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Added progress report to console when running sourmash compute with --singleton #84

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Added progress report to console when running sourmash compute with --singleton #84

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932f1fd
Added progress report to console when running `sourmash compute`
lgautier Jan 3, 2017
02cb44f
Made the step size for reporting progress when running
lgautier Jan 3, 2017
3fb7871
<sigh> compatibilty with Python 2 <sigh>
lgautier Jan 3, 2017
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18 changes: 17 additions & 1 deletion sourmash_lib/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -171,6 +171,9 @@ def compute(self, args):
parser.add_argument('--name-from-first', action='store_true')
parser.add_argument('--with-cardinality', action='store_true')
parser.add_argument('--track-abundance', action='store_true')
parser.add_argument('--progress-stepsize', type=int,
default = 10000,
help='number of entries in input after which progress is printed to stderr.')
args = parser.parse_args(args)

if args.input_is_protein and args.dna:
Expand Down Expand Up @@ -294,13 +297,26 @@ def save_siglist(siglist, output_fp, filename=None):
if args.singleton:
siglist = []
for n, record in enumerate(screed.open(filename)):
if n % args.progress_stepsize == 0:
if sys.version_info[0] < 3:
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Hmm, I think we should avoid adding too many of these checks to the code. Is it too bad to just not flush the output?

And not for this PR, but we should definitely start using the logging module for this kind of output, instead of printing stuff. Also makes it easier to filter what output we want (INFO for printing progress, for example?)

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Hmm, I think we should avoid adding too many of these checks to the code. Is it too bad to just not flush the output?

It is a progress report. Not flushing the output kind of defeats the purpose.

And not for this PR, but we should definitely start using the logging module for this kind of output, instead of printing stuff. Also makes it easier to filter what output we want (INFO for printing progress, for example?)

Big yes about using logging (I am trying to match the current code base and not have changes and new features are the same time to the extent possible - I am happy to go both if not creating too much trouble). Note: Flushing is implicitly done by logging with each call, I believe.

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Why not call sys.stderr.flush() in both cases?

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Would work... although it doesn't make the implicit point that Python 2 should eventually go ;-)

print('%s: %i entries' % (filename, n+1), file=sys.stderr, end='\r')
sys.stderr.flush()
else:
print('%s: %i entries' % (filename, n+1), file=sys.stderr, end='\r', flush=True)

# make estimators for each sequence
Elist = make_estimators()
add_seq(Elist, record.sequence,
args.input_is_protein, args.check_sequence)

siglist += build_siglist(args.email, Elist, filename,
name=record.name)
if sys.version_info[0] < 3:
print('%s: %i entries' % (filename, n+1), file=sys.stderr, end='\r')
sys.stderr.flush()
else:
print('%s: %i entries' % (filename, n+1), file=sys.stderr, end='\r', flush=True)

print('calculated {} signatures for {} sequences in {}'.\
format(len(siglist), n + 1, filename))
else:
Expand All @@ -312,7 +328,7 @@ def save_siglist(siglist, output_fp, filename=None):
file=sys.stderr)
name = None
for n, record in enumerate(screed.open(filename)):
if n % 10000 == 0:
if n % args.progress_stepsize == 0:
if n:
print('...', filename, n, file=sys.stderr)
elif args.name_from_first:
Expand Down