP file written to `{0}`.".format(agpfile))
def scaffold(args):
"""
%prog scaffold ctgfasta agpfile
Build scaffolds based on ordering in the AGP file.
"""
from jcvi.formats.agp import AGP, bed, order_to_agp, build
from jcvi.formats.bed import Bed
p = OptionParser(scaffold.__doc__)
p.add_option("--prefix", default=False, action="store_true",
help="Keep IDs with same prefix together [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
ctgfasta, agpfile = args
sizes = Sizes(ctgfasta).mapping
pf = ctgfasta.rsplit(".", 1)[0]
phasefile = pf + ".phases"
fwphase = open(phasefile, "w")
newagpfile = pf + ".new.agp"
fwagp = open(newagpfile, "w")
scaffoldbuckets = defaultdict(list)
seqnames = sorted(sizes.keys())
bedfile = bed([agpfile, "--nogaps", "--outfile=tmp"])
bb = Bed(bedfile)
for s, partialorder in bb.sub_beds():
name = partialorder[0].accn
bname = name.rsplit("_", 1)[0] if opts.prefix else s
scaffoldbuckets[bname].append([(b.accn, b.strand) for b in partialorder])
# Now the buckets contain a mixture of singletons and partially resolved
# scaffolds. Print the scaffolds first then remaining singletons.
for bname, scaffolds in sorted(scaffoldbuckets.items()):
ctgorder = []
singletons = set()
for scaf in sorted(scaffolds):
for node, orientation in scaf:
ctgorder.append((node, orientation))
if len(scaf) == 1:
singletons.add(node)
nscaffolds = len(scaffolds)
nsingletons = len(singletons)
if nsingletons == 1 and nscaffolds == 0:
phase = 3
elif nsingletons == 0 and nscaffolds == 1:
phase = 2
else:
phase = 1
msg = "{0}: Scaffolds={1} Singletons={2} Phase={3}".\
format(bname, nscaffolds, nsingletons, phase)
print >> sys.stderr, msg
print >> fwphase, "\t".join((bname, str(phase)))
order_to_agp(bname, ctgorder, sizes, fwagp)
fwagp.close()
os.remove(bedfile)
fastafile = "final.fasta"
build([newagpfile, ctgfasta, fastafile])
tidy([fastafile])
def covfilter(args):
"""
%prog covfilter blastfile fastafile
Fastafile is used to get the sizes of the queries. Two filters can be
applied, the id% and cov%.
"""
p = OptionParser(covfilter.__doc__)
p.add_option("--pctid",
dest="pctid",
default=90,
type="int",
help="Percentage identity cutoff [default: %default]")
p.add_option("--pctcov",
dest="pctcov",
default=50,
type="int",
help="Percentage identity cutoff [default: %default]")
p.add_option("--ids",
dest="ids",
default=None,
help="Print out the ids that satisfy [default: %default]")
p.add_option("--list",
dest="list",
default=False,
action="store_true",
help="List the id% and cov% per gene [default: %default]")
set_outfile(p, outfile=None)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
from jcvi.algorithms.supermap import supermap
blastfile, fastafile = args
sizes = Sizes(fastafile).mapping
querysupermap = blastfile + ".query.supermap"
if not op.exists(querysupermap):
supermap(blastfile, filter="query")
blastfile = querysupermap
assert op.exists(blastfile)
covered = 0
mismatches = 0
gaps = 0
alignlen = 0
queries = set()
valid = set()
blast = BlastSlow(querysupermap)
for query, blines in blast.iter_hits():
blines = list(blines)
queries.add(query)
# per gene report
this_covered = 0
this_alignlen = 0
this_mismatches = 0
this_gaps = 0
for b in blines:
this_covered += abs(b.qstart - b.qstop + 1)
this_alignlen += b.hitlen
this_mismatches += b.nmismatch
this_gaps += b.ngaps
this_identity = 100. - (this_mismatches +
this_gaps) * 100. / this_alignlen
this_coverage = this_covered * 100. / sizes[query]
if opts.list:
print "{0}\t{1:.1f}\t{2:.1f}".format(query, this_identity,
this_coverage)
if this_identity >= opts.pctid and this_coverage >= opts.pctcov:
valid.add(query)
covered += this_covered
mismatches += this_mismatches
gaps += this_gaps
alignlen += this_alignlen
mapped_count = len(queries)
valid_count = len(valid)
cutoff_message = "(id={0.pctid}% cov={0.pctcov}%)".format(opts)
print >> sys.stderr, "Identity: {0} mismatches, {1} gaps, {2} alignlen".\
format(mismatches, gaps, alignlen)
total = len(sizes.keys())
print >> sys.stderr, "Total mapped: {0} ({1:.1f}% of {2})".\
format(mapped_count, mapped_count * 100. / total, total)
print >> sys.stderr, "Total valid {0}: {1} ({2:.1f}% of {3})".\
format(cutoff_message, valid_count, valid_count * 100. / total, total)
print >> sys.stderr, "Average id = {0:.2f}%".\
format(100 - (mismatches + gaps) * 100. / alignlen)
queries_combined = sum(sizes[x] for x in queries)
print >> sys.stderr, "Coverage: {0} covered, {1} total".\
format(covered, queries_combined)
print >> sys.stderr, "Average coverage = {0:.2f}%".\
format(covered * 100. / queries_combined)
if opts.ids:
filename = opts.ids
fw = must_open(filename, "w")
for id in valid:
print >> fw, id
logging.debug("Queries beyond cutoffs {0} written to `{1}`.".\
format(cutoff_message, filename))
outfile = opts.outfile
if not outfile:
return
fp = open(blastfile)
fw = must_open(outfile, "w")
blast = Blast(blastfile)
for b in blast.iter_line():
if b.query in valid:
print >> fw, b
def scaffold(args):
"""
%prog scaffold ctgfasta linksfile
Use the linksfile to build scaffolds. The linksfile can be
generated by calling assembly.bundle.link() or assembly.bundle.bundle().
Use --prefix to place the sequences with same prefix together. The final
product is an AGP file.
"""
from jcvi.algorithms.graph import nx
from jcvi.formats.agp import order_to_agp
p = OptionParser(scaffold.__doc__)
p.add_option("--prefix",
default=False,
action="store_true",
help="Keep IDs with same prefix together [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
ctgfasta, linksfile = args
sizes = Sizes(ctgfasta).mapping
logfile = "scaffold.log"
fwlog = open(logfile, "w")
pf = ctgfasta.rsplit(".", 1)[0]
agpfile = pf + ".agp"
fwagp = open(agpfile, "w")
clinks = []
g = nx.MultiGraph() # use this to get connected components
fp = open(linksfile)
for row in fp:
c = LinkLine(row)
distance = max(c.distance, 50)
g.add_edge(c.aseqid,
c.bseqid,
orientation=c.orientation,
distance=distance)
def get_bname(sname, prefix=False):
return sname.rsplit("_", 1)[0] if prefix else "chr0"
scaffoldbuckets = defaultdict(list)
seqnames = sorted(sizes.keys())
for h in nx.connected_component_subgraphs(g):
partialorder = solve_component(h, sizes, fwlog)
name = partialorder[0][0]
bname = get_bname(name, prefix=opts.prefix)
scaffoldbuckets[bname].append(partialorder)
ctgbuckets = defaultdict(set)
for name in seqnames:
bname = get_bname(name, prefix=opts.prefix)
ctgbuckets[bname].add(name)
# Now the buckets contain a mixture of singletons and partially resolved
# scaffolds. Print the scaffolds first then remaining singletons.
scafname = "{0}.scf_{1:04d}"
for bname, ctgs in sorted(ctgbuckets.items()):
scaffolds = scaffoldbuckets[bname]
scaffolded = set()
ctgorder = []
for scafID, scaf in enumerate(scaffolds):
ctgorder = []
for node, start, end, orientation in scaf:
ctgorder.append((node, orientation))
scaffolded.add(node)
scaf = scafname.format(bname, scafID)
order_to_agp(scaf, ctgorder, sizes, fwagp)
singletons = sorted(ctgbuckets[bname] - scaffolded)
nscaffolds = len(scaffolds)
nsingletons = len(singletons)
msg = "{0}: Scaffolds={1} Singletons={2}".\
format(bname, nscaffolds, nsingletons)
print >> sys.stderr, msg
for singleton in singletons:
ctgorder = [(singleton, "+")]
order_to_agp(singleton, ctgorder, sizes, fwagp)
fwagp.close()
logging.debug("AGP file written to `{0}`.".format(agpfile))