def test01(self):
infile = 'testfiles/474_0_0.txt'
names, seqs = zip(*(line.split() for line in open(infile) if line.strip()))
d1 = dedup(seqs)
d2 = dedup(seqs, chunksize=500)
as_strings = lambda idx: set(seqs[i] for i in idx)
self.assertTrue(as_strings(d1.keys()) == as_strings(d1.keys()))
parents = [seqs[i] for i in d1.keys()]
# canonical sequences should all be unique
self.assertTrue(len(parents) == len(set(parents)))
dp = dedup(parents)
self.assertTrue(len(dp) == len(parents))
def test01(self):
infile = 'testfiles/474_0_0.txt'
names, seqs = zip(*(line.split() for line in open(infile)
if line.strip()))
d1 = dedup(seqs)
d2 = dedup(seqs, chunksize=500)
as_strings = lambda idx: set(seqs[i] for i in idx)
self.assertTrue(as_strings(d1.keys()) == as_strings(d1.keys()))
parents = [seqs[i] for i in d1.keys()]
# canonical sequences should all be unique
self.assertTrue(len(parents) == len(set(parents)))
dp = dedup(parents)
self.assertTrue(len(dp) == len(parents))
def main():
usage = """%prog [options]
Read sequences in fasta format and identify a single sequence to
represent each set of substrings or identical sequences.
"""
parser = OptionParser(usage=usage, version="$Id$")
parser.set_defaults(
infile=None,
verbose=0,
nchunks=0,
chunksize=None,
compare_type='contains',
outfile=None,
r_file=None,
as_is=False,
name_style='list',
)
parser.add_option("-f",
"--fasta-file",
dest="infile",
help='Input file containing sequences in fasta format',
metavar='FILE')
parser.add_option("-o",
"--outfile",
dest="outfile",
help='Output file in fasta format',
metavar='FILE')
parser.add_option(
"-r",
"--r-output",
dest="r_file",
help='Output file containing an R-language list of character vectors',
metavar='FILE')
parser.add_option('-n',
'--nchunks',
dest='nchunks',
metavar='INT',
type='int',
help='Number of partitions [default: %default].')
parser.add_option(
'-c',
'--chunksize',
dest='chunksize',
metavar='INT',
type='int',
help=
'Number of strings in each partition (overrides --nchunks) [default: %default].'
)
parser.add_option(
'-t',
'--compare-type',
dest='compare_type',
metavar='VAL',
type='choice',
choices=['eq', 'contains'],
help=('Type of comparison: "contains"'
'(finds longest sequences containing sets of substrings)'
' or "eq" (selects single representatives from groups of'
' identical sequences) [default: %default].'))
parser.add_option(
"-a",
"--as-is",
action="store_true",
dest="as_is",
help='If True, do not degap input sequences [default: %default].')
parser.add_option(
'-N',
'--name-style',
dest='name_style',
type='choice',
choices=['list', 'count'],
help=
('Naming style of sequences.'
'"list" - name of canonical sequence representing each group followed by list of members'
' or "count" - as above, with the count of group members appended to the seq name'
' identical sequences) [default: %default].'))
parser.add_option(
"-v",
"--verbose",
action="count",
dest="verbose",
help=
"increase verbosity of screen output (eg, -v is verbose, -vv is more so)"
)
options, args = parser.parse_args()
loglevel = {
0: logging.WARNING,
1: logging.INFO,
2: logging.DEBUG
}.get(options.verbose, logging.DEBUG)
verbose_format = '%(levelname)s %(funcName)s %(lineno)s %(message)s'
logformat = {
0: '%(message)s',
1: verbose_format,
2: verbose_format
}.get(options.verbose, verbose_format)
if __debug__:
logformat = verbose_format
# set up logging
logging.basicConfig(file=sys.stdout, format=logformat, level=loglevel)
comp = options.compare_type
infile = options.infile
if not infile:
log.error('Please provide an input file using -f/--fasta-file\n')
parser.print_usage()
sys.exit(1)
seqs = readfasta(infile, degap=True)
strings = tuple(seq[1] for seq in seqs)
nstrings = len(strings)
log.warning('Input contains %s items' % nstrings)
start = time.time()
if options.chunksize:
chunksize = options.chunksize
elif options.nchunks and options.nchunks > 1:
chunksize = int(nstrings / options.nchunks) + 1
else:
chunksize = nstrings
log.warning('chunksize = %s' % chunksize)
d = deduplicate.dedup(strings, comp, chunksize)
log.warning(
'Input data can be represented by %s superstrings (%.2f%% of the input number)'
% (len(d), 100 * (len(d) / float(nstrings))))
log.warning('grand total is %.2f secs' % (time.time() - start))
def main():
usage = """%prog [options]
Read sequences in fasta format and identify a single sequence to
represent each set of substrings or identical sequences.
"""
parser = OptionParser(usage=usage, version="$Id$")
parser.set_defaults(
infile=None,
verbose=0,
nchunks=0,
chunksize=None,
compare_type='contains',
outfile=None,
r_file=None,
as_is=False,
name_style = 'list',
)
parser.add_option("-f", "--fasta-file", dest="infile",
help='Input file containing sequences in fasta format',
metavar='FILE')
parser.add_option("-o", "--outfile", dest="outfile",
help='Output file in fasta format',
metavar='FILE')
parser.add_option("-r", "--r-output", dest="r_file",
help='Output file containing an R-language list of character vectors',
metavar='FILE')
parser.add_option('-n','--nchunks', dest='nchunks', metavar='INT', type='int',
help='Number of partitions [default: %default].')
parser.add_option('-c','--chunksize', dest='chunksize', metavar='INT',
type='int',
help='Number of strings in each partition (overrides --nchunks) [default: %default].')
parser.add_option('-t','--compare-type',dest='compare_type',metavar='VAL',
type='choice',choices=['eq','contains'],
help=('Type of comparison: "contains"'
'(finds longest sequences containing sets of substrings)'
' or "eq" (selects single representatives from groups of'
' identical sequences) [default: %default].'))
parser.add_option("-a","--as-is", action="store_true", dest="as_is",
help='If True, do not degap input sequences [default: %default].')
parser.add_option('-N','--name-style',dest='name_style',
type='choice',choices=['list','count'],
help=('Naming style of sequences.'
'"list" - name of canonical sequence representing each group followed by list of members'
' or "count" - as above, with the count of group members appended to the seq name'
' identical sequences) [default: %default].'
))
parser.add_option("-v", "--verbose",
action="count", dest="verbose",
help="increase verbosity of screen output (eg, -v is verbose, -vv is more so)")
options, args = parser.parse_args()
loglevel = {0:logging.WARNING,
1:logging.INFO,
2:logging.DEBUG}.get(options.verbose, logging.DEBUG)
verbose_format = '%(levelname)s %(funcName)s %(lineno)s %(message)s'
logformat = {0:'%(message)s',
1:verbose_format,
2:verbose_format}.get(options.verbose, verbose_format)
if __debug__:
logformat = verbose_format
# set up logging
logging.basicConfig(file=sys.stdout,
format=logformat,
level=loglevel)
comp = options.compare_type
infile = options.infile
if not infile:
log.error('Please provide an input file using -f/--fasta-file\n')
parser.print_usage()
sys.exit(1)
seqs = readfasta(infile, degap=True)
strings = tuple(seq[1] for seq in seqs)
nstrings = len(strings)
log.warning('Input contains %s items' % nstrings)
start = time.time()
if options.chunksize:
chunksize = options.chunksize
elif options.nchunks and options.nchunks > 1:
chunksize = int(nstrings/options.nchunks) + 1
else:
chunksize = nstrings
log.warning('chunksize = %s' % chunksize)
d = deduplicate.dedup(strings, comp, chunksize)
log.warning('Input data can be represented by %s superstrings (%.2f%% of the input number)' % (len(d), 100*(len(d)/float(nstrings))))
log.warning('grand total is %.2f secs' % (time.time()-start))