def bes(args):
"""
%prog bes bacfasta clonename
Use the clone name to download BES gss sequences from Genbank, map and then
visualize.
"""
from jcvi.apps.align import run_blat
p = OptionParser(bes.__doc__)
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
bacfasta, clonename = args
entrez([clonename, "--database=nucgss", "--skipcheck"])
besfasta = clonename + ".fasta"
blatfile = clonename + ".bes.blat"
run_blat(
infile=besfasta,
outfile=blatfile,
db=bacfasta,
pctid=95,
hitlen=100,
cpus=opts.cpus,
)
aid, asize = next(Fasta(bacfasta).itersizes())
width = 50
msg = "=" * width
msg += " " + aid
print(msg, file=sys.stderr)
ratio = width * 1.0 / asize
_ = lambda x: int(round(x * ratio, 0))
blasts = [BlastLine(x) for x in open(blatfile)]
for b in blasts:
if b.orientation == "+":
msg = " " * _(b.sstart) + "->"
else:
msg = " " * (_(b.sstop) - 2) + "<-"
msg += " " * (width - len(msg) + 2)
msg += b.query
if b.orientation == "+":
msg += " (hang={0})".format(b.sstart - 1)
else:
msg += " (hang={0})".format(asize - b.sstop)
print(msg, file=sys.stderr)
def bes(args):
"""
%prog bes bacfasta clonename
Use the clone name to download BES gss sequences from Genbank, map and then
visualize.
"""
from jcvi.apps.align import run_blat
p = OptionParser(bes.__doc__)
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
bacfasta, clonename = args
entrez([clonename, "--database=nucgss", "--skipcheck"])
besfasta = clonename + ".fasta"
blatfile = clonename + ".bes.blat"
run_blat(infile=besfasta, outfile=blatfile, db=bacfasta, \
pctid=95, hitlen=100, cpus=opts.cpus)
aid, asize = Fasta(bacfasta).itersizes().next()
width = 50
msg = "=" * width
msg += " " + aid
print >> sys.stderr, msg
ratio = width * 1. / asize
_ = lambda x: int(round(x * ratio, 0))
blasts = [BlastLine(x) for x in open(blatfile)]
for b in blasts:
if b.orientation == '+':
msg = " " * _(b.sstart) + "->"
else:
msg = " " * (_(b.sstop) - 2) + "<-"
msg += " " * (width - len(msg) + 2)
msg += b.query
if b.orientation == '+':
msg += " (hang={0})".format(b.sstart - 1)
else:
msg += " (hang={0})".format(asize - b.sstop)
print >> sys.stderr, msg