diff --git a/doc/command-line.md b/doc/command-line.md index a3900e9825..df875dd60e 100644 --- a/doc/command-line.md +++ b/doc/command-line.md @@ -989,20 +989,25 @@ Display signature details. For example, ``` -sourmash sig describe tests/test-data/47.fa.sig +sourmash sig describe tests/test-data/track_abund/47.fa.sig ``` will display: ``` -signature filename: tests/test-data/47.fa.sig +signature filename: tests/test-data/track_abund/47.fa.sig signature: NC_009665.1 Shewanella baltica OS185, complete genome -source file: 47.fa +source file: podar-ref/47.fa md5: 09a08691ce52952152f0e866a59f6261 -k=31 molecule=DNA num=0 scaled=1000 seed=42 track_abundance=0 +k=31 molecule=DNA num=0 scaled=1000 seed=42 track_abundance=1 size: 5177 +sum hashes: 5292 signature license: CC0 ``` +Here, the `size` is the number of distinct hashes in the sketch, and +`sum_hashes` is the total number of hashes in the sketch, with abundances. +When `track_abundance` is 0, `size` is always the same as `sum_hashes`. + ### `sourmash signature fileinfo` - display a summary of the contents of a sourmash collection Display signature file, database, or collection. diff --git a/src/sourmash/cli/sig/describe.py b/src/sourmash/cli/sig/describe.py index ca382732d8..e07b3204aa 100644 --- a/src/sourmash/cli/sig/describe.py +++ b/src/sourmash/cli/sig/describe.py @@ -1,7 +1,7 @@ """show details of signature""" from sourmash.cli.utils import (add_moltype_args, add_ksize_arg, - add_picklist_args) + add_picklist_args, add_pattern_args) def subparser(subparsers): @@ -26,6 +26,7 @@ def subparser(subparsers): add_ksize_arg(subparser, 31) add_moltype_args(subparser) add_picklist_args(subparser) + add_pattern_args(subparser) def main(args): diff --git a/src/sourmash/sig/__main__.py b/src/sourmash/sig/__main__.py index 5c8106076d..f7c4302d36 100644 --- a/src/sourmash/sig/__main__.py +++ b/src/sourmash/sig/__main__.py @@ -205,6 +205,7 @@ def describe(args): set_quiet(args.quiet) moltype = sourmash_args.calculate_moltype(args) picklist = sourmash_args.load_picklist(args) + pattern_search = sourmash_args.load_include_exclude_db_patterns(args) _extend_signatures_with_from_file(args) # write CSV? @@ -214,11 +215,11 @@ def describe(args): csv_obj = sourmash_args.FileOutputCSV(args.csv) csv_fp = csv_obj.open() - # CTB: might want to switch to sourmash_args.FileOutputCSV here? w = csv.DictWriter(csv_fp, ['signature_file', 'md5', 'ksize', 'moltype', 'num', 'scaled', 'n_hashes', 'seed', - 'with_abundance', 'name', 'filename', 'license'], + 'with_abundance', 'name', 'filename', 'license', + 'sum_hashes'], extrasaction='ignore') w.writeheader() @@ -230,10 +231,12 @@ def describe(args): picklist=picklist, progress=progress, yield_all_files=args.force, - force=args.force) + force=args.force, + pattern=pattern_search) for sig, location in loader: # extract info, write as appropriate. + signature_file = location mh = sig.minhash ksize = mh.ksize moltype = mh.moltype @@ -241,6 +244,7 @@ def describe(args): num = mh.num seed = mh.seed n_hashes = len(mh) + sum_hashes = sum(mh.hashes.values()) with_abundance = 0 if mh.track_abundance: with_abundance = 1 @@ -262,6 +266,7 @@ def describe(args): md5: {md5} k={ksize} molecule={moltype} num={num} scaled={scaled} seed={seed} track_abundance={with_abundance} size: {n_hashes} +sum hashes: {sum_hashes} signature license: {license} ''', **locals()) diff --git a/tests/test-data/47.abunds.fa.sig b/tests/test-data/47.abunds.fa.sig deleted file mode 100644 index 74a9f495cb..0000000000 --- a/tests/test-data/47.abunds.fa.sig +++ /dev/null @@ -1 +0,0 @@ -[{"class":"sourmash_signature","email":"","filename":"47.fa","hash_function":"0.murmur64","license":"CC0","name":"NC_009665.1 Shewanella baltica OS185, complete 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\ No newline at end of file diff --git a/tests/test_bugs.py b/tests/test_bugs.py index dea352db0a..e0f3c5daf0 100644 --- a/tests/test_bugs.py +++ b/tests/test_bugs.py @@ -3,7 +3,7 @@ @utils.in_tempdir def test_bug_803(c): # can we do a 'sourmash search' on an LCA database and a query with abundance? - query = utils.get_test_data('47.abunds.fa.sig') + query = utils.get_test_data('track_abund/47.fa.sig') lca_db = utils.get_test_data('lca/47+63.lca.json') c.run_sourmash('search', query, lca_db, '--ignore-abundance') diff --git a/tests/test_cmd_signature.py b/tests/test_cmd_signature.py index 9d5b1eaa0b..5e03011ba5 100644 --- a/tests/test_cmd_signature.py +++ b/tests/test_cmd_signature.py @@ -2800,7 +2800,7 @@ def test_sig_describe_1_hp(c): c.run_sourmash('sig', 'describe', computed_sig) out = c.last_result.out - print(c.last_result) + print(c.last_result.out) # Add final trailing slash for this OS testdata_dirname = os.path.dirname(testdata) + os.sep @@ -2814,6 +2814,7 @@ def test_sig_describe_1_hp(c): md5: e45a080101751e044d6df861d3d0f3fd k=7 molecule=protein num=500 scaled=0 seed=42 track_abundance=0 size: 500 +sum hashes: 500 signature license: CC0 --- @@ -2823,6 +2824,7 @@ def test_sig_describe_1_hp(c): md5: c027e96c3379d38942639219daa24fdc k=7 molecule=dayhoff num=500 scaled=0 seed=42 track_abundance=0 size: 500 +sum hashes: 500 signature license: CC0 --- @@ -2841,6 +2843,7 @@ def test_sig_describe_1_hp(c): md5: 1136a8a68420bd93683e45cdaf109b80 k=21 molecule=DNA num=500 scaled=0 seed=42 track_abundance=0 size: 500 +sum hashes: 500 signature license: CC0 --- @@ -2850,6 +2853,7 @@ def test_sig_describe_1_hp(c): md5: 4244d1612598af044e799587132f007e k=10 molecule=protein num=500 scaled=0 seed=42 track_abundance=0 size: 500 +sum hashes: 500 signature license: CC0 --- @@ -2859,6 +2863,7 @@ def test_sig_describe_1_hp(c): md5: 396dcb7c1875f48ca31e0759bec72ee1 k=10 molecule=dayhoff num=500 scaled=0 seed=42 track_abundance=0 size: 500 +sum hashes: 500 signature license: CC0 --- @@ -2868,6 +2873,7 @@ def test_sig_describe_1_hp(c): md5: 4c43878296459783dbd6a4a071ab7e9d k=10 molecule=hp num=500 scaled=0 seed=42 track_abundance=0 size: 500 +sum hashes: 500 signature license: CC0 --- @@ -2877,6 +2883,7 @@ def test_sig_describe_1_hp(c): md5: 71f7c111c01785e5f38efad45b00a0e1 k=30 molecule=DNA num=500 scaled=0 seed=42 track_abundance=0 size: 500 +sum hashes: 500 signature license: CC0 """.splitlines() @@ -2982,6 +2989,29 @@ def test_sig_describe_1_zipfile(c): assert line.strip() in out +def test_sig_describe_1_sig_abund(runtmp): + # check output of sig describe on a sketch with abundances + c = runtmp + + sigfile = utils.get_test_data('track_abund/47.fa.sig') + c.run_sourmash('sig', 'describe', sigfile) + + out = c.last_result.out + print(c.last_result.out) + + expected_output = """\ +signature: NC_009665.1 Shewanella baltica OS185, complete genome +source file: podar-ref/47.fa +md5: 09a08691ce52952152f0e866a59f6261 +k=31 molecule=DNA num=0 scaled=1000 seed=42 track_abundance=1 +size: 5177 +sum hashes: 5292 +signature license: CC0 +""".splitlines() + for line in expected_output: + assert line.strip() in out + + @utils.in_thisdir def test_sig_describe_stdin(c): sig = utils.get_test_data('prot/protein/GCA_001593925.1_ASM159392v1_protein.faa.gz.sig') @@ -3045,6 +3075,37 @@ def test_sig_describe_2_csv(runtmp): assert n == 2 +def test_sig_describe_2_csv_abund(runtmp): + # output info in CSV spreadsheet, for abund sig + c = runtmp + + sig47 = utils.get_test_data('track_abund/47.fa.sig') + c.run_sourmash('sig', 'describe', sig47, '--csv', 'out.csv') + + with open(c.output('out.csv'), 'rt') as fp: + r = csv.DictReader(fp) + + n = 0 + + rows = list(r) + assert len(rows) == 1 + row = rows[0] + + assert row['signature_file'] == sig47 + assert row['md5'] == "09a08691ce52952152f0e866a59f6261" + assert row['ksize'] == "31" + assert row['moltype'] == "DNA" + assert row['num'] == "0" + assert row['scaled'] == "1000" + assert row['n_hashes'] == "5177" + assert row['seed'] == "42" + assert row['with_abundance'] == "1" + assert row['name'] == "NC_009665.1 Shewanella baltica OS185, complete genome" + assert row['filename'] == "podar-ref/47.fa" + assert row['license'] == "CC0" + assert row['sum_hashes'] == "5292" + + def test_sig_describe_2_csv_as_picklist(runtmp): # generate an output CSV from describe and then use it as a manifest # pickfile @@ -3074,6 +3135,54 @@ def test_sig_describe_2_csv_as_picklist(runtmp): assert line.strip() in out +def test_sig_describe_2_include_db_pattern(runtmp): + # test sig describe --include-db-pattern + c = runtmp + + allzip = utils.get_test_data('prot/all.zip') + + c.run_sourmash('sig', 'describe', allzip, + '--include-db-pattern', 'os185') + + out = c.last_result.out + print(c.last_result) + + expected_output = """\ +signature: NC_009665.1 Shewanella baltica OS185, complete genome +source file: 47.fa +md5: 09a08691ce52952152f0e866a59f6261 +k=31 molecule=DNA num=0 scaled=1000 seed=42 track_abundance=0 +size: 5177 +signature license: CC0 +""".splitlines() + for line in expected_output: + assert line.strip() in out + + +def test_sig_describe_2_exclude_db_pattern(runtmp): + # test sig describe --exclude-db-pattern + c = runtmp + + allzip = utils.get_test_data('prot/all.zip') + + c.run_sourmash('sig', 'describe', allzip, '--dna', '-k', '31', + '--exclude-db-pattern', 'os223') + + out = c.last_result.out + print(c.last_result) + + expected_output = """\ +signature: NC_009665.1 Shewanella baltica OS185, complete genome +source file: 47.fa +md5: 09a08691ce52952152f0e866a59f6261 +k=31 molecule=DNA num=0 scaled=1000 seed=42 track_abundance=0 +size: 5177 +signature license: CC0 +""".splitlines() + for line in expected_output: + assert line.strip() in out + + @utils.in_tempdir def test_sig_overlap(c): # get overlap details diff --git a/tests/test_cmd_signature_fileinfo.py b/tests/test_cmd_signature_fileinfo.py index 534360712b..cf6155f036 100644 --- a/tests/test_cmd_signature_fileinfo.py +++ b/tests/test_cmd_signature_fileinfo.py @@ -63,7 +63,7 @@ def test_fileinfo_1_sig_summarize(runtmp): def test_fileinfo_1_sig_abund(runtmp): # get basic info on a signature with abundance - sig47 = utils.get_test_data('47.abunds.fa.sig') + sig47 = utils.get_test_data('track_abund/47.fa.sig') shutil.copyfile(sig47, runtmp.output('sig47.sig')) runtmp.run_sourmash('sig', 'fileinfo', 'sig47.sig')