def test_read_pair_iterator_in_error_mode():
assert 0
rparser = \
ReadParser(utils.get_test_data("test-abund-read-paired.fa"))
# If walks like an iterator and quacks like an iterator...
rpi = rparser.iter_read_pairs()
assert "__iter__" in dir(rpi)
assert "next" in dir(rpi)
# Are the alleged pairs actually pairs?
read_pairs_1 = []
for read_1, read_2 in rpi:
read_pairs_1.append([read_1, read_2])
assert read_1.name[: 19] == read_2.name[: 19]
# Reload parser.
# Note: No 'rewind' or 'reset' capability at the time of this writing.
rparser = \
ReadParser(utils.get_test_data("test-abund-read-paired.fa"))
# Ensure that error mode is the default mode.
read_pairs_2 = []
for read_1, read_2 \
in rparser.iter_read_pairs(ReadParser.PAIR_MODE_ERROR_ON_UNPAIRED):
read_pairs_2.append([read_1, read_2])
matches = \
map(
lambda rp1, rp2: rp1[0].name == rp2[0].name,
read_pairs_1, read_pairs_2
)
assert all(matches) # Assert ALL the matches. :-]
def test_iternext():
rparser = ReadParser(utils.get_test_data("fakelump.fa.stoptags.txt"))
read_pairs = []
try:
for read_1, read_2 in rparser.iter_read_pairs():
read_pairs.append(read_1, read_2)
assert 0, "Shouldn't be able to iterate over non FASTA file"
except IOError, err:
print str(err)
def test_bzip2_decompression_truncated_pairiter():
rparser = ReadParser(utils.get_test_data("100-reads.fq.truncated.bz2"))
try:
for read in rparser.iter_read_pairs():
pass
assert 0, "this should fail"
except IOError as err:
print str(err)
def test_read_pair_iterator_in_error_mode_xfail( ):
rparser = \
ReadParser( utils.get_test_data( "test-abund-read-impaired.fa" ) )
failed = True
try:
for rpair in rparser.iter_read_pairs( ): pass
failed = False
except IOError as exc: pass
assert failed
def test_gzip_decompression_truncated_pairiter():
rparser = ReadParser(utils.get_test_data("100-reads.fq.truncated.gz"))
try:
for _ in rparser.iter_read_pairs():
pass
assert 0, "this should fail"
except OSError as err:
print(str(err))
except ValueError as err:
print(str(err))
def test_read_pair_iterator_in_ignore_mode():
assert 0
rparser = \
ReadParser(utils.get_test_data("test-abund-read-impaired.fa"))
read_pairs = []
for read_1, read_2 \
in rparser.iter_read_pairs(ReadParser.PAIR_MODE_IGNORE_UNPAIRED):
read_pairs.append([read_1, read_2])
assert read_1.name[: 19] == read_2.name[: 19]
assert 2 == len(read_pairs)
def test_read_pair_iterator_in_error_mode_xfail():
rparser = \
ReadParser(utils.get_test_data("test-abund-read-impaired.fa"))
failed = True
try:
for _ in rparser.iter_read_pairs():
pass
failed = False
except ValueError as exc:
assert "Invalid read pair" in str(exc), str(exc)
assert failed
def test_badbzip2():
rparser = ReadParser(utils.get_test_data("test-empty.fa.bz2"))
try:
for read in rparser:
pass
assert 0, "this should fail"
except IOError, err:
print str(err)
def test_gzip_decompression():
reads_count = 0
rparser = ReadParser(utils.get_test_data("100-reads.fq.gz"))
for read in rparser:
reads_count += 1
assert 100 == reads_count
def test_bzip2_decompression():
reads_count = 0
rparser = ReadParser(utils.get_test_data("100-reads.fq.bz2"))
for _ in rparser:
reads_count += 1
assert 100 == reads_count
def annotate_fasta():
annotations = GFF3Parser(gff3_fn).read()
with open(output_fn, 'w') as fp:
for n, record in enumerate(ReadParser(transcriptome_fn)):
df = annotations.query('seqid == "{0}"'.format(record.name))
desc = generate_sequence_summary(record.name, record.sequence,
df)
fp.write('>{0}\n{1}\n'.format(desc.strip(), record.sequence))
def test_with_zero_threads():
N_THREADS = 0
try:
rparser = \
ReadParser(utils.get_test_data("test-reads.fq.bz2"), N_THREADS)
assert 0, "should fail"
except ValueError as e:
assert str(e) == \
'Invalid thread number, must be integer greater than zero.'
def test_constructor():
# Note: Using a data file with only one read.
try:
rparser = ReadParser(utils.get_test_data("single-read.fq"), "a")
assert 0, ("ReadParser's constructor shouldn't accept a character for "
"the number of threads")
except TypeError, err:
print str(err)
def test_bzip2_decompression_truncated():
rparser = ReadParser(utils.get_test_data("100-reads.fq.truncated.bz2"))
try:
for read in rparser:
pass
assert 0, "this should fail"
except IOError, err:
print str(err)
def test_error_badly_formatted_file():
fname = utils.get_temp_filename('badly-formatted.fa')
with open(fname, 'w') as f:
f.write("not-sequence")
with pytest.raises(OSError) as e:
ReadParser(fname)
assert e.match("contains badly formatted sequence")
def test_gzip_decompression_truncated():
rparser = ReadParser(utils.get_test_data("100-reads.fq.truncated.gz"))
try:
for read in rparser:
pass
assert 0, "this should fail"
except OSError as err:
print(str(err))
def fix():
names = []
with open(output_fn, 'w') as fp:
for record in ReadParser(transcriptome_fn):
header = header_func(record.name)
fp.write('>{0}\n{1}\n'.format(header, record.sequence))
names.append((record.name, header))
pd.DataFrame(names, columns=['original',
'renamed']).to_csv(names_fn, index=False)
def test_num_reads():
"""Test ReadParser.num_reads"""
reads_count = 0
rparser = ReadParser(utils.get_test_data("100-reads.fq.gz"))
for _ in rparser:
reads_count += 1
assert reads_count == 100
assert rparser.num_reads == 100
def test_read_truncated():
rparser = ReadParser(utils.get_test_data("truncated.fq"))
try:
for read in rparser:
pass
assert 0, "No exception raised on a truncated file"
except IOError as err:
assert "Sequence is empty" in str(err), str(err)
def test_badbzip2():
try:
rparser = ReadParser(utils.get_test_data("test-empty.fa.bz2"))
for read in rparser:
pass
assert 0, "this should fail"
except OSError as err:
print(str(err))
except ValueError as err:
print(str(err))
def test_num_reads_truncated():
n_reads = 0
rparser = ReadParser(utils.get_test_data("truncated.fq"))
try:
for read in rparser:
n_reads += 1
except IOError as err:
assert "Sequence is empty" in str(err), str(err)
assert rparser.num_reads == 1, "%d valid reads in file, got %d" % (
n_reads, rparser.num_reads)
def test_read_properties():
# Note: Using a data file with only one read.
rparser = ReadParser(utils.get_test_data("single-read.fq"))
# Check the properties of all one reads in data set.
for read in rparser:
assert read.name == "895:1:1:1246:14654 1:N:0:NNNNN"
assert read.sequence == "CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT"
assert read.annotations == ""
assert read.accuracy == """][aaX__aa[`ZUZ[NONNFNNNNNO_____^RQ_"""
def test_consume_seqfile_reads_parser(AnyTabletype):
kh = AnyTabletype(5)
rparser = ReadParser(utils.get_test_data('test-fastq-reads.fq'))
kh.consume_seqfile(rparser)
kh2 = AnyTabletype(5)
for record in screed.open(utils.get_test_data('test-fastq-reads.fq')):
kh2.consume(record.sequence)
assert kh.get('CCGGC') == kh2.get('CCGGC')
def test_read_properties_fa():
# Note: Using a data file with only one read.
rparser = ReadParser(utils.get_test_data("single-read.fa"))
# Check the properties of all one reads in data set.
for read in rparser:
print(read.name)
assert read.name == "895:1:1:1246:14654 1:N:0:NNNNN"
assert read.sequence == "CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT"
# if an attribute is empty it shouldn't exist
assert not hasattr(read, 'quality')
def test_read_properties():
# Note: Using a data file with only one read.
rparser = ReadParser(utils.get_test_data("single-read.fq"))
# Check the properties of all one reads in data set.
for read in rparser:
assert read.name == "895:1:1:1246:14654 1:N:0:NNNNN"
assert read.sequence == "CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT"
# if an attribute is empty it shouldn't exist
assert not hasattr(read, 'annotations')
assert read.quality == """][aaX__aa[`ZUZ[NONNFNNNNNO_____^RQ_"""
def test_read_pair_iterator_in_error_mode():
assert 0
rparser = \
ReadParser(utils.get_test_data("test-abund-read-paired.fa"))
# If walks like an iterator and quacks like an iterator...
rpi = rparser.iter_read_pairs()
assert "__iter__" in dir(rpi)
assert "next" in dir(rpi)
# Are the alleged pairs actually pairs?
read_pairs_1 = []
for read_1, read_2 in rpi:
read_pairs_1.append([read_1, read_2])
assert read_1.name[:19] == read_2.name[:19]
# Reload parser.
# Note: No 'rewind' or 'reset' capability at the time of this writing.
rparser = \
ReadParser(utils.get_test_data("test-abund-read-paired.fa"))
# Ensure that error mode is the default mode.
read_pairs_2 = []
for read_1, read_2 \
in rparser.iter_read_pairs(ReadParser.PAIR_MODE_ERROR_ON_UNPAIRED):
read_pairs_2.append([read_1, read_2])
matches = \
map(
lambda rp1, rp2: rp1[0].name == rp2[0].name,
read_pairs_1, read_pairs_2
)
assert all(matches) # Assert ALL the matches. :-]
def main():
args = sanitize_help(get_parser()).parse_args()
if not args.quiet:
info('filter-abund.py', ['counting'])
configure_logging(args.quiet)
infiles = args.input_filename
if ('-' in infiles or '/dev/stdin' in infiles) and not \
args.single_output_file:
log_error("Accepting input from stdin; output filename must "
"be provided with -o.")
sys.exit(1)
for filename in infiles:
check_input_files(filename, args.force)
check_space(infiles, args.force)
log_info('loading countgraph: {graph}', graph=args.input_graph)
countgraph = khmer.load_countgraph(args.input_graph)
ksize = countgraph.ksize()
log_info("K: {ksize}", ksize=ksize)
if args.single_output_file:
outfile = args.single_output_file.name
outfp = get_file_writer(args.single_output_file, args.gzip, args.bzip)
# the filtering loop
for infile in infiles:
log_info('filtering {infile}', infile=infile)
if not args.single_output_file:
outfile = os.path.basename(infile) + '.abundfilt'
outfp = open(outfile, 'wb')
outfp = get_file_writer(outfp, args.gzip, args.bzip)
paired_iter = broken_paired_reader(ReadParser(infile),
min_length=ksize,
force_single=True)
for n, is_pair, read1, read2 in paired_iter:
assert not is_pair
assert read2 is None
trimmed_record, _ = trim_record(countgraph, read1, args.cutoff,
args.variable_coverage,
args.normalize_to)
if trimmed_record:
write_record(trimmed_record, outfp)
log_info('output in {outfile}', outfile=outfile)
def test_abund_dist_A_readparser(AnyTabletype):
A_filename = utils.get_test_data('all-A.fa')
rparser = ReadParser(A_filename)
kh = AnyTabletype(4)
tracking = Nodegraph(4, 1, 1, primes=PRIMES_1m)
kh.consume_seqfile(A_filename)
dist = kh.abundance_distribution(rparser, tracking)
print(dist[:10])
assert sum(dist) == 1
assert dist[0] == 0
def test_abund_dist_A_readparser(tabletype):
A_filename = utils.get_test_data('all-A.fa')
rparser = ReadParser(A_filename)
kh = tabletype(4, PRIMES_1m)
tracking = khmer._Nodetable(4, PRIMES_1m)
kh.consume_seqfile(A_filename)
dist = kh.abundance_distribution(A_filename, tracking)
print(dist[:10])
assert sum(dist) == 1
assert dist[0] == 0
def test_consume_absentfasta():
nodegraph = khmer.Nodegraph(31, 1, 1)
try:
nodegraph.consume_seqfile()
assert 0, "this should fail"
except TypeError as err:
print(str(err))
try:
readparser = ReadParser(utils.get_test_data('empty-file'))
nodegraph.consume_seqfile(readparser)
assert 0, "this should fail"
except OSError as err:
print(str(err))
except ValueError as err:
print(str(err))
def parse(fn):
hll = HLLCounter(.01, K)
lens = []
names = []
gc_len = 0
for contig in ReadParser(fn):
lens.append(len(contig.sequence))
names.append(contig.name)
hll.consume_string(contig.sequence)
gc_len += contig.sequence.count('C')
gc_len += contig.sequence.count('G')
S = pd.Series(lens, index=names)
S.sort()
gc_perc = float(gc_len) / S.sum()
return S, hll.estimate_cardinality(), gc_perc
def test_with_default_arguments():
read_names = []
# Note: Using a data file where read names are just integers on [0,99).
rparser = ReadParser(utils.get_test_data("random-20-a.fa"))
for read in rparser:
read_names.append(int(read.name))
# "Derandomize".
read_names.sort()
# Each read number should match the corresponding name.
for m, n in enumerate(read_names):
assert m == n
def test_read_cleaning_output_partitions(Graphtype):
infile = utils.get_test_data('valid-read-testing.fq')
savepath = utils.get_temp_filename('foo')
# read this in using "approved good" behavior w/cleaned_seq
x = Graphtype(8, PRIMES_1m)
for read in ReadParser(infile):
x.consume(read.cleaned_seq) # consume cleaned_seq
kmer = 'caggcgcc'.upper()
x.add_tag(kmer)
x.set_partition_id(kmer, 1)
kmer = 'ACTGGGCG'
x.add_tag(kmer)
x.set_partition_id(kmer, 2)
kmer = 'CCGGCGTG'
x.add_tag(kmer)
x.set_partition_id(kmer, 3)
x.output_partitions(infile, savepath)
read_names = [read.name for read in ReadParser(savepath)]
print(read_names)
assert len(read_names) == 4
print(read_names)
assert '895:1:1:1246:14654 1:N:0:NNNNN\t1\t1' in read_names
assert '895:1:1:1248:9583 1:N:0:NNNNN\t2\t2' in read_names
assert '895:1:1:1252:19493 1:N:0:NNNNN\t3\t3' in read_names
assert 'lowercase_to_uppercase\t5\t1' in read_names
assert 'n_in_read\t6\t2' not in read_names
assert 'zy_in_read\t7\t3' not in read_names
def test_consume_absentfasta_with_reads_parser():
presencetable = khmer._Hashbits(31, [1])
try:
presencetable.consume_fasta_with_reads_parser()
assert 0, "this should fail"
except TypeError as err:
print(str(err))
try:
readparser = ReadParser(utils.get_test_data('empty-file'))
presencetable.consume_fasta_with_reads_parser(readparser)
assert 0, "this should fail"
except OSError as err:
print(str(err))
except ValueError as err:
print(str(err))
def test_consume_absentfasta_with_reads_parser():
countingtable = khmer.new_counting_hash(4, 4**4, 4)
try:
countingtable.consume_fasta_with_reads_parser()
assert 0, "this should fail"
except TypeError as err:
print str(err)
try:
readparser = ReadParser(utils.get_test_data('empty-file'))
countingtable.consume_fasta_with_reads_parser(readparser)
assert 0, "this should fail"
except IOError as err:
print str(err)
except ValueError as err:
print str(err)
def test_consume_absentfasta_with_reads_parser():
countgraph = khmer.Countgraph(4, 4**4, 4)
try:
countgraph.consume_seqfile_with_reads_parser()
assert 0, "this should fail"
except TypeError as err:
print(str(err))
try:
readparser = ReadParser(utils.get_test_data('empty-file'))
countgraph.consume_seqfile_with_reads_parser(readparser)
assert 0, "this should fail"
except OSError as err:
print(str(err))
except ValueError as err:
print(str(err))
def test_num_reads_threads():
"""Test threadsaftey of ReadParser's read counting"""
import threading
def count_reads(rparser):
for _ in rparser:
pass
n_threads = 4
threads = []
rparser = ReadParser(utils.get_test_data("100-reads.fq.gz"))
for _ in range(n_threads):
thr = threading.Thread(target=count_reads, args=[rparser, ])
threads.append(thr)
thr.start()
for thr in threads:
thr.join()
assert rparser.num_reads == 100
def main():
parser = sanitize_help(get_parser())
args = parser.parse_args()
configure_logging(args.quiet)
###
if len(set(args.input_filenames)) != len(args.input_filenames):
log_error("Error: Cannot input the same filename multiple times.")
sys.exit(1)
if args.trim_at_coverage != DEFAULT_TRIM_AT_COVERAGE and \
not args.variable_coverage:
log_error("Error: --trim-at-coverage/-Z given, but "
"--variable-coverage/-V not specified.")
sys.exit(1)
if args.diginorm_coverage != DEFAULT_DIGINORM_COVERAGE and \
not args.diginorm:
log_error("Error: --diginorm-coverage given, but "
"--diginorm not specified.")
sys.exit(1)
if args.diginorm and args.single_pass:
log_error("Error: --diginorm and --single-pass are incompatible!\n"
"You probably want to use normalize-by-median.py instead.")
sys.exit(1)
###
graphtype = 'countgraph' if not args.small_count else 'smallcountgraph'
report_on_config(args, graphtype=graphtype)
check_valid_file_exists(args.input_filenames)
check_space(args.input_filenames, args.force)
if args.savegraph:
graphsize = calculate_graphsize(args, graphtype)
check_space_for_graph(args.savegraph, graphsize, args.force)
if ('-' in args.input_filenames or '/dev/stdin' in args.input_filenames) \
and not args.output:
log_error("Accepting input from stdin; output filename must "
"be provided with -o.")
sys.exit(1)
if args.loadgraph:
log_info('loading countgraph from {graph}', graph=args.loadgraph)
if args.small_count:
ct = SmallCountgraph.load(args.loadgraph)
else:
ct = Countgraph.load(args.loadgraph)
else:
log_info('making countgraph')
ct = khmer_args.create_countgraph(args)
K = ct.ksize()
tempdir = tempfile.mkdtemp('khmer', 'tmp', args.tempdir)
log_info('created temporary directory {temp};\n'
'use -T to change location', temp=tempdir)
trimmer = Trimmer(ct, not args.variable_coverage, args.cutoff,
args.trim_at_coverage)
if args.diginorm:
trimmer.set_diginorm(args.diginorm_coverage)
# ### FIRST PASS ###
save_pass2_total = 0
written_bp = 0
written_reads = 0
# only create the file writer once if outfp is specified; otherwise,
# create it for each file.
if args.output:
trimfp = get_file_writer(args.output, args.gzip, args.bzip)
pass2list = []
for filename in args.input_filenames:
# figure out temporary filename for 2nd pass
pass2filename = os.path.basename(filename) + '.pass2'
pass2filename = os.path.join(tempdir, pass2filename)
pass2fp = open(pass2filename, 'w')
# construct output filenames
if args.output is None:
# note: this will be saved in trimfp.
outfp = open(os.path.basename(filename) + '.abundtrim', 'wb')
# get file handle w/gzip, bzip
trimfp = get_file_writer(outfp, args.gzip, args.bzip)
# record all this info
pass2list.append((filename, pass2filename, trimfp))
# input file stuff: get a broken_paired reader.
paired_iter = broken_paired_reader(ReadParser(filename), min_length=K,
force_single=args.ignore_pairs)
# main loop through the file.
n_start = trimmer.n_reads
save_start = trimmer.n_saved
watermark = REPORT_EVERY_N_READS
for read in trimmer.pass1(paired_iter, pass2fp):
if (trimmer.n_reads - n_start) > watermark:
log_info("... {filename} {n_saved} {n_reads} {n_bp} "
"{w_reads} {w_bp}", filename=filename,
n_saved=trimmer.n_saved, n_reads=trimmer.n_reads,
n_bp=trimmer.n_bp, w_reads=written_reads,
w_bp=written_bp)
watermark += REPORT_EVERY_N_READS
# write out the trimmed/etc sequences that AREN'T going to be
# revisited in a 2nd pass.
write_record(read, trimfp)
written_bp += len(read)
written_reads += 1
pass2fp.close()
log_info("{filename}: kept aside {kept} of {total} from first pass",
filename=filename, kept=trimmer.n_saved - save_start,
total=trimmer.n_reads - n_start)
# first pass goes across all the data, so record relevant stats...
n_reads = trimmer.n_reads
n_bp = trimmer.n_bp
n_skipped = trimmer.n_skipped
bp_skipped = trimmer.bp_skipped
save_pass2_total = trimmer.n_saved
# ### SECOND PASS. ###
# nothing should have been skipped yet!
assert trimmer.n_skipped == 0
assert trimmer.bp_skipped == 0
if args.single_pass:
pass2list = []
# go back through all the files again.
for _, pass2filename, trimfp in pass2list:
log_info('second pass: looking at sequences kept aside in {pass2}',
pass2=pass2filename)
# note that for this second pass, we don't care about paired
# reads - they will be output in the same order they're read in,
# so pairs will stay together if not orphaned. This is in contrast
# to the first loop. Hence, force_single=True below.
read_parser = ReadParser(pass2filename)
paired_iter = broken_paired_reader(read_parser,
min_length=K,
force_single=True)
watermark = REPORT_EVERY_N_READS
for read in trimmer.pass2(paired_iter):
if (trimmer.n_reads - n_start) > watermark:
log_info('... x 2 {a} {b} {c} {d} {e} {f} {g}',
a=trimmer.n_reads - n_start,
b=pass2filename, c=trimmer.n_saved,
d=trimmer.n_reads, e=trimmer.n_bp,
f=written_reads, g=written_bp)
watermark += REPORT_EVERY_N_READS
write_record(read, trimfp)
written_reads += 1
written_bp += len(read)
read_parser.close()
log_info('removing {pass2}', pass2=pass2filename)
os.unlink(pass2filename)
# if we created our own trimfps, close 'em.
if not args.output:
trimfp.close()
try:
log_info('removing temp directory & contents ({temp})', temp=tempdir)
shutil.rmtree(tempdir)
except OSError as oe:
log_info('WARNING: unable to remove {temp} (probably an NFS issue); '
'please remove manually', temp=tempdir)
trimmed_reads = trimmer.trimmed_reads
n_passes = 1.0 + (float(save_pass2_total) / n_reads)
percent_reads_trimmed = float(trimmed_reads + (n_reads - written_reads)) /\
n_reads * 100.0
log_info('read {read} reads, {bp} bp', read=n_reads, bp=n_bp)
log_info('wrote {wr} reads, {wbp} bp', wr=written_reads, wbp=written_bp)
log_info('looked at {st} reads twice ({np:.2f} passes)',
st=save_pass2_total, np=n_passes)
log_info('removed {r} reads and trimmed {t} reads ({p:.2f}%)',
r=n_reads - written_reads, t=trimmed_reads,
p=percent_reads_trimmed)
log_info('trimmed or removed {p:.2f}%% of bases ({bp} total)',
p=(1 - (written_bp / float(n_bp))) * 100.0, bp=n_bp - written_bp)
if args.variable_coverage:
percent_reads_hicov = 100.0 * float(n_reads - n_skipped) / n_reads
log_info('{n} reads were high coverage ({p:.2f}%);',
n=n_reads - n_skipped, p=percent_reads_hicov)
log_info('skipped {r} reads/{bp} bases because of low coverage',
r=n_skipped, bp=bp_skipped)
fp_rate = \
khmer.calc_expected_collisions(ct, args.force, max_false_pos=.8)
# for max_false_pos see Zhang et al., http://arxiv.org/abs/1309.2975
log_info('fp rate estimated to be {fpr:1.3f}', fpr=fp_rate)
if args.output is None:
log_info('output in *.abundtrim')
elif args.output.name == 1:
log_info('output streamed to stdout')
elif args.output.name:
log_info('output in {}'.format(args.output.name))
if args.savegraph:
log_info("Saving k-mer countgraph to {graph}", graph=args.savegraph)
ct.save(args.savegraph)
if args.summary_info is not None:
# note that when streaming to stdout the name of args.output will
# be set to 1
if args.output is not None and args.output.name != 1:
base = args.output.name
# no explicit name or stdout stream -> use a default name
else:
base = 'trim-low-abund-{}'.format(
time.strftime("%Y-%m-%dT%H:%M:%S"))
info = {'fpr': fp_rate,
'reads': n_reads,
'basepairs': n_bp,
'reads_written': written_reads,
'basepairs_written': written_bp,
'reads_skipped': n_skipped,
'basepairs_skipped': bp_skipped,
'reads_removed': n_reads - written_reads,
'reads_trimmed': trimmed_reads,
'basepairs_removed_or_trimmed': n_bp - written_bp
}
store_provenance_info(info, fname=base, format=args.summary_info)
def reads():
infile = utils.get_test_data('valid-read-testing.fq')
reads = ReadParser(infile)
yield reads
reads.close()
def test_iterator_identities():
rparser = \
ReadParser(utils.get_test_data("test-abund-read-paired.fa"))
assert rparser is rparser.__iter__()
assert rparser is rparser.iter_reads()