Merge branch 'kdmurray91-feature/load-into-counting_tsv-output'

ChangeLog

@@ -1,3 +1,8 @@
+2014-12-01  Kevin Murray  <spam@kdmurray.id.au>
+
+    * load-into-counting.py: Add a CLI parameter to output a machine-readable
+    summary of the run, including number of k-mers, FPR, input files etc in
+    json or TSV format.
 
 2014-12-01  Titus Brown  <t@idyll.org>
 

scripts/load-into-counting.py

@@ -13,6 +13,8 @@
 Use '-h' for parameter help.
 """
 
+import json
+import os
 import sys
 import threading
 import textwrap
@@ -40,7 +42,7 @@ def get_parser():
 
     Example::
 
-        load_into_counting.py -k 20 -x 5e7 -T 4 out.kh data/100k-filtered.fa
+        load-into-counting.py -k 20 -x 5e7 -T 4 out.kh data/100k-filtered.fa
     """
 
     parser = build_counting_args("Build a k-mer counting table from the given"
@@ -54,6 +56,10 @@ def get_parser():
     parser.add_argument('-b', '--no-bigcount', dest='bigcount', default=True,
                         action='store_false',
                         help='Do not count k-mers past 255')
+    parser.add_argument('--summary-info', '-s', default=None, metavar="FORMAT",
+                        choices=['json', 'tsv'],
+                        help="What format should the machine readable run "
+                        "summary be in? (json or tsv, disabled by default)")
     parser.add_argument('--report-total-kmers', '-t', action='store_true',
                         help="Prints the total number of k-mers to stderr")
     return parser
@@ -62,6 +68,7 @@ def get_parser():
 def main():
 
     info('load-into-counting.py', ['counting'])
+
     args = get_parser().parse_args()
     report_on_config(args)
 
@@ -74,9 +81,13 @@ def main():
     check_space(args.input_sequence_filename)
     check_space_for_hashtable(args.n_tables * args.min_tablesize)
 
-    print >>sys.stderr, 'Saving k-mer counting table to %s' % base
+    print >>sys.stderr, 'Saving k-mer counting table to %s' %  base
     print >>sys.stderr, 'Loading kmers from sequences in %s' % repr(filenames)
 
+    # clobber the '.info' file now, as we always open in append mode below
+    if os.path.exists(base + '.info'):
+        os.remove(base + '.info')
+
     print >>sys.stderr, 'making k-mer counting table'
     htable = khmer.new_counting_hash(args.ksize, args.min_tablesize,
                                      args.n_tables, args.threads)
@@ -108,32 +119,56 @@ def main():
             check_space_for_hashtable(args.n_tables * args.min_tablesize)
             print >>sys.stderr, 'mid-save', base
             htable.save(base)
-            open(base + '.info', 'w').write('through %s' % filename)
+        with open(base + '.info', 'a') as info_fh:
+            print >> info_fh, 'through', filename
 
+    n_kmers = htable.n_unique_kmers()
     if args.report_total_kmers:
-        print >> sys.stderr, 'Total number of unique k-mers: {0}'.format(
-            htable.n_unique_kmers())
+        print >> sys.stderr, 'Total number of unique k-mers:', n_kmers
+        with open(base + '.info', 'a') as info_fp:
+            print >>info_fp, 'Total number of unique k-mers:', n_kmers
 
     print >>sys.stderr, 'saving', base
     htable.save(base)
 
-    info_fp = open(base + '.info', 'w')
-    info_fp.write('through end: %s\n' % filename)
-
-    # Change 0.2 only if you really grok it.  HINT: You don't.
     fp_rate = khmer.calc_expected_collisions(htable)
-    print >>sys.stderr, 'fp rate estimated to be %1.3f' % fp_rate
-    print >> info_fp, 'fp rate estimated to be %1.3f' % fp_rate
 
+    with open(base + '.info', 'a') as info_fp:
+        print >> info_fp, 'fp rate estimated to be %1.3f\n' % fp_rate
+
+    if args.summary_info:
+        mr_fmt = args.summary_info.lower()
+        mr_file = base + '.info.' + mr_fmt
+        print >> sys.stderr, "Writing summmary info to", mr_file
+        with open(mr_file, 'w') as mr_fh:
+            if mr_fmt == 'json':
+                mr_data = {
+                    "ht_name": os.path.basename(base),
+                    "fpr": fp_rate,
+                    "num_kmers": n_kmers,
+                    "files": filenames,
+                    "mrinfo_version": "0.1.0",
+                }
+                json.dump(mr_data, mr_fh)
+                mr_fh.write('\n')
+            elif mr_fmt == 'tsv':
+                mr_fh.write("ht_name\tfpr\tnum_kmers\tfiles\n")
+                mr_fh.write("{b:s}\t{fpr:1.3f}\t{k:d}\t{fls:s}\n".format(
+                    b=os.path.basename(base), fpr=fp_rate, k=n_kmers,
+                    fls=";".join(filenames)))
+
+    print >> sys.stderr, 'fp rate estimated to be %1.3f' % fp_rate
+
+    # Change 0.2 only if you really grok it.  HINT: You don't.
     if fp_rate > 0.20:
         print >> sys.stderr, "**"
-        print >> sys.stderr, ("** ERROR: the k-mer counting table is too small"
-                              " this data set.  Increase tablesize/# tables.")
+        print >> sys.stderr, "** ERROR: the k-mer counting table is too small",
+        print >> sys.stderr, "for this data set. Increase tablesize/# tables."
         print >> sys.stderr, "**"
         sys.exit(1)
 
     print >>sys.stderr, 'DONE.'
-    print>>sys.stderr, 'wrote to: ' + base + '.info'
+    print >>sys.stderr, 'wrote to:', base + '.info'
 
 if __name__ == '__main__':
     main()

tests/test_scripts.py

@@ -7,6 +7,7 @@
 
 # pylint: disable=C0111,C0103,E1103,W0612
 
+import json
 import sys
 import os
 import shutil
@@ -66,6 +67,71 @@ def test_load_into_counting_fail():
     assert "ERROR:" in err
 
 
+def test_load_into_counting_tsv():
+    script = scriptpath('load-into-counting.py')
+    args = ['-x', '1e7', '-N', '2', '-k', '20', '-t', '-s', 'tsv']
+
+    outfile = utils.get_temp_filename('out.kh')
+    tabfile = outfile + '.info.tsv'
+    infile = utils.get_test_data('test-abund-read-2.fa')
+
+    args.extend([outfile, infile])
+
+    (status, out, err) = utils.runscript(script, args)
+    assert 'Total number of unique k-mers: 95' in err, err
+    assert os.path.exists(outfile)
+    assert os.path.exists(tabfile)
+    with open(tabfile) as tabfh:
+        tabfile_lines = tabfh.readlines()
+    assert len(tabfile_lines) == 2
+    outbase = os.path.basename(outfile)
+    expected_tsv_line = '\t'.join([outbase, '0.000', '95', infile]) + '\n'
+    assert tabfile_lines[1] == expected_tsv_line, tabfile_lines
+
+
+def test_load_into_counting_json():
+    script = scriptpath('load-into-counting.py')
+    args = ['-x', '1e7', '-N', '2', '-k', '20', '-t', '-s', 'json']
+
+    outfile = utils.get_temp_filename('out.kh')
+    jsonfile = outfile + '.info.json'
+    infile = utils.get_test_data('test-abund-read-2.fa')
+
+    args.extend([outfile, infile])
+
+    (status, out, err) = utils.runscript(script, args)
+    assert 'Total number of unique k-mers: 95' in err, err
+    assert os.path.exists(outfile)
+    assert os.path.exists(jsonfile)
+
+    with open(jsonfile) as jsonfh:
+        got_json = json.load(jsonfh)
+    outbase = os.path.basename(outfile)
+    expected_json = {
+        "files": [infile],
+        "ht_name": outbase,
+        "num_kmers": 95,
+        "fpr": 9.024965705097741e-11,
+        "mrinfo_version": "0.1.0",
+    }
+
+    assert got_json == expected_json, got_json
+
+
+def test_load_into_counting_bad_summary_fmt():
+    script = scriptpath('load-into-counting.py')
+    args = ['-x', '1e7', '-N', '2', '-k', '20', '-s', 'badfmt']
+
+    outfile = utils.get_temp_filename('out.kh')
+    infile = utils.get_test_data('test-abund-read-2.fa')
+
+    args.extend([outfile, infile])
+
+    (status, out, err) = utils.runscript(script, args, fail_ok=True)
+    assert status != 0, status
+    assert "invalid choice: 'badfmt'" in err, err
+
+
 def _make_counting(infilename, SIZE=1e7, N=2, K=20, BIGCOUNT=True):
     script = scriptpath('load-into-counting.py')
     args = ['-x', str(SIZE), '-N', str(N), '-k', str(K)]