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# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2011-2015, Michigan State University.
# Copyright (C) 2015, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
#
# * Neither the name of the Michigan State University nor the names
# of its contributors may be used to endorse or promote products
# derived from this software without specific prior written
# permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project@idyll.org
# pylint: disable=missing-docstring,invalid-name
from khmer.thread_utils import ThreadedSequenceProcessor, SequenceGroup
from io import StringIO
from screed.fasta import fasta_iter
from screed.fastq import fastq_iter
import screed
# stdlib queue module was renamed on Python 3
try:
import queue
except ImportError:
import Queue as queue
def load_records(stringio_fp):
records = list(fasta_iter(StringIO(stringio_fp.getvalue())))
return records
def load_records_fastq(stringio_fp):
records = list(fastq_iter(StringIO(stringio_fp.getvalue())))
return records
def load_records_d(stringio_fp):
return dict([(r.name, r.sequence)
for r in load_records(stringio_fp)])
# simple processing function: keep all sequences.
def idem(record):
return record['name'], record['sequence']
# keep every *other* sequence
odd_counter = 0
def every_other(record):
global odd_counter # pylint: disable=global-statement
odd_counter += 1
if odd_counter % 2 == 1:
return None, None
return record['name'], record['sequence']
#
def test_basic():
tsp = ThreadedSequenceProcessor(idem, 1, 1, verbose=False)
inseqs = [screed.Record(name='a', sequence='AAA'),
screed.Record(name='b', sequence='TTT'), ]
outfp = StringIO()
tsp.start(inseqs, outfp)
x = load_records_d(outfp)
assert len(x) == 2, x
assert x['a'] == 'AAA'
assert x['b'] == 'TTT'
def test_basic_fastq_like():
tsp = ThreadedSequenceProcessor(idem, 1, 1, verbose=False)
inseqs = [screed.Record(name='a', sequence='AAA', quality='###'),
screed.Record(name='b', sequence='TTT', quality='###'), ]
outfp = StringIO()
tsp.start(inseqs, outfp)
x = load_records_fastq(outfp)
for i in x:
assert i['quality'] == '###'
def test_odd():
tsp = ThreadedSequenceProcessor(every_other, 1, 1, verbose=False)
inseqs = [screed.Record(name='a', sequence='AAA'),
screed.Record(name='b', sequence='TTT'), ]
outfp = StringIO()
tsp.start(inseqs, outfp)
x = load_records_d(outfp)
assert len(x) == 1, x
assert x['b'] == 'TTT'
def test_basic_2thread():
tsp = ThreadedSequenceProcessor(idem, 2, 1, verbose=False)
inseqs = [screed.Record(name='a', sequence='AAA'),
screed.Record(name='b', sequence='TTT'), ]
outfp = StringIO()
tsp.start(inseqs, outfp)
x = load_records_d(outfp)
assert len(x) == 2, x
assert x['a'] == 'AAA'
assert x['b'] == 'TTT'
def test_paired_2thread():
class TSP_TestPairedProcess(ThreadedSequenceProcessor):
# write a new do_process function that ensures paired ends are kept.
def do_process(self):
inq = self.inqueue
while not self.done or not inq.empty():
try:
g = inq.get(True, 1)
except queue.Empty:
continue
assert len(g.seqlist) == 2
first_rec = g.seqlist[0]
second_rec = g.seqlist[1]
assert first_rec['name'][:-1] == second_rec['name'][:-1]
assert first_rec['name'][-1] == '1'
assert second_rec['name'][-1] == '2'
keep = []
for record in g.seqlist:
name, sequence = self.process_fn(record)
if name:
keep.append((name, sequence, None))
self.outqueue.put(SequenceGroup(0, keep))
# end of thread; exit, decrement worker count.
self.worker_count -= 1
#
tsp = TSP_TestPairedProcess(idem, 1, 1, verbose=False)
inseqs = [screed.Record(name='a/1', sequence='AAA'),
screed.Record(name='a/2', sequence='TTT'), ]
outfp = StringIO()
tsp.start(inseqs, outfp)
x = load_records_d(outfp)
assert len(x) == 2, x
assert x['a/1'] == 'AAA'
assert x['a/2'] == 'TTT'
def test_paired_2thread_more_seq():
class TSP_TestPairedProcess(ThreadedSequenceProcessor):
# write a new do_process function that ensures paired ends are kept.
def do_process(self):
inq = self.inqueue
while not self.done or not inq.empty():
try:
g = inq.get(True, 1)
except queue.Empty:
continue
if len(g.seqlist) == 2:
first_rec = g.seqlist[0]
second_rec = g.seqlist[1]
assert first_rec['name'][:-1] == second_rec['name'][:-1]
assert first_rec['name'][-1] == '1'
assert second_rec['name'][-1] == '2'
keep = []
for record in g.seqlist:
name, sequence = self.process_fn(record)
if name:
keep.append((name, sequence, None))
self.outqueue.put(SequenceGroup(0, keep))
# end of thread; exit, decrement worker count.
self.worker_count -= 1
#
tsp = TSP_TestPairedProcess(idem, 1, 1, verbose=False)
inseqs = [screed.Record(name='b/1', sequence='AAA'),
screed.Record(name='a/1', sequence='AAA'),
screed.Record(name='a/2', sequence='TTT'),
screed.Record(name='c/2', sequence='AAA'), ]
outfp = StringIO()
tsp.start(inseqs, outfp)
x = load_records_d(outfp)
assert len(x) == 4, x
assert x['a/1'] == 'AAA'
assert x['a/2'] == 'TTT'
assert x['b/1'] == 'AAA'
assert x['c/2'] == 'AAA'
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