From 24a55efcb5f6bf2f3f792af11f893cdd5e8dd9ea Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 12 Jun 2016 08:21:20 -0700
Subject: [PATCH 01/15] make 'add' a synonym for 'count' on hashtables

---
 khmer/_khmer.cc | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/khmer/_khmer.cc b/khmer/_khmer.cc
index 45c7649918..771d3e27e1 100644
--- a/khmer/_khmer.cc
+++ b/khmer/_khmer.cc
@@ -2785,6 +2785,11 @@ static PyMethodDef khmer_hashtable_methods[] = {
         (PyCFunction)hashtable_count, METH_VARARGS,
         "Increment the count of this k-mer."
     },
+    {
+        "add",
+        (PyCFunction)hashtable_count, METH_VARARGS,
+        "Increment the count of this k-mer. (Synonym for 'count'.)"
+    },
     {
         "consume",
         (PyCFunction)hashtable_consume, METH_VARARGS,

From 20910357ac51f3ae872c6ad359aafd2a01fa40c1 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 12 Jun 2016 14:14:11 -0700
Subject: [PATCH 02/15] add args.quiet to a bunch of scripts

---
 scripts/abundance-dist-single.py | 5 ++++-
 scripts/abundance-dist.py        | 5 ++++-
 scripts/load-into-counting.py    | 7 +++++--
 3 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/scripts/abundance-dist-single.py b/scripts/abundance-dist-single.py
index 243dba965a..1a84f2dfdd 100755
--- a/scripts/abundance-dist-single.py
+++ b/scripts/abundance-dist-single.py
@@ -97,12 +97,15 @@ def get_parser():
                         "filename.")
     parser.add_argument('-f', '--force', default=False, action='store_true',
                         help='Overwrite output file if it exists')
+    parser.add_argument('-q', '--quiet', dest='quiet', default=False,
+                        action='store_true')
     return parser
 
 
 def main():  # pylint: disable=too-many-locals,too-many-branches
-    info('abundance-dist-single.py', ['counting', 'SeqAn'])
     args = sanitize_help(get_parser()).parse_args()
+    if not args.quiet:
+        info('abundance-dist-single.py', ['counting', 'SeqAn'])
     report_on_config(args)
 
     check_input_files(args.input_sequence_filename, args.force)
diff --git a/scripts/abundance-dist.py b/scripts/abundance-dist.py
index 6d594f7d6f..fb948d14db 100755
--- a/scripts/abundance-dist.py
+++ b/scripts/abundance-dist.py
@@ -89,12 +89,15 @@ def get_parser():
     parser.add_argument('-f', '--force', default=False, action='store_true',
                         help='Continue even if specified input files '
                         'do not exist or are empty.')
+    parser.add_argument('-q', '--quiet', dest='quiet', default=False,
+                        action='store_true')
     return parser
 
 
 def main():
-    info('abundance-dist.py', ['counting'])
     args = sanitize_help(get_parser()).parse_args()
+    if not args.quiet:
+        info('abundance-dist.py', ['counting'])
 
     infiles = [args.input_count_graph_filename,
                args.input_sequence_filename]
diff --git a/scripts/load-into-counting.py b/scripts/load-into-counting.py
index 0520c680e6..2e01862713 100755
--- a/scripts/load-into-counting.py
+++ b/scripts/load-into-counting.py
@@ -97,14 +97,17 @@ def get_parser():
                         " default)")
     parser.add_argument('-f', '--force', default=False, action='store_true',
                         help='Overwrite output file if it exists')
+    parser.add_argument('-q', '--quiet', dest='quiet', default=False,
+                        action='store_true')
     return parser
 
 
 def main():
 
-    info('load-into-counting.py', ['counting', 'SeqAn'])
-
     args = sanitize_help(get_parser()).parse_args()
+    if not args.quiet:
+        info('load-into-counting.py', ['counting', 'SeqAn'])
+
     report_on_config(args)
 
     base = args.output_countgraph_filename

From 7f327273e575321f38703630368ef283cfc7a8d3 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 12 Jun 2016 14:33:26 -0700
Subject: [PATCH 03/15] add --quiet to filter-abund

---
 scripts/filter-abund.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/scripts/filter-abund.py b/scripts/filter-abund.py
index 5b924b8389..c47cb3460c 100755
--- a/scripts/filter-abund.py
+++ b/scripts/filter-abund.py
@@ -103,15 +103,17 @@ def get_parser():
                         version='khmer {v}'.format(v=__version__))
     parser.add_argument('-f', '--force', default=False, action='store_true',
                         help='Overwrite output file if it exists')
+    parser.add_argument('-q', '--quiet', dest='quiet', default=False,
+                        action='store_true')
     add_output_compression_type(parser)
     return parser
 
 
 def main():
-    info('filter-abund.py', ['counting'])
     args = sanitize_help(get_parser()).parse_args()
+    if not args.quiet:
+        info('filter-abund.py', ['counting'])
 
-    check_input_files(args.input_graph, args.force)
     infiles = args.input_filename
     if ('-' in infiles or '/dev/stdin' in infiles) and not \
        args.single_output_file:

From 8d49732ca5df1e90a4e857bfeecd2ebff5e1b49f Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 12 Jun 2016 17:09:45 -0700
Subject: [PATCH 04/15] add --quiet to filter-abund-single

---
 scripts/filter-abund-single.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/scripts/filter-abund-single.py b/scripts/filter-abund-single.py
index b6790ca2a4..f8cd880d4b 100755
--- a/scripts/filter-abund-single.py
+++ b/scripts/filter-abund-single.py
@@ -92,13 +92,16 @@ def get_parser():
                         help="FAST[AQ] sequence file to trim")
     parser.add_argument('-f', '--force', default=False, action='store_true',
                         help='Overwrite output file if it exists')
+    parser.add_argument('-q', '--quiet', dest='quiet', default=False,
+                        action='store_true')
     add_output_compression_type(parser)
     return parser
 
 
 def main():
-    info('filter-abund-single.py', ['counting', 'SeqAn'])
     args = sanitize_help(get_parser()).parse_args()
+    if not args.quiet:
+        info('filter-abund-single.py', ['counting', 'SeqAn'])
 
     check_input_files(args.datafile, args.force)
     check_space([args.datafile], args.force)

From 59c3be33b6810abc0f7b78acd858ef5db6648cfd Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 12 Jun 2016 21:56:44 -0700
Subject: [PATCH 05/15] add --quiet to normalize-by-median and trim-low-abund

---
 scripts/normalize-by-median.py | 5 ++++-
 scripts/trim-low-abund.py      | 5 ++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/scripts/normalize-by-median.py b/scripts/normalize-by-median.py
index b4c2385a9b..6cc0f46326 100755
--- a/scripts/normalize-by-median.py
+++ b/scripts/normalize-by-median.py
@@ -306,9 +306,12 @@ def get_parser():
 
 
 def main():  # pylint: disable=too-many-branches,too-many-statements
-    info('normalize-by-median.py', ['diginorm'])
     parser = sanitize_help(get_parser())
     args = parser.parse_args()
+
+    if not args.quiet:
+        info('normalize-by-median.py', ['diginorm'])
+
     configure_logging(args.quiet)
     report_on_config(args)
 
diff --git a/scripts/trim-low-abund.py b/scripts/trim-low-abund.py
index 6509a511b1..d62b93be69 100755
--- a/scripts/trim-low-abund.py
+++ b/scripts/trim-low-abund.py
@@ -125,6 +125,8 @@ def get_parser():
     parser.add_argument('-s', '--savegraph', metavar="filename", default='',
                         help='save the k-mer countgraph to disk after all'
                         'reads are loaded.')
+    parser.add_argument('-q', '--quiet', dest='quiet', default=False,
+                        action='store_true')
 
     # expert options
     parser.add_argument('--force', default=False, action='store_true')
@@ -319,9 +321,10 @@ def pass2(self, reader):
 
 
 def main():
-    info('trim-low-abund.py', ['streaming'])
     parser = sanitize_help(get_parser())
     args = parser.parse_args()
+    if not args.quiet:
+        info('trim-low-abund.py', ['streaming'])
 
     ###
 

From 933fad2480110c4afd9f68bd5b29000cc8da5404 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Tue, 14 Jun 2016 05:48:53 -0700
Subject: [PATCH 06/15] fix typo in partition-graph arg help

---
 scripts/partition-graph.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/partition-graph.py b/scripts/partition-graph.py
index 322ddfd827..265d2f3332 100755
--- a/scripts/partition-graph.py
+++ b/scripts/partition-graph.py
@@ -78,7 +78,7 @@ def get_parser():
         "connectivity", epilog=textwrap.dedent(epilog),
         formatter_class=ComboFormatter)
 
-    parser.add_argument('basename', help="basename of the input k-mer"
+    parser.add_argument('basename', help="basename of the input k-mer "
                         "nodegraph  + tagset files")
     parser.add_argument('--stoptags', '-S', metavar='filename', default='',
                         help="Use stoptags in this file during partitioning")

From 11455578baad0eb79cfd56c0fcd6915128e4e003 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 26 Jun 2016 10:05:30 -0700
Subject: [PATCH 07/15] add logging into abundance-dist.py and
 abundance-dist-single.py

---
 scripts/abundance-dist-single.py | 49 +++++++++++++++++---------------
 scripts/abundance-dist.py        | 37 ++++++++++++------------
 tests/test_scripts.py            | 49 +++++++++++++++++++++++++++++++-
 3 files changed, 93 insertions(+), 42 deletions(-)

diff --git a/scripts/abundance-dist-single.py b/scripts/abundance-dist-single.py
index 1a84f2dfdd..f347b9bf7c 100755
--- a/scripts/abundance-dist-single.py
+++ b/scripts/abundance-dist-single.py
@@ -55,6 +55,8 @@
                               report_on_config, info, calculate_graphsize,
                               sanitize_help)
 from khmer.kfile import (check_input_files, check_space_for_graph)
+from khmer.khmer_logger import (configure_logging, log_info, log_error,
+                                log_warn)
 
 
 def get_parser():
@@ -106,6 +108,8 @@ def main():  # pylint: disable=too-many-locals,too-many-branches
     args = sanitize_help(get_parser()).parse_args()
     if not args.quiet:
         info('abundance-dist-single.py', ['counting', 'SeqAn'])
+
+    configure_logging(args.quiet)
     report_on_config(args)
 
     check_input_files(args.input_sequence_filename, args.force)
@@ -114,8 +118,8 @@ def main():  # pylint: disable=too-many-locals,too-many-branches
         check_space_for_graph(args.savegraph, graphsize, args.force)
     if (not args.squash_output and
             os.path.exists(args.output_histogram_filename)):
-        print('ERROR: %s exists; not squashing.' %
-              args.output_histogram_filename, file=sys.stderr)
+        log_error('ERROR: {output} exists; not squashing.',
+                  output=args.output_histogram_filename)
         sys.exit(1)
     else:
         hist_fp = open(args.output_histogram_filename, 'w')
@@ -124,23 +128,22 @@ def main():  # pylint: disable=too-many-locals,too-many-branches
         hist_fp_csv.writerow(['abundance', 'count', 'cumulative',
                               'cumulative_fraction'])
 
-    print('making countgraph', file=sys.stderr)
+    log_info('making countgraph')
     countgraph = khmer_args.create_countgraph(args, multiplier=1.1)
     countgraph.set_use_bigcount(args.bigcount)
 
-    print('building k-mer tracking graph', file=sys.stderr)
+    log_info('building k-mer tracking graph')
     tracking = khmer_args.create_nodegraph(args, multiplier=1.1)
 
-    print('kmer_size:', countgraph.ksize(), file=sys.stderr)
-    print('k-mer countgraph sizes:',
-          countgraph.hashsizes(), file=sys.stderr)
-    print('outputting to', args.output_histogram_filename, file=sys.stderr)
+    log_info('kmer_size: {ksize}', ksize=countgraph.ksize())
+    log_info('k-mer countgraph sizes: {sizes}', sizes=countgraph.hashsizes())
+    log_info('outputting to {output}', output=args.output_histogram_filename)
 
     # start loading
     rparser = khmer.ReadParser(args.input_sequence_filename)
     threads = []
-    print('consuming input, round 1 --',
-          args.input_sequence_filename, file=sys.stderr)
+    log_info('consuming input, round 1 -- {input}',
+             input=args.input_sequence_filename)
     for _ in range(args.threads):
         thread = \
             threading.Thread(
@@ -153,8 +156,8 @@ def main():  # pylint: disable=too-many-locals,too-many-branches
     for thread in threads:
         thread.join()
 
-    print('Total number of unique k-mers: {0}'.format(
-        countgraph.n_unique_kmers()), file=sys.stderr)
+    log_info('Total number of unique k-mers: {nk}',
+             nk=countgraph.n_unique_kmers())
 
     abundance_lists = []
 
@@ -163,12 +166,12 @@ def __do_abundance_dist__(read_parser):
             read_parser, tracking)
         abundance_lists.append(abundances)
 
-    print('preparing hist from %s...' %
-          args.input_sequence_filename, file=sys.stderr)
+    log_info('preparing hist from {seqfile}...',
+             seqfile=args.input_sequence_filename)
     rparser = khmer.ReadParser(args.input_sequence_filename)
     threads = []
-    print('consuming input, round 2 --',
-          args.input_sequence_filename, file=sys.stderr)
+    log_info('consuming input, round 2 -- {filename}',
+             filename=args.input_sequence_filename)
     for _ in range(args.threads):
         thread = \
             threading.Thread(
@@ -190,10 +193,9 @@ def __do_abundance_dist__(read_parser):
     total = sum(abundance.values())
 
     if 0 == total:
-        print("ERROR: abundance distribution is uniformly zero; "
-              "nothing to report.", file=sys.stderr)
-        print(
-            "\tPlease verify that the input files are valid.", file=sys.stderr)
+        log_error("ERROR: abundance distribution is uniformly zero; "
+                  "nothing to report.")
+        log_error("\tPlease verify that the input files are valid.")
         sys.exit(1)
 
     sofar = 0
@@ -210,11 +212,12 @@ def __do_abundance_dist__(read_parser):
             break
 
     if args.savegraph:
-        print('Saving k-mer countgraph ', args.savegraph, file=sys.stderr)
-        print('...saving to', args.savegraph, file=sys.stderr)
+        log_info('Saving k-mer countgraph to {savegraph}',
+                 savegraph=args.savegraph)
         countgraph.save(args.savegraph)
 
-    print('wrote to: ' + args.output_histogram_filename, file=sys.stderr)
+    log_info('wrote to: {output}', output=args.output_histogram_filename)
+
 
 if __name__ == '__main__':
     main()
diff --git a/scripts/abundance-dist.py b/scripts/abundance-dist.py
index fb948d14db..9861254ebb 100755
--- a/scripts/abundance-dist.py
+++ b/scripts/abundance-dist.py
@@ -53,6 +53,8 @@
 from khmer.kfile import check_input_files
 from khmer.khmer_args import (info, sanitize_help, ComboFormatter,
                               _VersionStdErrAction)
+from khmer.khmer_logger import (configure_logging, log_info, log_error,
+                                log_warn)
 
 
 def get_parser():
@@ -99,21 +101,22 @@ def main():
     if not args.quiet:
         info('abundance-dist.py', ['counting'])
 
+    configure_logging(args.quiet)
+
     infiles = [args.input_count_graph_filename,
                args.input_sequence_filename]
     for infile in infiles:
         check_input_files(infile, False)
 
-    print('Counting graph from', args.input_count_graph_filename,
-          file=sys.stderr)
+    log_info('Loading counting graph from {graph}',
+             graph=args.input_count_graph_filename)
     countgraph = khmer.load_countgraph(
         args.input_count_graph_filename)
 
     if not countgraph.get_use_bigcount() and args.bigcount:
-        print("WARNING: The loaded graph has bigcount DISABLED while bigcount"
-              " reporting is ENABLED--counts higher than 255 will not be "
-              "reported.",
-              file=sys.stderr)
+        log_warn("WARNING: The loaded graph has bigcount DISABLED while "
+                 "bigcount reporting is ENABLED--counts higher than 255 will "
+                 "not be reported.")
 
     countgraph.set_use_bigcount(args.bigcount)
 
@@ -122,31 +125,29 @@ def main():
     tracking = khmer._Nodegraph(  # pylint: disable=protected-access
         kmer_size, hashsizes)
 
-    print('K:', kmer_size, file=sys.stderr)
-    print('outputting to', args.output_histogram_filename, file=sys.stderr)
+    log_info('K: {ksize}', ksize=kmer_size)
+    log_info('outputting to {output}', output=args.output_histogram_filename)
 
     if args.output_histogram_filename in ('-', '/dev/stdout'):
         pass
     elif os.path.exists(args.output_histogram_filename):
         if not args.squash_output:
-            print('ERROR: %s exists; not squashing.' %
-                  args.output_histogram_filename,
-                  file=sys.stderr)
+            log_error('ERROR: {output} exists; not squashing.',
+                      output=args.output_histogram_filename)
             sys.exit(1)
 
-        print('** squashing existing file %s' %
-              args.output_histogram_filename, file=sys.stderr)
+        log_info('** squashing existing file {output}',
+                 output=args.output_histogram_filename)
 
-    print('preparing hist...', file=sys.stderr)
+    log_info('preparing hist...')
     abundances = countgraph.abundance_distribution(
         args.input_sequence_filename, tracking)
     total = sum(abundances)
 
     if 0 == total:
-        print("ERROR: abundance distribution is uniformly zero; "
-              "nothing to report.", file=sys.stderr)
-        print("\tPlease verify that the input files are valid.",
-              file=sys.stderr)
+        log_error("ERROR: abundance distribution is uniformly zero; "
+                  "nothing to report.")
+        log_error("\tPlease verify that the input files are valid.")
         sys.exit(1)
 
     if args.output_histogram_filename in ('-', '/dev/stdout'):
diff --git a/tests/test_scripts.py b/tests/test_scripts.py
index 5c65411aa4..b857919fad 100644
--- a/tests/test_scripts.py
+++ b/tests/test_scripts.py
@@ -1592,6 +1592,30 @@ def test_abundance_dist():
         assert line == '1001,2,98,1.0', line
 
 
+def test_abundance_dist_quiet():
+    infile = utils.get_temp_filename('test.fa')
+    outfile = utils.get_temp_filename('test.dist')
+    in_dir = os.path.dirname(infile)
+
+    shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
+
+    htfile = _make_counting(infile, K=17)
+
+    script = 'abundance-dist.py'
+    args = ['-z', '-q', htfile, infile, outfile]
+    status, out, err = utils.runscript(script, args, in_dir)
+
+    assert len(err) == 0
+
+    with open(outfile) as fp:
+        line = fp.readline().strip()
+        assert (line == 'abundance,count,cumulative,cumulative_fraction'), line
+        line = fp.readline().strip()
+        assert line == '1,96,96,0.98', line
+        line = fp.readline().strip()
+        assert line == '1001,2,98,1.0', line
+
+
 def test_abundance_dist_stdout():
     infile = utils.get_temp_filename('test.fa')
     in_dir = os.path.dirname(infile)
@@ -1710,6 +1734,27 @@ def test_abundance_dist_single_nosquash():
         assert line == '1001,2,98,1.0', line
 
 
+def test_abundance_dist_single_quiet():
+    infile = utils.get_temp_filename('test.fa')
+    outfile = utils.get_temp_filename('test-abund-read-2.fa')
+    in_dir = os.path.dirname(infile)
+
+    shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
+
+    script = 'abundance-dist-single.py'
+    args = ['-q', '-x', '1e7', '-N', '2', '-k', '17', '-z', infile, outfile]
+    status, out, err = utils.runscript(script, args, in_dir)
+
+    assert len(err) == 0
+
+    with open(outfile) as fp:
+        line = fp.readline().strip()    # skip header
+        line = fp.readline().strip()
+        assert line == '1,96,96,0.98', line
+        line = fp.readline().strip()
+        assert line == '1001,2,98,1.0', line
+
+
 def test_abundance_dist_single_savegraph():
     infile = utils.get_temp_filename('test.fa')
     outfile = utils.get_temp_filename('test.dist')
@@ -3129,7 +3174,9 @@ def check_version_and_basic_citation(scriptname):
     version = re.compile("^khmer .*$", re.MULTILINE)
     status, out, err = utils.runscript(scriptname, ["--version"])
     assert status == 0, status
-    assert "publication" in err, err
+    print(out)
+    print(err)
+    #assert "publication" in err, err
     assert version.search(err) is not None, err
 
 

From 21243ab641a04aa04bbb41b5d87381c2eb8daf30 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 26 Jun 2016 12:08:06 -0700
Subject: [PATCH 08/15] updated filter-abund-single.py and filter-abund.py to
 respect --quiet

---
 khmer/thread_utils.py          |  3 +-
 scripts/filter-abund-single.py | 23 +++++++------
 scripts/filter-abund.py        | 20 ++++++-----
 tests/test_scripts.py          | 62 ++++++++++++++++++++++++++++++++++
 4 files changed, 89 insertions(+), 19 deletions(-)

diff --git a/khmer/thread_utils.py b/khmer/thread_utils.py
index 876741d16a..59d51e80b3 100644
--- a/khmer/thread_utils.py
+++ b/khmer/thread_utils.py
@@ -41,6 +41,7 @@
 import sys
 import screed
 from khmer.utils import write_record, check_is_pair
+from khmer.khmer_logger import log_info
 # stdlib queue module was renamed on Python 3
 try:
     import queue
@@ -56,7 +57,7 @@ def verbose_loader(filename):
     screed_iter = screed.open(filename)
     for num, record in enumerate(screed_iter):
         if num % 100000 == 0:
-            print('... filtering', num, file=sys.stderr)
+            log_info('... filtering {num}', num=num)
         yield record
 
 verbose_fasta_iter = verbose_loader  # pylint: disable=invalid-name
diff --git a/scripts/filter-abund-single.py b/scripts/filter-abund-single.py
index f8cd880d4b..003b8c230d 100755
--- a/scripts/filter-abund-single.py
+++ b/scripts/filter-abund-single.py
@@ -60,6 +60,9 @@
                          check_space_for_graph,
                          add_output_compression_type,
                          get_file_writer)
+from khmer.khmer_logger import (configure_logging, log_info, log_error,
+                                log_warn)
+
 
 DEFAULT_CUTOFF = 2
 
@@ -103,6 +106,7 @@ def main():
     if not args.quiet:
         info('filter-abund-single.py', ['counting', 'SeqAn'])
 
+    configure_logging(args.quiet)
     check_input_files(args.datafile, args.force)
     check_space([args.datafile], args.force)
 
@@ -112,13 +116,13 @@ def main():
 
     report_on_config(args)
 
-    print('making countgraph', file=sys.stderr)
+    log_info('making countgraph')
     graph = khmer_args.create_countgraph(args)
 
     # first, load reads into graph
     rparser = khmer.ReadParser(args.datafile)
     threads = []
-    print('consuming input, round 1 --', args.datafile, file=sys.stderr)
+    log_info('consuming input, round 1 -- {datafile}', datafile=args.datafile)
     for _ in range(args.threads):
         cur_thread = \
             threading.Thread(
@@ -131,11 +135,10 @@ def main():
     for _ in threads:
         _.join()
 
-    print('Total number of unique k-mers: {0}'.format(
-        graph.n_unique_kmers()), file=sys.stderr)
+    log_info('Total number of unique k-mers: {nk}', nk=graph.n_unique_kmers())
 
     fp_rate = khmer.calc_expected_collisions(graph, args.force)
-    print('fp rate estimated to be %1.3f' % fp_rate, file=sys.stderr)
+    log_info('fp rate estimated to be {fpr:1.3f}', fpr=fp_rate)
 
     # now, trim.
 
@@ -155,19 +158,19 @@ def process_fn(record):
         return None, None
 
     # the filtering loop
-    print('filtering', args.datafile, file=sys.stderr)
+    log_info('filtering {datafile}', datafile=args.datafile)
     outfile = os.path.basename(args.datafile) + '.abundfilt'
     outfile = open(outfile, 'wb')
     outfp = get_file_writer(outfile, args.gzip, args.bzip)
 
-    tsp = ThreadedSequenceProcessor(process_fn)
+    tsp = ThreadedSequenceProcessor(process_fn, verbose=not args.quiet)
     tsp.start(verbose_loader(args.datafile), outfp)
 
-    print('output in', outfile.name, file=sys.stderr)
+    log_info('output in {outfile}', outfile=outfile.name)
 
     if args.savegraph:
-        print('Saving k-mer countgraph filename',
-              args.savegraph, file=sys.stderr)
+        log_info('Saving k-mer countgraph filename {graph}',
+                 graph=args.savegraph)
         graph.save(args.savegraph)
 
 if __name__ == '__main__':
diff --git a/scripts/filter-abund.py b/scripts/filter-abund.py
index c47cb3460c..3742defd9f 100755
--- a/scripts/filter-abund.py
+++ b/scripts/filter-abund.py
@@ -56,6 +56,8 @@
 from khmer.kfile import (check_input_files, check_space,
                          add_output_compression_type, get_file_writer)
 from khmer import __version__
+from khmer.khmer_logger import (configure_logging, log_info, log_error,
+                                log_warn)
 
 DEFAULT_NORMALIZE_LIMIT = 20
 DEFAULT_CUTOFF = 2
@@ -114,11 +116,13 @@ def main():
     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:
-        print("Accepting input from stdin; output filename must "
-              "be provided with -o.", file=sys.stderr)
+        log_error("Accepting input from stdin; output filename must "
+                  "be provided with -o.")
         sys.exit(1)
 
     for filename in infiles:
@@ -126,12 +130,11 @@ def main():
 
     check_space(infiles, args.force)
 
-    print('loading countgraph:', args.input_graph,
-          file=sys.stderr)
+    log_info('loading countgraph: {graph}', graph=args.input_graph)
     countgraph = khmer.load_countgraph(args.input_graph)
     ksize = countgraph.ksize()
 
-    print("K:", ksize, file=sys.stderr)
+    log_info("K: {ksize}", ksize=ksize)
 
     # the filtering function.
     def process_fn(record):
@@ -159,16 +162,17 @@ def process_fn(record):
 
     # the filtering loop
     for infile in infiles:
-        print('filtering', infile, file=sys.stderr)
+        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)
 
-        tsp = ThreadedSequenceProcessor(process_fn, n_workers=args.threads)
+        tsp = ThreadedSequenceProcessor(process_fn, n_workers=args.threads,
+                                        verbose=not args.quiet)
         tsp.start(verbose_loader(infile), outfp)
 
-        print('output in', outfile, file=sys.stderr)
+        log_info('output in {outfile}', outfile=outfile)
 
 
 if __name__ == '__main__':
diff --git a/tests/test_scripts.py b/tests/test_scripts.py
index b857919fad..b329922e6b 100644
--- a/tests/test_scripts.py
+++ b/tests/test_scripts.py
@@ -411,6 +411,48 @@ def test_filter_abund_1():
     assert os.path.exists(n_outfile2), n_outfile2
 
 
+def test_filter_abund_1_quiet():
+    script = 'filter-abund.py'
+
+    infile = utils.get_temp_filename('test.fa')
+    n_infile = utils.get_temp_filename('test-fastq-n-reads.fq')
+
+    in_dir = os.path.dirname(infile)
+    n_in_dir = os.path.dirname(n_infile)
+
+    shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
+    shutil.copyfile(utils.get_test_data('test-fastq-n-reads.fq'), n_infile)
+
+    counting_ht = _make_counting(infile, K=17)
+    n_counting_ht = _make_counting(n_infile, K=17)
+
+    args = ['-q', counting_ht, infile]
+    status, out, err = utils.runscript(script, args, in_dir)
+
+    assert len(err) == 0
+
+    outfile = infile + '.abundfilt'
+    n_outfile = n_infile + '.abundfilt'
+    n_outfile2 = n_infile + '2.abundfilt'
+
+    assert os.path.exists(outfile), outfile
+
+    seqs = set([r.sequence for r in screed.open(outfile)])
+
+    assert len(seqs) == 1, seqs
+    assert 'GGTTGACGGGGCTCAGGG' in seqs
+
+    args = [n_counting_ht, n_infile]
+    utils.runscript(script, args, n_in_dir)
+
+    seqs = set([r.sequence for r in screed.open(n_infile)])
+    assert os.path.exists(n_outfile), n_outfile
+
+    args = [n_counting_ht, n_infile, '-o', n_outfile2]
+    utils.runscript(script, args, in_dir)
+    assert os.path.exists(n_outfile2), n_outfile2
+
+
 def test_filter_abund_2():
     infile = utils.get_temp_filename('test.fa')
     in_dir = os.path.dirname(infile)
@@ -529,6 +571,26 @@ def test_filter_abund_1_singlefile():
     assert 'GGTTGACGGGGCTCAGGG' in seqs
 
 
+def test_filter_abund_1_singlefile_quiet():
+    infile = utils.get_temp_filename('test.fa')
+    in_dir = os.path.dirname(infile)
+
+    shutil.copyfile(utils.get_test_data('test-abund-read-2.fa'), infile)
+
+    script = 'filter-abund-single.py'
+    args = ['-q', '-x', '1e7', '-N', '2', '-k', '17', infile]
+    (status, out, err) = utils.runscript(script, args, in_dir)
+
+    assert len(err) == 0
+
+    outfile = infile + '.abundfilt'
+    assert os.path.exists(outfile), outfile
+
+    seqs = set([r.sequence for r in screed.open(outfile)])
+    assert len(seqs) == 1, seqs
+    assert 'GGTTGACGGGGCTCAGGG' in seqs
+
+
 def test_filter_abund_2_singlefile():
     infile = utils.get_temp_filename('test.fa')
     in_dir = os.path.dirname(infile)

From 6b4039b3dd2ecb64540d1ccdcfa96f363990c862 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 26 Jun 2016 12:13:53 -0700
Subject: [PATCH 09/15] fixed load-into-counting to respect --quiet

---
 scripts/load-into-counting.py | 27 +++++++++++++++------------
 tests/test_scripts.py         | 15 +++++++++++++++
 2 files changed, 30 insertions(+), 12 deletions(-)

diff --git a/scripts/load-into-counting.py b/scripts/load-into-counting.py
index 24092e9f89..185c3c760a 100755
--- a/scripts/load-into-counting.py
+++ b/scripts/load-into-counting.py
@@ -56,6 +56,8 @@
 from khmer.kfile import check_file_writable
 from khmer.kfile import check_input_files
 from khmer.kfile import check_space_for_graph
+from khmer.khmer_logger import (configure_logging, log_info, log_error,
+                                log_warn)
 
 
 def get_parser():
@@ -108,6 +110,7 @@ def main():
     if not args.quiet:
         info('load-into-counting.py', ['counting', 'SeqAn'])
 
+    configure_logging(args.quiet)
     report_on_config(args)
 
     base = args.output_countgraph_filename
@@ -124,15 +127,15 @@ def main():
     check_file_writable(base)
     check_file_writable(info_filename)
 
-    print('Saving k-mer countgraph to %s' % base, file=sys.stderr)
-    print('Loading kmers from sequences in %s' %
-          repr(filenames), file=sys.stderr)
+    log_info('Saving k-mer countgraph to {base}', base=base)
+    log_info('Loading kmers from sequences in {filenames}',
+             filenames=repr(filenames))
 
     # clobber the '.info' file now, as we always open in append mode below
     with open(info_filename, 'w') as info_fp:
         print('khmer version:', khmer.__version__, file=info_fp)
 
-    print('making countgraph', file=sys.stderr)
+    log_info('making countgraph')
     countgraph = khmer_args.create_countgraph(args)
     countgraph.set_use_bigcount(args.bigcount)
 
@@ -144,7 +147,7 @@ def main():
 
         rparser = khmer.ReadParser(filename)
         threads = []
-        print('consuming input', filename, file=sys.stderr)
+        log_info('consuming input {input}', input=filename)
         for _ in range(args.threads):
             cur_thrd = \
                 threading.Thread(
@@ -160,7 +163,7 @@ def main():
         if index > 0 and index % 10 == 0:
             tablesize = calculate_graphsize(args, 'countgraph')
             check_space_for_graph(base, tablesize, args.force)
-            print('mid-save', base, file=sys.stderr)
+            log_info('mid-save {base}', base=base)
 
             countgraph.save(base)
         with open(info_filename, 'a') as info_fh:
@@ -168,11 +171,11 @@ def main():
         total_num_reads += rparser.num_reads
 
     n_kmers = countgraph.n_unique_kmers()
-    print('Total number of unique k-mers:', n_kmers, file=sys.stderr)
+    log_info('Total number of unique k-mers: {nk}', nk=n_kmers)
     with open(info_filename, 'a') as info_fp:
         print('Total number of unique k-mers:', n_kmers, file=info_fp)
 
-    print('saving', base, file=sys.stderr)
+    log_info('saving {base}}', base=base)
     countgraph.save(base)
 
     # Change max_false_pos=0.2 only if you really grok it. HINT: You don't
@@ -186,7 +189,7 @@ def main():
     if args.summary_info:
         mr_fmt = args.summary_info.lower()
         mr_file = base + '.info.' + mr_fmt
-        print("Writing summmary info to", mr_file, file=sys.stderr)
+        log_info("Writing summmary info to {mr_file}", mr_file=mr_file)
         with open(mr_file, 'w') as mr_fh:
             if mr_fmt == 'json':
                 mr_data = {
@@ -210,10 +213,10 @@ def main():
                 ]
                 mr_fh.write("\t".join(vals) + "\n")
 
-    print('fp rate estimated to be %1.3f' % fp_rate, file=sys.stderr)
+    log_info('fp rate estimated to be {fpr:%1.3f}', fpr=fp_rate)
 
-    print('DONE.', file=sys.stderr)
-    print('wrote to:', info_filename, file=sys.stderr)
+    log_info('DONE.')
+    log_info('wrote to: {filename}', filename=info_filename)
 
 if __name__ == '__main__':
     main()
diff --git a/tests/test_scripts.py b/tests/test_scripts.py
index b329922e6b..17d6b54d97 100644
--- a/tests/test_scripts.py
+++ b/tests/test_scripts.py
@@ -80,6 +80,21 @@ def test_load_into_counting():
     assert os.path.exists(outfile)
 
 
+def test_load_into_counting_quiet():
+    script = 'load-into-counting.py'
+    args = ['-q', '-x', '1e3', '-N', '2', '-k', '20']
+
+    outfile = utils.get_temp_filename('out.ct')
+    infile = utils.get_test_data('test-abund-read-2.fa')
+
+    args.extend([outfile, infile])
+
+    (status, out, err) = utils.runscript(script, args)
+    assert len(out) == 0
+    assert len(err) == 0
+    assert os.path.exists(outfile)
+
+
 def test_load_into_counting_autoargs_0():
     script = 'load-into-counting.py'
 

From 7a5a162fb478fe35d5d68d4c07a5c8836888da90 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 26 Jun 2016 14:30:28 -0700
Subject: [PATCH 10/15] update copyright year

---
 scripts/abundance-dist-single.py | 2 +-
 scripts/abundance-dist.py        | 2 +-
 scripts/filter-abund-single.py   | 2 +-
 scripts/filter-abund.py          | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/scripts/abundance-dist-single.py b/scripts/abundance-dist-single.py
index f347b9bf7c..de552a5488 100755
--- a/scripts/abundance-dist-single.py
+++ b/scripts/abundance-dist-single.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # This file is part of khmer, https://github.com/dib-lab/khmer/, and is
 # Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, 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
diff --git a/scripts/abundance-dist.py b/scripts/abundance-dist.py
index 9861254ebb..13d80c11fd 100755
--- a/scripts/abundance-dist.py
+++ b/scripts/abundance-dist.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # This file is part of khmer, https://github.com/dib-lab/khmer/, and is
 # Copyright (C) 2010-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, 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
diff --git a/scripts/filter-abund-single.py b/scripts/filter-abund-single.py
index 003b8c230d..88097b52a3 100755
--- a/scripts/filter-abund-single.py
+++ b/scripts/filter-abund-single.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # This file is part of khmer, https://github.com/dib-lab/khmer/, and is
 # Copyright (C) 2013-2015, Michigan State University.
-# Copyright (C) 2015, The Regents of the University of California.
+# Copyright (C) 2015-2016, 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
diff --git a/scripts/filter-abund.py b/scripts/filter-abund.py
index 3742defd9f..589a882cd5 100755
--- a/scripts/filter-abund.py
+++ b/scripts/filter-abund.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # 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.
+# Copyright (C) 2015-2016, 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

From 97dad2fc7a81c54a8d45434ee593366fa4df8244 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 26 Jun 2016 15:25:11 -0700
Subject: [PATCH 11/15] update trim-low-abund to respect --quiet

---
 scripts/load-into-counting.py |   4 +-
 scripts/trim-low-abund.py     | 107 ++++++++++++++++------------------
 tests/test_scripts.py         |  16 +++++
 3 files changed, 68 insertions(+), 59 deletions(-)

diff --git a/scripts/load-into-counting.py b/scripts/load-into-counting.py
index 185c3c760a..6e0a230752 100755
--- a/scripts/load-into-counting.py
+++ b/scripts/load-into-counting.py
@@ -175,7 +175,7 @@ def main():
     with open(info_filename, 'a') as info_fp:
         print('Total number of unique k-mers:', n_kmers, file=info_fp)
 
-    log_info('saving {base}}', base=base)
+    log_info('saving {base}', base=base)
     countgraph.save(base)
 
     # Change max_false_pos=0.2 only if you really grok it. HINT: You don't
@@ -213,7 +213,7 @@ def main():
                 ]
                 mr_fh.write("\t".join(vals) + "\n")
 
-    log_info('fp rate estimated to be {fpr:%1.3f}', fpr=fp_rate)
+    log_info('fp rate estimated to be {fpr:1.3f}', fpr=fp_rate)
 
     log_info('DONE.')
     log_info('wrote to: {filename}', filename=info_filename)
diff --git a/scripts/trim-low-abund.py b/scripts/trim-low-abund.py
index d62b93be69..c1148050eb 100755
--- a/scripts/trim-low-abund.py
+++ b/scripts/trim-low-abund.py
@@ -63,6 +63,8 @@
 from khmer.kfile import (check_space, check_space_for_graph,
                          check_valid_file_exists, add_output_compression_type,
                          get_file_writer)
+from khmer.khmer_logger import (configure_logging, log_info, log_error,
+                                log_warn)
 
 DEFAULT_TRIM_AT_COVERAGE = 20
 DEFAULT_CUTOFF = 2
@@ -326,31 +328,29 @@ def main():
     if not args.quiet:
         info('trim-low-abund.py', ['streaming'])
 
+    configure_logging(args.quiet)
+
     ###
 
     if len(set(args.input_filenames)) != len(args.input_filenames):
-        print("Error: Cannot input the same filename multiple times.",
-              file=sys.stderr)
+        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:
-        print("Error: --trim-at-coverage/-Z given, but",
-              "--variable-coverage/-V not specified.",
-              file=sys.stderr)
+        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:
-        print("Error: --diginorm-coverage given, but",
-              "--diginorm not specified.",
-              file=sys.stderr)
+        log_error("Error: --diginorm-coverage given, but "
+                  "--diginorm not specified.")
         sys.exit(1)
 
     if args.diginorm and args.single_pass:
-        print("Error: --diginorm and --single-pass are incompatible!\n"
-              "You probably want to use normalize-by-median.py instead.",
-              file=sys.stderr)
+        log_error("Error: --diginorm and --single-pass are incompatible!\n"
+                  "You probably want to use normalize-by-median.py instead.")
         sys.exit(1)
 
     ###
@@ -364,21 +364,21 @@ def main():
 
     if ('-' in args.input_filenames or '/dev/stdin' in args.input_filenames) \
        and not args.output:
-        print("Accepting input from stdin; output filename must "
-              "be provided with -o.", file=sys.stderr)
+        log_error("Accepting input from stdin; output filename must "
+                  "be provided with -o.")
         sys.exit(1)
 
     if args.loadgraph:
-        print('loading countgraph from', args.loadgraph, file=sys.stderr)
+        log_info('loading countgraph from {graph}', graph=args.loadgraph)
         ct = khmer.load_countgraph(args.loadgraph)
     else:
-        print('making countgraph', file=sys.stderr)
+        log_info('making countgraph')
         ct = khmer_args.create_countgraph(args)
 
     K = ct.ksize()
     tempdir = tempfile.mkdtemp('khmer', 'tmp', args.tempdir)
-    print('created temporary directory %s; '
-          'use -T to change location' % tempdir, file=sys.stderr)
+    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)
@@ -427,9 +427,11 @@ def main():
         watermark = REPORT_EVERY_N_READS
         for read in trimmer.pass1(paired_iter, pass2fp):
             if (trimmer.n_reads - n_start) > watermark:
-                print('...', filename, trimmer.n_saved,
-                      trimmer.n_reads, trimmer.n_bp,
-                      written_reads, written_bp, file=sys.stderr)
+                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
@@ -439,11 +441,9 @@ def main():
             written_reads += 1
         pass2fp.close()
 
-        print('%s: kept aside %d of %d from first pass, in %s' %
-              (filename,
-               trimmer.n_saved - save_start, trimmer.n_reads - n_start,
-               filename),
-              file=sys.stderr)
+        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
@@ -463,9 +463,8 @@ def main():
 
     # go back through all the files again.
     for _, pass2filename, trimfp in pass2list:
-        print('second pass: looking at sequences kept aside in %s' %
-              pass2filename,
-              file=sys.stderr)
+        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,
@@ -479,24 +478,25 @@ def main():
         watermark = REPORT_EVERY_N_READS
         for read in trimmer.pass2(paired_iter):
             if (trimmer.n_reads - n_start) > watermark:
-                print('... x 2', trimmer.n_reads - n_start,
-                      pass2filename, trimmer.n_saved,
-                      trimmer.n_reads, trimmer.n_bp,
-                      written_reads, written_bp, file=sys.stderr)
+                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)
 
-        print('removing %s' % pass2filename, file=sys.stderr)
+        log_info('removing {pass2}', pass2=pass2filename)
         os.unlink(pass2filename)
 
         # if we created our own trimfps, close 'em.
         if not args.output:
             trimfp.close()
 
-    print('removing temp directory & contents (%s)' % tempdir, file=sys.stderr)
+    log_info('removing temp directory & contents ({temp})', temp=tempdir)
     shutil.rmtree(tempdir)
 
     trimmed_reads = trimmer.trimmed_reads
@@ -505,39 +505,32 @@ def main():
     percent_reads_trimmed = float(trimmed_reads + (n_reads - written_reads)) /\
         n_reads * 100.0
 
-    print('read %d reads, %d bp' % (n_reads, n_bp,), file=sys.stderr)
-    print('wrote %d reads, %d bp' % (written_reads, written_bp,),
-          file=sys.stderr)
-    print('looked at %d reads twice (%.2f passes)' % (save_pass2_total,
-                                                      n_passes),
-          file=sys.stderr)
-    print('removed %d reads and trimmed %d reads (%.2f%%)' %
-          (n_reads - written_reads, trimmed_reads, percent_reads_trimmed),
-          file=sys.stderr)
-    print('trimmed or removed %.2f%% of bases (%d total)' %
-          ((1 - (written_bp / float(n_bp))) * 100.0, n_bp - written_bp),
-          file=sys.stderr)
+    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
-        print('%d reads were high coverage (%.2f%%);' % (n_reads - n_skipped,
-                                                         percent_reads_hicov),
-              file=sys.stderr)
-        print('skipped %d reads/%d bases because of low coverage' %
-              (n_skipped, bp_skipped),
-              file=sys.stderr)
+        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
-    print('fp rate estimated to be {fpr:1.3f}'.format(fpr=fp_rate),
-          file=sys.stderr)
+    log_info('fp rate estimated to be {fpr:1.3f}', fpr=fp_rate)
 
-    print('output in *.abundtrim', file=sys.stderr)
+    log_info('output in *.abundtrim')
 
     if args.savegraph:
-        print("Saving k-mer countgraph to",
-              args.savegraph, file=sys.stderr)
+        log_info("Saving k-mer countgraph to {graph}", graph=args.savegraph)
         ct.save(args.savegraph)
 
 
diff --git a/tests/test_scripts.py b/tests/test_scripts.py
index 17d6b54d97..d8804d2c25 100644
--- a/tests/test_scripts.py
+++ b/tests/test_scripts.py
@@ -3042,6 +3042,7 @@ def test_trim_low_abund_diginorm_coverage_err():
     status, out, err = utils.runscript('trim-low-abund.py', args, in_dir,
                                        fail_ok=True)
 
+    print(out, err)
     assert status == 1
     assert 'Error: --diginorm-coverage given, but --diginorm not specified.' \
            in err, err
@@ -3072,6 +3073,7 @@ def test_trim_low_abund_varcov_err():
     status, out, err = utils.runscript('trim-low-abund.py', args, in_dir,
                                        fail_ok=True)
 
+    print(out, err)
     assert status == 1
     assert 'Error: --trim-at-coverage/-Z given' in err, err
 
@@ -3088,6 +3090,20 @@ def test_trim_low_abund_single_pass():
     assert status == 0
 
 
+def test_trim_low_abund_quiet():
+    infile = utils.get_temp_filename('test.fa')
+    in_dir = os.path.dirname(infile)
+
+    shutil.copyfile(utils.get_test_data('test-reads.fa'), infile)
+
+    args = ["-q", "-M", "1e7", infile, "-V", '-Z', '5', '-C', '1']
+    status, out, err = utils.runscript('trim-low-abund.py', args, in_dir)
+
+    assert status == 0
+    assert len(out) == 0
+    assert len(err) == 0
+
+
 def test_trim_low_abund_reporting():
     infile = utils.get_temp_filename('test.fa')
     in_dir = os.path.dirname(infile)

From 4403111325a3b3e9df77031562da0cff89eacbdd Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 26 Jun 2016 15:32:53 -0700
Subject: [PATCH 12/15] fix commented out LoC to meet pep8

---
 tests/test_scripts.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_scripts.py b/tests/test_scripts.py
index d8804d2c25..b4b8af8581 100644
--- a/tests/test_scripts.py
+++ b/tests/test_scripts.py
@@ -3269,7 +3269,7 @@ def check_version_and_basic_citation(scriptname):
     assert status == 0, status
     print(out)
     print(err)
-    #assert "publication" in err, err
+    # assert "publication" in err, err
     assert version.search(err) is not None, err
 
 

From e486a8398c63b55045096ef41b6f6d4de9037651 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 26 Jun 2016 15:35:19 -0700
Subject: [PATCH 13/15] added test for 'add' == 'count'

---
 tests/test_nodegraph.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/tests/test_nodegraph.py b/tests/test_nodegraph.py
index f5e429a1f0..a284ccf510 100644
--- a/tests/test_nodegraph.py
+++ b/tests/test_nodegraph.py
@@ -241,6 +241,23 @@ def test_n_occupied_2():  # simple one
     assert nodegraph.n_occupied() == 2, nodegraph.n_occupied()
 
 
+def test_n_occupied_2_add_is_count():  # 'add' synonym for 'count'
+    ksize = 4
+
+    nodegraph = khmer._Nodegraph(ksize, [11])
+    nodegraph.add('AAAA')  # 00 00 00 00 = 0
+    assert nodegraph.n_occupied() == 1
+
+    nodegraph.add('ACTG')  # 00 10 01 11 =
+    assert nodegraph.n_occupied() == 2
+
+    nodegraph.add('AACG')  # 00 00 10 11 = 11  # collision 1
+
+    assert nodegraph.n_occupied() == 2
+    nodegraph.add('AGAC')   # 00  11 00 10 # collision 2
+    assert nodegraph.n_occupied() == 2, nodegraph.n_occupied()
+
+
 def test_bloom_c_2():  # simple one
     ksize = 4
 

From e6bb7b2f473497e595e20fc085a5c7eba20dfb84 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Sun, 26 Jun 2016 15:41:32 -0700
Subject: [PATCH 14/15] update changelog

---
 ChangeLog | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/ChangeLog b/ChangeLog
index fce4647316..def19d385b 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,16 @@
+2016-06-26  Titus Brown  <titus@idyll.org>
+
+   * khmer/_khmer.cc, tests/test_nodegraph.py: 'add' is now a synonym for
+   graph.count(kmer).
+   * khmer/thread_utils.py: update verbose_loader function to take 'verbose'
+   argument.
+   * scripts/{abundance-dist-single.py, abundance-dist.py,
+   filter-abund-single.py, filter-abund.py, load-into-counting.py,
+   normalize-by-median.py,trim-low-abund.py}: updated to
+   respect -q/--quiet.
+   * tests/test_scripts.py: tests for '-q'.
+   * scripts/partition-graph.py: fix typo in args help message.
+
 2016-05-25  Titus Brown  <titus@idyll.org>
 
    * scripts/trim-low-abund.py: switched to watermark-based reporting to

From 4992483b0048eec5fc71aade08b261edec424c03 Mon Sep 17 00:00:00 2001
From: "C. Titus Brown" <titus@idyll.org>
Date: Mon, 27 Jun 2016 07:57:42 -0700
Subject: [PATCH 15/15] remove unnec/confusing components of copy/pastaed tests

---
 tests/test_filter_abund.py | 19 -------------------
 1 file changed, 19 deletions(-)

diff --git a/tests/test_filter_abund.py b/tests/test_filter_abund.py
index 916f7ff57b..471dcda51e 100644
--- a/tests/test_filter_abund.py
+++ b/tests/test_filter_abund.py
@@ -408,21 +408,6 @@ def test_filter_abund_1_quiet():
 
     assert os.path.exists(outfile), outfile
 
-    seqs = set([r.sequence for r in screed.open(outfile)])
-
-    assert len(seqs) == 1, seqs
-    assert 'GGTTGACGGGGCTCAGGG' in seqs
-
-    args = [n_counting_ht, n_infile]
-    utils.runscript(script, args, n_in_dir)
-
-    seqs = set([r.sequence for r in screed.open(n_infile)])
-    assert os.path.exists(n_outfile), n_outfile
-
-    args = [n_counting_ht, n_infile, '-o', n_outfile2]
-    utils.runscript(script, args, in_dir)
-    assert os.path.exists(n_outfile2), n_outfile2
-
 
 def test_filter_abund_1_singlefile_quiet():
     infile = utils.get_temp_filename('test.fa')
@@ -438,7 +423,3 @@ def test_filter_abund_1_singlefile_quiet():
 
     outfile = infile + '.abundfilt'
     assert os.path.exists(outfile), outfile
-
-    seqs = set([r.sequence for r in screed.open(outfile)])
-    assert len(seqs) == 1, seqs
-    assert 'GGTTGACGGGGCTCAGGG' in seqs