import logging
from optparse import OptionParser
from itertools import groupby
from jcvi.formats.agp import AGP, TPF, get_phase
from jcvi.formats.base import BaseFile
from jcvi.formats.fasta import Fasta, SeqIO
from jcvi.formats.blast import BlastLine
from jcvi.formats.coords import Overlap_types
from jcvi.formats.base import must_open
from jcvi.utils.cbook import memoized
from jcvi.apps.entrez import fetch
from jcvi.apps.base import ActionDispatcher, debug, popen, mkdir, sh
debug()
GoodPct = 99
GoodOverlap = 500
GoodOverhang = 10000
class Overlap(object):
def __init__(self, blastline, asize, bsize):
b = blastline
aid = b.query
bid = b.subject
self.aid = aid.split("|")[3] if aid.count("|") >= 3 else aid
self.bid = bid.split("|")[3] if bid.count("|") >= 3 else bid
self.asize = asize
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Script to write and assist SOAPdenovo assembly.
"""
import os.path as op
import sys
from jcvi.formats.fastq import guessoffset, readlen
from jcvi.assembly.base import FastqNamings, Library, get_libs
from jcvi.apps.base import OptionParser, ActionDispatcher, debug, need_update, sh
debug()
class FillLine(object):
def __init__(self, row):
args = row.split()
self.start = int(args[0])
self.end = int(args[1])
self.leftextend = int(args[2])
self.rightextend = int(args[3])
self.closed = int(args[4]) == 1
self.extendlength = int(args[5])
self.before = int(args[6])
self.after = int(args[7])
# Convert from unsigned to signed
# <http://stackoverflow.com/questions/1375897/how-to-get-the-signed-integer-value-of-a-long-in-python>
if self.after > 0 and (self.after & 0x80000000):
#!/usr/bin/env python # -*- coding: UTF-8 -*- import sys import os.path as op import logging from optparse import OptionParser from jcvi.formats.base import must_open from jcvi.apps.base import ActionDispatcher, debug debug() default_template = """#!/usr/bin/env python # -*- coding: UTF-8 -*- \"\"\" \"\"\" import sys from optparse import OptionParser from jcvi.apps.base import ActionDispatcher, debug debug() def main():
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
import sys
import logging
from jcvi.formats.base import write_file
from jcvi.apps.base import OptionParser, debug
debug()
default_template = """
\"\"\"
\"\"\"
import sys
from jcvi.apps.base import OptionParser, ActionDispatcher, debug
debug()
def main():
actions = (
('app', ''),
)
p = ActionDispatcher(actions)
p.dispatch(globals())
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
import sys
import os.path as op
import logging
from optparse import OptionParser
from jcvi.formats.base import must_open
from jcvi.apps.base import ActionDispatcher, debug
debug()
default_template = """#!/usr/bin/env python
# -*- coding: UTF-8 -*-
\"\"\"
\"\"\"
import sys
from optparse import OptionParser
from jcvi.apps.base import ActionDispatcher, debug
debug()
def main():
actions = (
