diff --git a/README.md b/README.md index 7d127239f5..7e26343211 100644 --- a/README.md +++ b/README.md @@ -46,7 +46,7 @@ You can also use pip to install the pre-release like so: ``` pip install --pre sourmash ``` - + A quickstart tutorial [is available](https://sourmash.readthedocs.io/en/latest/tutorials.html). ### Requirements diff --git a/doc/api-example.md b/doc/api-example.md index 5603ec766d..90799f51fc 100644 --- a/doc/api-example.md +++ b/doc/api-example.md @@ -321,10 +321,12 @@ The hashing function used is identical between num and scaled signatures, so the hash values themselves are compatible - it's the comparison between collections of them that doesn't work. -But, in some circumstances, num signatures can be -extracted from scaled signatures, and vice versa. We haven't yet -implemented nice shortcuts for this in sourmash, but you can hack it -together yourself quite easily :). +But, in some circumstances, num signatures can be extracted from +scaled signatures, and vice versa. We haven't yet implemented a +Python API for this in sourmash, but you can hack it together yourself +quite easily, and a conversion utility is implemented through the command +line in `sourmash signature downsample`. + To extract a num MinHash object from a scaled MinHash, first create or load your MinHash, and then extract the hash values: @@ -367,6 +369,9 @@ more hash values in the scaled MinHash than num. Yoda sayeth: *When understand these two sentences you can, use this code may you.* +(You can also take a look at the logic in `sourmash signature +downsample` if you are interested.) + ## Working with fast search trees (Sequence Bloom Trees, or SBTs) Suppose we have a number of signatures calculated with `--scaled`, like so: diff --git a/doc/command-line.md b/doc/command-line.md index 01aefdf588..43d5c05484 100644 --- a/doc/command-line.md +++ b/doc/command-line.md @@ -233,7 +233,7 @@ genomes with no (or incomplete) taxonomic information. Use `sourmash lca summarize` and `sourmash lca gather` to classify a metagenome using a collection of genomes with taxonomic information. -## `sourmash lca` subcommands +## `sourmash lca` subcommands for taxonomic classification These commands use LCA databases (created with `lca index`, below, or prepared databases such as @@ -288,7 +288,7 @@ signature were classified as family *Shewanellaceae*, genus *Shewanella*, or species *Shewanella baltica*. Then the lowest compatible node (here species *Shewanella baltica*) would be reported, and the status of the classification would be `found`. However, if a -number of additional k-mers in the input signaturer were classified as +number of additional k-mers in the input signature were classified as *Shewanella oneidensis*, sourmash would be unable to resolve the taxonomic assignment below genus *Shewanella* and it would report a status of `disagree` with the genus-level assignment of *Shewanella*; @@ -343,7 +343,7 @@ and the following example summarize output to stdout: ``` The output is space-separated and consists of three columns: the -perrcentage of total k-mers that have this classification; the number of +percentage of total k-mers that have this classification; the number of k-mers that have this classification; and the lineage classification. K-mer classifications are reported hierarchically, so the percentages and totals contain all assignments that are at a lower taxonomic level - @@ -420,3 +420,188 @@ for an example use case. [1]:http://mash.readthedocs.io/en/latest/__ [2]:http://biorxiv.org/content/early/2015/10/26/029827 [3]:https://en.wikipedia.org/wiki/Jaccard_index + +## `sourmash signature` subcommands for signature manipulation + +These commands manipulate signatures from the command line. Currently +supported subcommands are `merge`, `rename`, `intersect`, +`extract`, `downsample`, `subtract`, `import`, `export`, `info`, and +`flatten`. + +All of the signature commands work only on compatible signatures, where +the k-mer size and nucleotide/protein sequences match. If working directly +with the hash values (e.g. `merge`, `intersect`, `subtract`) then the +scaled values must also match; you can use `downsample` to convert a bunch +of samples to the same scaled value. + +If there are multiple signatures in a file with different ksizes and/or +from nucleotide and protein sequences, you can choose amongst them with +`-k/--ksize` and `--dna` or `--protein`, as with other sourmash commands +such as `search`, `gather`, and `compare`. + +Note, you can use `sourmash sig` as shorthand for all of these commands. + +### `sourmash signature merge` + +Merge two (or more) signatures. + +For example, +``` +sourmash signature merge file1.sig file2.sig -o merged.sig +``` +will output the union of all the hashes in `file1.sig` and `file2.sig` +to `merged.sig`. + +All of the signatures passed to merge must either have been computed +with `--track-abundance`, or not. If they have `track_abundance` on, +then the merged signature will have the sum of all abundances across +the individual signatures. The `--flatten` flag will override this +behavior and allow merging of mixtures by removing all abundances. + +### `sourmash signature rename` + +Rename the display name for a signature - this is the name output for matches +in `compare`, `search`, `gather`, etc. + +For example, +``` +sourmash signature rename file1.sig "new name" -o renamed.sig +``` +will place a renamed copy of the hashes in `file1.sig` in the file +`renamed.sig`. + +### `sourmash signature subtract` + +Subtract all of the hash values from one signature that are in one or more +of the others. + +For example, + +``` +sourmash signature subtract file1.sig file2.sig file3.sig -o subtracted.sig +``` +will subtract all of the hashes in `file2.sig` and `file3.sig` from +`file1.sig`, and save the new signature to `subtracted.sig`. + +To use `subtract` on signatures calculated with +`--track-abundance`, you must specify `--flatten`. + +### `sourmash signature intersect` + +Output the intersection of the hash values in multiple signature files. + +For example, + +``` +sourmash signature intersect file1.sig file2.sig file3.sig -o intersect.sig +``` +will output the intersection of all the hashes in those three files to +`intersect.sig`. + +The `intersect` command flattens all signatures, i.e. the abundances +in any signatures will be ignored and the output signature will have +`track_abundance` turned off. + +### `sourmash signature downsample` + +Downsample one or more signatures. + +With `downsample`, you can -- + +* increase the `--scaled` value for a signature computed with `--scaled`, shrinking it in size; +* decrease the `num` value for a traditional num MinHash, shrinking it in size; +* try to convert a `--scaled` signature to a `num` signature; +* try to convert a `num` signature to a `--scaled` signature. + +For example, +``` +sourmash signature downsample file1.sig file2.sig --scaled 100000 -o downsampled.sig +``` +will output each signature, downsampled to a scaled value of 100000, to +`downsampled.sig`; and +``` +sourmash signature downsample --num 500 scaled_file.sig -o downsampled.sig +``` +will try to convert a scaled MinHash to a num MinHash. + +### `sourmash signature extract` + +Extract the specified signature(s) from a collection of signatures. + +For example, +``` +sourmash signature extract *.sig -k 21 --dna -o extracted.sig +``` +will extract all nucleotide signatures calculated at k=21 from all +.sig files in the current directory. + +There are currently two other useful selectors for `extract`: you can specify +(part of) an md5sum, as output in the CSVs produced by `search` and `gather`; +and you can specify (part of) a name. + +For example, +``` +sourmash signature extract tests/test-data/*.fa.sig --md5 09a0869 +``` +will extract the signature from `47.fa.sig` which has an md5sum of +`09a08691ce52952152f0e866a59f6261`; and +``` +sourmash signature extract tests/test-data/*.fa.sig --name NC_009665 +``` +will extract the same signature, which has an accession number of +`NC_009665.1`. + +### `sourmash signature flatten` + +Flatten the specified signature(s), removing abundances and setting +track_abundance to False. + +For example, +``` +sourmash signature flatten *.sig -o flattened.sig +``` +will remove all abundances from all of the .sig files in the current +directory. + +The `flatten` command accepts the same selectors as `extract`. + +### `sourmash signature import` + +Import signatures into sourmash format. Currently only supports mash, +and can import mash sketches output by `mash info -d `. + +For example, +``` +sourmash signature import filename.msh.json -o imported.sig +``` +will import the contents of `filename.msh.json` into `imported.sig`. + +### `sourmash signature export` + +Export signatures from sourmash format. Currently only supports +mash dump format. + +For example, +``` +sourmash signature export filename.sig -o filename.sig.msh.json +``` + +### `sourmash signature overlap` + +Display a detailed comparison of two signatures. This computes the +Jaccard similarity (as in `sourmash compare` or `sourmash search`) and +the Jaccard containment in both directions (as with `--containment`). +It also displays the number of hash values in the union and +intersection of the two signatures, as well as the number of disjoint +hash values in each signature. + +This command has two uses - first, it is helpful for understanding how +similarity and containment are calculated, and second, it is useful for +analyzing signatures with very small overlaps, where the similarity +and/or containment might be very close to zero. + +For example, +``` +sourmash signature overlap file1.sig file2.sig +``` +will display the detailed comparison of `file1.sig` and `file2.sig`. diff --git a/sourmash/__main__.py b/sourmash/__main__.py index 05ec2a9806..867cf5f214 100644 --- a/sourmash/__main__.py +++ b/sourmash/__main__.py @@ -11,6 +11,7 @@ gather, index, sbt_combine, search, plot, watch, info, storage, migrate, multigather) from .lca import main as lca_main +from .sig import main as sig_main usage=''' sourmash [] @@ -35,9 +36,10 @@ categorize Identify best matches for many signatures using an SBT. watch Classify a stream of sequences. -** Other information: +** Other commands: -info Sourmash version and other information. +info Display sourmash version and other information. +signature Sourmash signature manipulation utilities. Use '-h' to get subcommand-specific help, e.g. @@ -59,7 +61,9 @@ def main(): 'storage': storage, 'lca': lca_main, 'migrate': migrate, - 'multigather': multigather} + 'multigather': multigather, + 'sig': sig_main, + 'signature': sig_main} parser = argparse.ArgumentParser( description='work with compressed sequence representations') parser.add_argument('command', nargs='?') diff --git a/sourmash/commands.py b/sourmash/commands.py index af6f466349..1c23c44dd8 100644 --- a/sourmash/commands.py +++ b/sourmash/commands.py @@ -1006,7 +1006,7 @@ def gather(args): sourmash_args.add_moltype_args(parser) args = parser.parse_args(args) - set_quiet(args.quiet) + set_quiet(args.quiet, args.debug) moltype = sourmash_args.calculate_moltype(args) # load the query signature & figure out all the things diff --git a/sourmash/lca/command_classify.py b/sourmash/lca/command_classify.py index 28ccd8c63c..5d5a8c4a6d 100644 --- a/sourmash/lca/command_classify.py +++ b/sourmash/lca/command_classify.py @@ -9,9 +9,9 @@ from collections import Counter from .. import sourmash_args, load_signatures -from ..logging import notify, error +from ..logging import notify, error, debug, set_quiet from . import lca_utils -from .lca_utils import debug, set_debug, check_files_exist +from .lca_utils import check_files_exist DEFAULT_THRESHOLD=5 # how many counts of a taxid at min @@ -88,7 +88,10 @@ def classify(args): p.add_argument('--scaled', type=float) p.add_argument('--traverse-directory', action='store_true', help='load all signatures underneath directories.') - p.add_argument('-d', '--debug', action='store_true') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + p.add_argument('-d', '--debug', action='store_true', + help='output debugging output') args = p.parse_args(args) if not args.db: @@ -99,8 +102,7 @@ def classify(args): error('Error! must specify at least one query signature with --query') sys.exit(-1) - if args.debug: - set_debug(args.debug) + set_quiet(args.quiet, args.debug) # flatten --db and --query args.db = [item for sublist in args.db for item in sublist] diff --git a/sourmash/lca/command_compare_csv.py b/sourmash/lca/command_compare_csv.py index ff8b1aa582..ab1903538b 100644 --- a/sourmash/lca/command_compare_csv.py +++ b/sourmash/lca/command_compare_csv.py @@ -8,9 +8,9 @@ from collections import defaultdict from .. import sourmash_args -from ..logging import notify, error, print_results +from ..logging import notify, error, print_results, set_quiet from . import lca_utils -from .lca_utils import debug, set_debug, zip_lineage +from .lca_utils import zip_lineage from .command_index import load_taxonomy_assignments @@ -18,7 +18,10 @@ def compare_csv(args): p = argparse.ArgumentParser(prog="sourmash lca compare_csv") p.add_argument('csv1', help='taxonomy spreadsheet output by classify') p.add_argument('csv2', help='custom taxonomy spreadsheet') - p.add_argument('-d', '--debug', action='store_true') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + p.add_argument('-d', '--debug', action='store_true', + help='output debugging output') p.add_argument('-C', '--start-column', default=2, type=int, help='column at which taxonomic assignments start') p.add_argument('--tabs', action='store_true', @@ -32,8 +35,7 @@ def compare_csv(args): error('error, --start-column cannot be less than 2') sys.exit(-1) - if args.debug: - set_debug(args.debug) + set_quiet(args.quiet, args.debug) # first, load classify-style spreadsheet notify('loading classify output from: {}', args.csv1) diff --git a/sourmash/lca/command_gather.py b/sourmash/lca/command_gather.py index 4a39053000..644212ef86 100644 --- a/sourmash/lca/command_gather.py +++ b/sourmash/lca/command_gather.py @@ -11,9 +11,9 @@ from collections import Counter, defaultdict, namedtuple from .. import sourmash_args, save_signatures, SourmashSignature -from ..logging import notify, error, print_results +from ..logging import notify, error, print_results, set_quiet, debug from . import lca_utils -from .lca_utils import debug, set_debug, check_files_exist +from .lca_utils import check_files_exist from ..search import format_bp LCAGatherResult = namedtuple('LCAGatherResult', @@ -186,17 +186,19 @@ def gather_main(args): p = argparse.ArgumentParser(prog="sourmash lca gather") p.add_argument('query') p.add_argument('db', nargs='+') - p.add_argument('-d', '--debug', action='store_true') p.add_argument('-o', '--output', type=argparse.FileType('wt'), help='output CSV containing matches to this file') p.add_argument('--output-unassigned', type=argparse.FileType('wt'), help='output unassigned portions of the query as a signature to this file') p.add_argument('--ignore-abundance', action='store_true', help='do NOT use k-mer abundances if present') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + p.add_argument('-d', '--debug', action='store_true', + help='output debugging output') args = p.parse_args(args) - if args.debug: - set_debug(args.debug) + set_quiet(args.quiet, args.debug) if not check_files_exist(args.query, *args.db): sys.exit(-1) diff --git a/sourmash/lca/command_index.py b/sourmash/lca/command_index.py index 6172b787a1..ce15388500 100644 --- a/sourmash/lca/command_index.py +++ b/sourmash/lca/command_index.py @@ -9,9 +9,9 @@ from collections import defaultdict from .. import sourmash_args, load_signatures -from ..logging import notify, error +from ..logging import notify, error, debug, set_quiet from . import lca_utils -from .lca_utils import debug, set_debug, LineagePair +from .lca_utils import LineagePair def load_taxonomy_assignments(filename, delimiter=',', start_column=2, @@ -118,7 +118,10 @@ def index(args): help='one or more sourmash signatures') p.add_argument('--scaled', default=10000, type=float) p.add_argument('-k', '--ksize', default=31, type=int) - p.add_argument('-d', '--debug', action='store_true') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + p.add_argument('-d', '--debug', action='store_true', + help='output debugging output') p.add_argument('-C', '--start-column', default=2, type=int, help='column at which taxonomic assignments start') p.add_argument('--tabs', action='store_true', @@ -137,8 +140,7 @@ def index(args): error('error, --start-column cannot be less than 2') sys.exit(-1) - if args.debug: - set_debug(args.debug) + set_quiet(args.quiet, args.debug) args.scaled = int(args.scaled) diff --git a/sourmash/lca/command_rankinfo.py b/sourmash/lca/command_rankinfo.py index 78dca38b29..889232c1c4 100644 --- a/sourmash/lca/command_rankinfo.py +++ b/sourmash/lca/command_rankinfo.py @@ -7,9 +7,8 @@ import argparse from collections import defaultdict -from ..logging import error +from ..logging import error, debug, set_quiet from . import lca_utils -from .lca_utils import debug, set_debug def make_lca_counts(dblist): @@ -52,15 +51,17 @@ def rankinfo_main(args): p = argparse.ArgumentParser(prog="sourmash lca rankinfo") p.add_argument('db', nargs='+') p.add_argument('--scaled', type=float) - p.add_argument('-d', '--debug', action='store_true') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + p.add_argument('-d', '--debug', action='store_true', + help='output debugging output') args = p.parse_args(args) if not args.db: error('Error! must specify at least one LCA database with --db') sys.exit(-1) - if args.debug: - set_debug(args.debug) + set_quiet(args.quiet, args.debug) if args.scaled: args.scaled = int(args.scaled) diff --git a/sourmash/lca/command_summarize.py b/sourmash/lca/command_summarize.py index 7681274a6d..55e8839cb3 100644 --- a/sourmash/lca/command_summarize.py +++ b/sourmash/lca/command_summarize.py @@ -9,9 +9,9 @@ from collections import defaultdict, Counter from .. import sourmash_args, load_signatures -from ..logging import notify, error, print_results +from ..logging import notify, error, print_results, set_quiet, debug from . import lca_utils -from .lca_utils import debug, set_debug, check_files_exist +from .lca_utils import check_files_exist DEFAULT_THRESHOLD=5 @@ -67,7 +67,10 @@ def summarize_main(args): p.add_argument('-o', '--output', type=argparse.FileType('wt'), help='CSV output') p.add_argument('--scaled', type=float) - p.add_argument('-d', '--debug', action='store_true') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + p.add_argument('-d', '--debug', action='store_true', + help='output debugging output') args = p.parse_args(args) if not args.db: @@ -78,8 +81,7 @@ def summarize_main(args): error('Error! must specify at least one query signature with --query') sys.exit(-1) - if args.debug: - set_debug(args.debug) + set_quiet(args.quiet, args.debug) if args.scaled: args.scaled = int(args.scaled) diff --git a/sourmash/lca/lca_utils.py b/sourmash/lca/lca_utils.py index 5132b4236c..f6c041fa14 100644 --- a/sourmash/lca/lca_utils.py +++ b/sourmash/lca/lca_utils.py @@ -1,7 +1,7 @@ """ Utility functions for lowest-common-ancestor analysis tools. """ -from __future__ import print_function +from __future__ import print_function, division import sys import json import gzip @@ -19,7 +19,7 @@ import pprint from .._minhash import get_max_hash_for_scaled -from ..logging import notify, error +from ..logging import notify, error, debug # type to store an element in a taxonomic lineage LineagePair = namedtuple('LineagePair', ['rank', 'name']) @@ -90,16 +90,6 @@ def zip_lineage(lineage, include_strain=True, truncate_empty=False): null_names = set(['[Blank]', 'na', 'null']) -_print_debug = False -def set_debug(state): - global _print_debug - _print_debug = True - -def debug(*args): - if _print_debug: - pprint.pprint(args) - - def build_tree(assignments, initial=None): """ Builds a tree of dictionaries from lists of LineagePair objects @@ -316,6 +306,7 @@ def find(self, minhash, threshold, containment=False, ignore_scaled=False): raise ValueError("lca db scaled is {} vs query {}; must downsample".format(self.scaled, minhash.scaled)) if not hasattr(self, 'signatures'): + debug('creating signatures for LCA DB...') sigd = defaultdict(minhash.copy_and_clear) for (k, v) in self.hashval_to_idx.items(): @@ -324,6 +315,9 @@ def find(self, minhash, threshold, containment=False, ignore_scaled=False): self.signatures = sigd + debug('=> {} signatures!', len(self.signatures)) + + # build idx_to_ident from ident_to_idx if not hasattr(self, 'idx_to_ident'): idx_to_ident = {} for k, v in self.ident_to_idx.items(): @@ -333,24 +327,33 @@ def find(self, minhash, threshold, containment=False, ignore_scaled=False): query_mins = set(minhash.get_mins()) + # collect matching hashes: c = Counter() for hashval in query_mins: idx_list = self.hashval_to_idx.get(hashval, []) for idx in idx_list: c[idx] += 1 + debug('number of matching signatures for hashes: {}', len(c)) + for idx, count in c.items(): ident = self.idx_to_ident[idx] name = self.ident_to_name[ident] + debug('looking at {} ({})', ident, name) match_mh = self.signatures[idx] match_size = len(match_mh) + debug('count: {}; query_mins: {}; match size: {}', + count, len(query_mins), match_size) + if containment: score = count / len(query_mins) else: score = count / (len(query_mins) + match_size - count) + debug('score: {} (containment? {})', score, containment) + if score >= threshold: # reconstruct signature... ugh. from .. import SourmashSignature diff --git a/sourmash/logging.py b/sourmash/logging.py index 98bb5dbe23..2c1de32d2a 100644 --- a/sourmash/logging.py +++ b/sourmash/logging.py @@ -3,9 +3,11 @@ from io import StringIO _quiet = False -def set_quiet(val): - global _quiet +_debug = False +def set_quiet(val, print_debug=False): + global _quiet, _debug _quiet = bool(val) + _debug = bool(print_debug) def print_results(s, *args, **kwargs): @@ -30,7 +32,7 @@ def notify(s, *args, **kwargs): def debug(s, *args, **kwargs): "A debug logging function => stderr." - if _quiet: + if _quiet or not _debug: return print(u'\r\033[K', end=u'', file=sys.stderr) diff --git a/sourmash/sig/__init__.py b/sourmash/sig/__init__.py new file mode 100644 index 0000000000..afdccbee52 --- /dev/null +++ b/sourmash/sig/__init__.py @@ -0,0 +1 @@ +from .__main__ import main diff --git a/sourmash/sig/__main__.py b/sourmash/sig/__main__.py new file mode 100644 index 0000000000..cf9adf8dc4 --- /dev/null +++ b/sourmash/sig/__main__.py @@ -0,0 +1,722 @@ +""" +Command-line entry point for 'python -m sourmash.sig' +""" +from __future__ import print_function, unicode_literals +import sys +import argparse +import csv +import json + +import sourmash +import copy + +from ..logging import set_quiet, error, notify, set_quiet, print_results +from .. import sourmash_args +from ..sourmash_args import DEFAULT_LOAD_K +from .._minhash import get_max_hash_for_scaled + +usage=''' +sourmash signature [] - manipulate/work with signature files. + +** Commands can be: + +describe [ ... ] - show details of signature +downsample [ ... ] - downsample one or more signatures +extract [ ... ] - extract one or more signatures +flatten [ ... ] - remove abundances +intersect [ ...] - intersect one or more signatures +merge [ ...] - merge one or more signatures +rename - rename signature +subtract [...] - subtract one or more signatures +import [ ... ] - import a mash or other signature +export - export a signature, e.g. to mash +overlap - see detailed comparison of sigs + +** Use '-h' to get subcommand-specific help, e.g. + +sourmash signature merge -h +''' + + +def _check_abundance_compatibility(sig1, sig2): + if sig1.minhash.track_abundance != sig2.minhash.track_abundance: + raise ValueError("incompatible signatures: track_abundance is {} in first sig, {} in second".format(sig1.minhash.track_abundance, sig2.minhash.track_abundance)) + + +def _flatten(mh): + "turn off track_abundance on a MinHash object" + mh_params = list(mh.__getstate__()) + mh_params[5] = False + mh.__setstate__(mh_params) + assert not mh.track_abundance + + +def _set_num_scaled(mh, num, scaled): + "set num and scaled values on a MinHash object" + mh_params = list(mh.__getstate__()) + mh_params[0] = num + mh_params[6] = get_max_hash_for_scaled(scaled) + mh.__setstate__(mh_params) + assert mh.num == num + assert mh.scaled == scaled + + +##### actual command line functions + + +def describe(args): + """ + provide basic info on signatures + """ + p = argparse.ArgumentParser(prog='sourmash signature describe') + p.add_argument('signatures', nargs='+') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + p.add_argument('--csv', type=argparse.FileType('wt'), + help='output information to a CSV file') + + args = p.parse_args(args) + set_quiet(args.quiet) + + siglist = [] + for sigfile in args.signatures: + this_siglist = [] + try: + this_siglist = sourmash.load_signatures(sigfile, quiet=True, do_raise=True) + for k in this_siglist: + siglist.append((k, sigfile)) + except Exception as exc: + error('\nError while reading signatures from {}:'.format(sigfile)) + error(str(exc)) + error('(continuing)') + + notify('loaded {} signatures from {}...', len(siglist), sigfile, + end='\r') + + notify('loaded {} signatures total.', len(siglist)) + + # write CSV? + w = None + if args.csv: + w = csv.DictWriter(args.csv, + ['signature_file', 'md5', 'ksize', 'moltype', 'num', + 'scaled', 'n_hashes', 'seed', 'with_abundance', + 'name', 'filename', 'license'], + extrasaction='ignore') + w.writeheader() + + # extract info, write as appropriate. + for (sig, signature_file) in siglist: + mh = sig.minhash + ksize = mh.ksize + moltype = 'DNA' + if mh.is_protein: + moltype = 'protein' + scaled = mh.scaled + num = mh.num + seed = mh.seed + n_hashes = len(mh) + with_abundance = 0 + if mh.track_abundance: + with_abundance = 1 + md5 = sig.md5sum() + name = sig.name() + filename = sig.d.get('filename', '') + license = sig.d['license'] + + if w: + w.writerow(locals()) + + print_results('''\ +--- +signature filename: {signature_file} +signature: {name} +source file: {filename} +md5: {md5} +k={ksize} molecule={moltype} num={num} scaled={scaled} seed={seed} track_abundance={with_abundance} +size: {n_hashes} +signature license: {license} +''', **locals()) + + +def overlap(args): + """ + provide detailed comparison of two signatures + """ + p = argparse.ArgumentParser(prog='sourmash signature overlap') + p.add_argument('signature1') + p.add_argument('signature2') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + + sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K) + sourmash_args.add_moltype_args(p) + args = p.parse_args(args) + set_quiet(args.quiet) + + moltype = sourmash_args.calculate_moltype(args) + + sig1 = sourmash.load_one_signature(args.signature1, ksize=args.ksize, + select_moltype=moltype) + sig2 = sourmash.load_one_signature(args.signature2, ksize=args.ksize, + select_moltype=moltype) + + notify('loaded one signature each from {} and {}', args.signature1, + args.signature2) + + try: + similarity = sig1.similarity(sig2) + except ValueError: + raise + + cont1 = sig1.contained_by(sig2) + cont2 = sig2.contained_by(sig1) + + sig1_file = args.signature1 + sig2_file = args.signature2 + + name1 = sig1.name() + name2 = sig2.name() + + md5_1 = sig1.md5sum() + md5_2 = sig2.md5sum() + + ksize = sig1.minhash.ksize + moltype = 'DNA' + if sig1.minhash.is_protein: + moltype = 'protein' + + num = sig1.minhash.num + size1 = len(sig1.minhash) + size2 = len(sig2.minhash) + + scaled = sig1.minhash.scaled + + hashes_1 = set(sig1.minhash.get_mins()) + hashes_2 = set(sig2.minhash.get_mins()) + + num_common = len(hashes_1.intersection(hashes_2)) + disjoint_1 = len(hashes_1 - hashes_2) + disjoint_2 = len(hashes_2 - hashes_1) + num_union = len(hashes_1.union(hashes_2)) + + print('''\ +first signature: + signature filename: {sig1_file} + signature: {name1} + md5: {md5_1} + k={ksize} molecule={moltype} num={num} scaled={scaled} + +second signature: + signature filename: {sig2_file} + signature: {name2} + md5: {md5_2} + k={ksize} molecule={moltype} num={num} scaled={scaled} + +similarity: {similarity:.5f} +first contained in second: {cont1:.5f} +second contained in first: {cont2:.5f} + +number of hashes in first: {size1} +number of hashes in second: {size2} + +number of hashes in common: {num_common} +only in first: {disjoint_1} +only in second: {disjoint_2} +total (union): {num_union} +'''.format(**locals())) + + +def merge(args): + """ + merge one or more signatures. + """ + p = argparse.ArgumentParser(prog='sourmash signature merge') + p.add_argument('signatures', nargs='+') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + p.add_argument('-o', '--output', type=argparse.FileType('wt'), + default=sys.stdout, + help='output signature to this file') + p.add_argument('--flatten', action='store_true', + help='Remove abundances from all signatures.') + sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K) + sourmash_args.add_moltype_args(p) + + args = p.parse_args(args) + set_quiet(args.quiet) + moltype = sourmash_args.calculate_moltype(args) + + first_sig = None + mh = None + total_loaded = 0 + + # iterate over all the sigs from all the files. + for sigfile in args.signatures: + notify('loading signatures from {}...', sigfile, end='\r') + this_n = 0 + for sigobj in sourmash.load_signatures(sigfile, ksize=args.ksize, + select_moltype=moltype, + do_raise=True): + # first signature? initialize a bunch of stuff + if first_sig is None: + first_sig = sigobj + mh = first_sig.minhash.copy_and_clear() + + # forcibly remove abundance? + if mh.track_abundance and args.flatten: + _flatten(mh) + + try: + if not args.flatten: + _check_abundance_compatibility(first_sig, sigobj) + + mh.merge(sigobj.minhash) + except: + error("ERROR when merging signature '{}' ({}) from file {}", + sigobj.name(), sigobj.md5sum()[:8], sigfile) + raise + + this_n += 1 + total_loaded += 1 + if this_n: + notify('loaded and merged {} signatures from {}...', this_n, sigfile, end='\r') + + if not total_loaded: + error("no signatures to merge!?") + sys.exit(-1) + + merged_sigobj = sourmash.SourmashSignature(mh) + + output_json = sourmash.save_signatures([merged_sigobj], fp=args.output) + + notify('loaded and merged {} signatures', total_loaded) + + +def intersect(args): + """ + intersect one or more signatures by taking the intersection of hashes. + + This function always removes abundances. + """ + p = argparse.ArgumentParser(prog='sourmash signature intersect') + p.add_argument('signatures', nargs='+') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + p.add_argument('-o', '--output', type=argparse.FileType('wt'), + default=sys.stdout, + help='output signature to this file') + sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K) + sourmash_args.add_moltype_args(p) + args = p.parse_args(args) + set_quiet(args.quiet) + moltype = sourmash_args.calculate_moltype(args) + + first_sig = None + mins = None + total_loaded = 0 + + for sigfile in args.signatures: + for sigobj in sourmash.load_signatures(sigfile, ksize=args.ksize, + select_moltype=moltype, + do_raise=True): + if first_sig is None: + first_sig = sigobj + mins = set(sigobj.minhash.get_mins()) + + mins.intersection_update(sigobj.minhash.get_mins()) + total_loaded += 1 + notify('loaded and intersected signatures from {}...', sigfile, end='\r') + + if total_loaded == 0: + error("no signatures to merge!?") + sys.exit(-1) + + # forcibly turn off track_abundance + intersect_mh = first_sig.minhash.copy_and_clear() + _flatten(intersect_mh) + intersect_mh.add_many(mins) + intersect_sigobj = sourmash.SourmashSignature(intersect_mh) + + output_json = sourmash.save_signatures([intersect_sigobj], fp=args.output) + + notify('loaded and intersected {} signatures', total_loaded) + + +def subtract(args): + """ + subtract one or more signatures from another + """ + p = argparse.ArgumentParser(prog='sourmash signature subtract') + p.add_argument('signature_from') + p.add_argument('subtraction_sigs', nargs='+') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + p.add_argument('-o', '--output', type=argparse.FileType('wt'), + default=sys.stdout, + help='output signature to this file') + p.add_argument('--flatten', action='store_true', + help='remove abundance from signatures before subtracting') + sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K) + sourmash_args.add_moltype_args(p) + args = p.parse_args(args) + set_quiet(args.quiet) + moltype = sourmash_args.calculate_moltype(args) + + from_sigfile = args.signature_from + from_sigobj = sourmash.load_one_signature(from_sigfile, ksize=args.ksize, select_moltype=moltype) + + from_mh = from_sigobj.minhash + if from_mh.track_abundance and not args.flatten: + error('Cannot use subtract on signatures with abundance tracking, sorry!') + sys.exit(1) + + subtract_mins = set(from_mh.get_mins()) + + notify('loaded signature from {}...', from_sigfile, end='\r') + + total_loaded = 0 + for sigfile in args.subtraction_sigs: + for sigobj in sourmash.load_signatures(sigfile, ksize=args.ksize, + select_moltype=moltype, + do_raise=True): + + if sigobj.minhash.track_abundance and not args.flatten: + error('Cannot use subtract on signatures with abundance tracking, sorry!') + sys.exit(1) + + subtract_mins -= set(sigobj.minhash.get_mins()) + + notify('loaded and subtracted signatures from {}...', sigfile, end='\r') + total_loaded += 1 + + if not total_loaded: + error("no signatures to subtract!?") + sys.exit(-1) + + + subtract_mh = from_sigobj.minhash.copy_and_clear() + subtract_mh.add_many(subtract_mins) + + subtract_sigobj = sourmash.SourmashSignature(subtract_mh) + + output_json = sourmash.save_signatures([subtract_sigobj], fp=args.output) + + notify('loaded and subtracted {} signatures', total_loaded) + + +def rename(args): + """ + rename a signature. + """ + p = argparse.ArgumentParser(prog='sourmash signature rename') + p.add_argument('signature') + p.add_argument('name') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + p.add_argument('-o', '--output', type=argparse.FileType('wt'), + default=sys.stdout, + help='output signature to this file') + sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K) + sourmash_args.add_moltype_args(p) + args = p.parse_args(args) + set_quiet(args.quiet) + moltype = sourmash_args.calculate_moltype(args) + + sigobj = sourmash.load_one_signature(args.signature, ksize=args.ksize, select_moltype=moltype) + sigobj.d['name'] = args.name + output_json = sourmash.save_signatures([sigobj], fp=args.output) + + notify("set name to '{}'", args.name) + + +def extract(args): + """ + extract signatures. + """ + p = argparse.ArgumentParser(prog='sourmash signature extract') + p.add_argument('signatures', nargs='+') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + p.add_argument('-o', '--output', type=argparse.FileType('wt'), + default=sys.stdout, + help='output signature to this file') + p.add_argument('--md5', default=None, + help='select signatures whose md5 contains this substring') + p.add_argument('--name', default=None, + help='select signatures whose name contains this substring') + + sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K) + sourmash_args.add_moltype_args(p) + args = p.parse_args(args) + set_quiet(args.quiet) + moltype = sourmash_args.calculate_moltype(args) + + outlist = [] + total_loaded = 0 + for filename in args.signatures: + siglist = sourmash.load_signatures(filename, ksize=args.ksize, + select_moltype=moltype, + do_raise=True) + siglist = list(siglist) + + total_loaded += len(siglist) + + # select! + if args.md5 is not None: + siglist = [ ss for ss in siglist if args.md5 in ss.md5sum() ] + if args.name is not None: + siglist = [ ss for ss in siglist if args.name in ss.name() ] + + outlist.extend(siglist) + + notify("loaded {} total that matched ksize & molecule type", + total_loaded) + if not outlist: + error("no matching signatures!") + sys.exit(-1) + + output_json = sourmash.save_signatures(outlist, fp=args.output) + + notify("extracted {} signatures from {} file(s)", len(outlist), + len(args.signatures)) + + +def flatten(args): + """ + flatten a signature, removing abundances. + """ + p = argparse.ArgumentParser(prog='sourmash signature flatten') + p.add_argument('signatures', nargs='+') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + p.add_argument('-o', '--output', type=argparse.FileType('wt'), + default=sys.stdout, + help='output signature to this file') + p.add_argument('--md5', default=None, + help='select signatures whose md5 contains this substring') + p.add_argument('--name', default=None, + help='select signatures whose name contains this substring') + + sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K) + sourmash_args.add_moltype_args(p) + args = p.parse_args(args) + set_quiet(args.quiet) + moltype = sourmash_args.calculate_moltype(args) + + outlist = [] + total_loaded = 0 + for filename in args.signatures: + siglist = sourmash.load_signatures(filename, ksize=args.ksize, + select_moltype=moltype, + do_raise=True) + siglist = list(siglist) + + total_loaded += len(siglist) + + # select! + if args.md5 is not None: + siglist = [ ss for ss in siglist if args.md5 in ss.md5sum() ] + if args.name is not None: + siglist = [ ss for ss in siglist if args.name in ss.name() ] + + for ss in siglist: + flattened_mh = ss.minhash.copy_and_clear() + _flatten(flattened_mh) + flattened_mh.add_many(ss.minhash.get_mins()) + + ss.minhash = flattened_mh + + outlist.extend(siglist) + + output_json = sourmash.save_signatures(outlist, fp=args.output) + + notify("loaded {} total that matched ksize & molecule type", + total_loaded) + notify("extracted {} signatures from {} file(s)", len(outlist), + len(args.signatures)) + + +def downsample(args): + """ + downsample a scaled signature. + """ + p = argparse.ArgumentParser(prog='sourmash signature downsample') + p.add_argument('signatures', nargs="+") + p.add_argument('--scaled', type=int, default=0, + help='scaled value to downsample to') + p.add_argument('--num', type=int, default=0, + help='num value to downsample to') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + p.add_argument('-o', '--output', type=argparse.FileType('wt'), + default=sys.stdout, + help='output signature to this file') + sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K) + sourmash_args.add_moltype_args(p) + args = p.parse_args(args) + set_quiet(args.quiet) + moltype = sourmash_args.calculate_moltype(args) + + if not args.num and not args.scaled: + error('must specify either --num or --scaled value') + sys.exit(-1) + + if args.num and args.scaled: + error('cannot specify both --num and --scaled') + sys.exit(-1) + + output_list = [] + total_loaded = 0 + for sigfile in args.signatures: + siglist = sourmash.load_signatures(sigfile, ksize=args.ksize, select_moltype=moltype, do_raise=True) + + for sigobj in siglist: + mh = sigobj.minhash + + notify('loading and downsampling signature from {}...', sigfile, end='\r') + total_loaded += 1 + if args.scaled: + if mh.scaled: + mh_new = mh.downsample_scaled(args.scaled) + else: # try to turn a num into a scaled + # first check: can we? + max_hash = get_max_hash_for_scaled(args.scaled) + mins = mh.get_mins() + if max(mins) < max_hash: + raise ValueError("this num MinHash does not have enough hashes to convert it into a scaled MinHash.") + + mh_new = copy.copy(mh) + _set_num_scaled(mh_new, 0, args.scaled) + elif args.num: + if mh.num: + mh_new = mh.downsample_n(args.num) + else: # try to turn a scaled into a num + # first check: can we? + if len(mh) < args.num: + raise ValueError("this scaled MinHash has only {} hashes") + + mh_new = copy.copy(mh) + _set_num_scaled(mh_new, args.num, 0) + + sigobj.minhash = mh_new + + output_list.append(sigobj) + + output_json = sourmash.save_signatures(output_list, fp=args.output) + + notify("loaded and downsampled {} signatures", total_loaded) + + +def sig_import(args): + """ + import a signature into sourmash format. + """ + p = argparse.ArgumentParser(prog='sourmash signature import') + p.add_argument('filenames', nargs='+') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + p.add_argument('-o', '--output', type=argparse.FileType('wt'), + default=sys.stdout, + help='output signature to this file') + args = p.parse_args(args) + set_quiet(args.quiet) + + siglist = [] + for filename in args.filenames: + with open(filename) as fp: + x = json.loads(fp.read()) + + ksize = x['kmer'] + num = x['sketchSize'] + + assert x['hashType'] == "MurmurHash3_x64_128" + assert x['hashBits'] == 64 + assert x['hashSeed'] == 42 + + xx = x['sketches'][0] + hashes = xx['hashes'] + + mh = sourmash.MinHash(ksize=ksize, n=num, is_protein=False) + mh.add_many(hashes) + + s = sourmash.SourmashSignature(mh, filename=filename) + siglist.append(s) + + sourmash.save_signatures(siglist, args.output) + + +def export(args): + """ + export a signature to mash format + """ + p = argparse.ArgumentParser(prog='sourmash signature export') + p.add_argument('filename') + p.add_argument('-q', '--quiet', action='store_true', + help='suppress non-error output') + p.add_argument('-o', '--output', type=argparse.FileType('wt'), + default=sys.stdout, + help='output signature to this file') + sourmash_args.add_ksize_arg(p, DEFAULT_LOAD_K) + sourmash_args.add_moltype_args(p) + args = p.parse_args(args) + set_quiet(args.quiet) + moltype = sourmash_args.calculate_moltype(args) + + total_loaded = 0 + ss = sourmash.load_one_signature(args.filename, ksize=args.ksize, + select_moltype=moltype) + mh = ss.minhash + + x = {} + x['kmer'] = mh.ksize + x['sketchSize'] = len(mh) + + x['hashType'] = "MurmurHash3_x64_128" + x['hashBits'] = 64 + x['hashSeed'] = mh.seed + + ll = list(mh.get_mins()) + x['sketches'] = [{ 'hashes': ll }] + + print(json.dumps(x), file=args.output) + notify("exported signature {} ({})", ss.name(), ss.md5sum()[:8]) + + +def main(sysv_args): + set_quiet(False) + + commands = {'merge': merge, + 'intersect': intersect, + 'rename': rename, + 'extract': extract, + 'flatten': flatten, + 'downsample': downsample, + 'subtract': subtract, + 'import': sig_import, + 'export': export, + 'describe': describe, + 'overlap': overlap} + + parser = argparse.ArgumentParser( + description='signature file manipulation utilities', usage=usage) + parser.add_argument('sig_command', nargs='?') + args = parser.parse_args(sysv_args[0:1]) + + if not args.sig_command: + print(usage) + sys.exit(1) + + if args.sig_command not in commands: + error('Unrecognized command: {}', args.sig_command) + parser.print_help() + sys.exit(1) + + cmd = commands.get(args.sig_command) + cmd(sysv_args[1:]) + + return 0 + + +if __name__ == '__main__': + sys.exit(main(sys.argv[1:])) diff --git a/sourmash/signature.py b/sourmash/signature.py index da0babe264..d4fd4ab3fe 100644 --- a/sourmash/signature.py +++ b/sourmash/signature.py @@ -175,7 +175,7 @@ def _guess_open(filename): def load_signatures(data, ksize=None, select_moltype=None, - ignore_md5sum=False, do_raise=False): + ignore_md5sum=False, do_raise=False, quiet=False): """Load a JSON string with signatures into classes. Returns list of SourmashSignature objects. @@ -205,7 +205,7 @@ def load_signatures(data, ksize=None, select_moltype=None, is_fp = True done = True except OSError as excinfo: - error(str(excinfo)) + if not quiet: error(str(excinfo)) if do_raise: raise return @@ -224,8 +224,9 @@ def load_signatures(data, ksize=None, select_moltype=None, sig.minhash.is_molecule_type(select_moltype): yield sig except Exception as e: - error("Error in parsing signature; quitting.") - error("Exception: {}", str(e)) + if not quiet: + error("Error in parsing signature; quitting.") + error("Exception: {}", str(e)) if do_raise: raise finally: diff --git a/tests/test-data/47+63-intersect.fa.sig b/tests/test-data/47+63-intersect.fa.sig new file mode 100644 index 0000000000..4d34cfca9d --- /dev/null +++ b/tests/test-data/47+63-intersect.fa.sig @@ -0,0 +1 @@ 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diff --git a/tests/test-data/47+63-multisig.sig b/tests/test-data/47+63-multisig.sig new file mode 100644 index 0000000000..32fff94b24 --- /dev/null +++ b/tests/test-data/47+63-multisig.sig @@ -0,0 +1 @@ +[{"class":"sourmash_signature","email":"","filename":"-","hash_function":"0.murmur64","license":"CC0","name":"NC_009665.1 Shewanella baltica OS185, complete 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Shewanella baltica OS185 plasmid pS18501, complete sequence","signatures":[{"abundances":[1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],"ksize":31,"max_hash":18446744073709552,"md5sum":"bde81a418745fb8b94b6b0bb5bda97e4","mins":[306041902505698,395356088720884,457671098462976,1339674524726757,1483592564337201,1996672784729607,2154825108832254,2296330477067902,2556506799873846,2947035710205399,3549947024705822,3705003329123112,4388622108830575,4421125787216995,4501876131664304,4641458089041250,4676205735481526,5335020091722251,5489284312856062,6304297838290460,6980494356161697,7134741662059672,7430512069482015,7987424295175338,8279996819873290,8333295411468735,8336794237476945,8444597753784738,8471415745047933,8478129640091772,8676906171988104,9630291603264391,9745464335501377,10196461247193047,10266820110531598,10691866174146243,11261264491503353,11401700519195899,11479308399516360,11950767340516423,11958460182520420,12157910100394424,12418785272430115,12574953991866005,12880367229968159,13099158956896694,13441217894362634,13485627420255013,13630191002096322,13669670567123455,13851419674057285,13860370948717274,13894176996423815,14775120243637151,14841572903295226,14981979822436646,15413173941024438,15911665623700279,16555675508895642,16850886838136612,16887131664281014,17420499051739414,17848382043638116,18258589056361348],"molecule":"DNA","num":0,"seed":42}],"version":0.4},{"class":"sourmash_signature","email":"","filename":"-","hash_function":"0.murmur64","license":"CC0","name":"NC_011663.1 Shewanella baltica OS223, complete 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Shewanella baltica OS223 plasmid pS22301, complete sequence","signatures":[{"abundances":[1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],"ksize":31,"max_hash":18446744073709552,"md5sum":"87a9aec4272972a74c14adc376ba6ef4","mins":[189372881188038,927733683191258,1339674524726757,1432423484009425,1596940098556068,1642353838656017,1800236363852916,1806220280793222,1961412299515744,1977965122461301,2050342367296606,2182965638264818,2230499997873756,2556506799873846,2798287443905216,2947035710205399,3103723994300125,3705003329123112,4381988283585309,4421125787216995,4676205735481526,4739486119895556,4934031744913600,5333588429074391,5381644047795232,5415695371666931,5435896905179181,6603801197985057,6980494356161697,7686401160104927,7880427676195188,7884420955280740,7965797077819465,7987424295175338,8333295411468735,8440361071453676,8444597753784738,8471415745047933,8676906171988104,8708531679191487,9630291603264391,9745464335501377,9837155339404081,10266820110531598,10322210269356740,10378785729437771,10969273755543103,11208848071296690,11261264491503353,11300136534963911,11376187659958324,11401700519195899,11479308399516360,11481525923581615,11641472090021925,11734135498068733,12157910100394424,12340480227036543,12370584345785125,12422291487048270,12518321496058049,12520923198368458,12753765690440504,12767461214123574,12868775358248804,12880367229968159,13099158956896694,13466324773783696,13630191002096322,13669670567123455,13851419674057285,13860370948717274,13939640716669681,14028210972184975,14424431392247406,14486688729309047,14841572903295226,14981979822436646,15180542353613847,15534018111390967,15609335762508274,15775430111926025,15911665623700279,16116526388299685,16436934401638026,16551950824707495,16850886838136612,17420499051739414,17654605406803051,18251366028776903],"molecule":"DNA","num":0,"seed":42}],"version":0.4},{"class":"sourmash_signature","email":"","filename":"-","hash_function":"0.murmur64","license":"CC0","name":"NC_011668.1 Shewanella baltica OS223 plasmid pS22302, complete sequence","signatures":[{"abundances":[1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],"ksize":31,"max_hash":18446744073709552,"md5sum":"837bf2a7db4c55de184bc88cdef2a093","mins":[117764718466551,312508185357838,444196295289556,457671098462976,623564286058606,717098217279451,736734785664407,1075576974119467,1278259882696625,1339674524726757,1377792461855597,1505096985478881,1719016742757524,1800236363852916,2154825108832254,2296330477067902,2566619437831302,2742141972024096,2798287443905216,2823296594306435,2947035710205399,2953540238859553,3056598953438835,3315214714717367,3320924500756368,4421125787216995,4501876131664304,4613982013879466,4975226570860151,5333588429074391,5685175185189040,5873135456761229,6340198968767374,6633360677360828,6642050646677695,7088092836502881,7430512069482015,7686401160104927,8005398354408904,8333295411468735,8336794237476945,8477713132692627,8519080382417862,8899181735854770,9089480345230505,9153419337108811,9306667536052907,10266820110531598,10322210269356740,10423223119950014,11320460996284466,11401700519195899,11403781057496463,11481525923581615,11734135498068733,11919527016797167,12287926682400907,12351058834484070,12370584345785125,13087887536529400,13283754265526543,13851419674057285,13860370948717274,13973873959866261,14003981992485830,14486688729309047,14594358540722423,14841572903295226,14867172379036342,15074812809725285,15947799685112623,16061260687253150,16100320419524573,16312770958996932,16344386984734169,16748052258655621,16887131664281014,17229146874971723],"molecule":"DNA","num":0,"seed":42}],"version":0.4},{"class":"sourmash_signature","email":"","filename":"-","hash_function":"0.murmur64","license":"CC0","name":"NC_011665.1 Shewanella baltica OS223 plasmid pS22303, complete sequence","signatures":[{"abundances":[1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],"ksize":31,"max_hash":18446744073709552,"md5sum":"485c3377a3057fba74d2d50419f80005","mins":[385242214102144,395356088720884,457671098462976,792800620274218,1339674524726757,1466391743844010,1535451811798960,1642353838656017,1658104204669725,1996672784729607,2154825108832254,2296330477067902,2823296594306435,2827393174086051,2947035710205399,3103723994300125,3173337239261818,3321523572005253,3549947024705822,3863738703644495,4421125787216995,4499856296475689,4501876131664304,4689320811962225,5012847090206147,5381644047795232,5415695371666931,5435896905179181,5601051424903560,6724547078953919,6906188072934282,7430512069482015,7686401160104927,7880427676195188,7987424295175338,8005398354408904,8336794237476945,8386972491027812,8995595104860000,9089480345230505,9306667536052907,9837155339404081,10071227734029562,10266820110531598,10322210269356740,10483468440563572,10506658427947222,10551722700063187,11208382996235211,11208848071296690,11257541020758021,11376187659958324,11401700519195899,12351058834484070,12518321496058049,12574953991866005,12868775358248804,13100332410846032,13573812546471498,13669670567123455,13851419674057285,13860370948717274,13894176996423815,13973873959866261,14424431392247406,14841572903295226,15534018111390967,16116526388299685,16436934401638026,16834585049588482,16887131664281014,16993284480102555,17939317258777532,17996626721764095,18212687689930990,18251366028776903],"molecule":"DNA","num":0,"seed":42}],"version":0.4}] \ No newline at end of file diff --git a/tests/test-data/47+63.fa.sig b/tests/test-data/47+63.fa.sig index 073e0bcbeb..57e1715570 100644 --- a/tests/test-data/47+63.fa.sig +++ b/tests/test-data/47+63.fa.sig @@ -1 +1 @@ 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\ No newline at end of file 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/dev/null +++ b/tests/test-data/track_abund/47.fa.sig @@ -0,0 +1 @@ +[{"class":"sourmash_signature","email":"","filename":"podar-ref/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-data/track_abund/63.fa.sig b/tests/test-data/track_abund/63.fa.sig new file mode 100644 index 0000000000..a44205a439 --- /dev/null +++ b/tests/test-data/track_abund/63.fa.sig @@ -0,0 +1 @@ +[{"class":"sourmash_signature","email":"","filename":"podar-ref/63.fa","hash_function":"0.murmur64","license":"CC0","name":"NC_011663.1 Shewanella baltica OS223, complete 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\ No newline at end of file diff --git a/tests/test__minhash.py b/tests/test__minhash.py index 3411a80b80..2c4159945a 100644 --- a/tests/test__minhash.py +++ b/tests/test__minhash.py @@ -41,11 +41,11 @@ import pytest -from sourmash_lib._minhash import (MinHash, hash_murmur, dotproduct, +from sourmash._minhash import (MinHash, hash_murmur, dotproduct, get_scaled_for_max_hash, get_max_hash_for_scaled) from . import sourmash_tst_utils as utils -from sourmash_lib import signature +from sourmash import signature # add: # * get default params from Python @@ -895,7 +895,7 @@ def test_scaled_property(track_abundance): def test_mh_subtract(track_abundance): - # test merging two identically configured minhashes + # test subtracting two identically configured minhashes a = MinHash(20, 10, track_abundance=track_abundance) for i in range(0, 40, 2): a.add_hash(i) diff --git a/tests/test_api.py b/tests/test_api.py index 0eb53d4057..2118c5ee40 100644 --- a/tests/test_api.py +++ b/tests/test_api.py @@ -1,6 +1,5 @@ from __future__ import print_function, unicode_literals - -import sourmash_lib as sourmash +import sourmash def test_sourmash_signature_api(): diff --git a/tests/test_cmd_signature.py b/tests/test_cmd_signature.py new file mode 100644 index 0000000000..4842534a6c --- /dev/null +++ b/tests/test_cmd_signature.py @@ -0,0 +1,682 @@ +""" +Tests for the 'sourmash signature' command line. +""" +from __future__ import print_function, unicode_literals +import csv + +import pytest + +from . import sourmash_tst_utils as utils +import sourmash + +## command line tests + + +def test_run_sourmash_signature_cmd(): + status, out, err = utils.runscript('sourmash', ['signature'], fail_ok=True) + assert status != 0 # no args provided, ok ;) + + +def test_run_sourmash_sig_cmd(): + status, out, err = utils.runscript('sourmash', ['sig'], fail_ok=True) + assert status != 0 # no args provided, ok ;) + + +@utils.in_tempdir +def test_sig_merge_1(c): + # merge of 47 & 63 should be union of mins + sig47 = utils.get_test_data('47.fa.sig') + sig63 = utils.get_test_data('63.fa.sig') + sig47and63 = utils.get_test_data('47+63.fa.sig') + c.run_sourmash('sig', 'merge', sig47, sig63) + + # stdout should be new signature + out = c.last_result.out + + test_merge_sig = sourmash.load_one_signature(sig47and63) + actual_merge_sig = sourmash.load_one_signature(out) + + print(test_merge_sig.minhash) + print(actual_merge_sig.minhash) + print(out) + + assert actual_merge_sig.minhash == test_merge_sig.minhash + + +@utils.in_tempdir +def test_sig_merge_1_multisig(c): + # merge of 47 & 63 should be union of mins; here, sigs are in same file. + multisig = utils.get_test_data('47+63-multisig.sig') + sig47and63 = utils.get_test_data('47+63.fa.sig') + c.run_sourmash('sig', 'merge', multisig, '--flatten') + + # stdout should be new signature + out = c.last_result.out + + test_merge_sig = sourmash.load_one_signature(sig47and63) + actual_merge_sig = sourmash.load_one_signature(out) + + print(test_merge_sig.minhash) + print(actual_merge_sig.minhash) + print(out) + + assert actual_merge_sig.minhash == test_merge_sig.minhash + + +@utils.in_tempdir +def test_sig_merge_1_ksize_moltype(c): + # check ksize, moltype args + sig47 = utils.get_test_data('47.fa.sig') + sig63 = utils.get_test_data('63.fa.sig') + sig47and63 = utils.get_test_data('47+63.fa.sig') + c.run_sourmash('sig', 'merge', sig47, sig63, '--dna', '-k', '31') + + # stdout should be new signature + out = c.last_result.out + + test_merge_sig = sourmash.load_one_signature(sig47and63) + actual_merge_sig = sourmash.load_one_signature(out) + + print(test_merge_sig.minhash) + print(actual_merge_sig.minhash) + print(out) + + assert actual_merge_sig.minhash == test_merge_sig.minhash + + +@utils.in_tempdir +def test_sig_merge_2(c): + # merge of 47 with nothing should be 47 + sig47 = utils.get_test_data('47.fa.sig') + c.run_sourmash('sig', 'merge', sig47) + + # stdout should be new signature + out = c.last_result.out + + test_merge_sig = sourmash.load_one_signature(sig47) + actual_merge_sig = sourmash.load_one_signature(out) + + print(out) + + assert actual_merge_sig.minhash == test_merge_sig.minhash + + +@utils.in_tempdir +def test_sig_merge_3_abund_ab_ok(c): + # merge of 47 and 63 with abund should work + sig47abund = utils.get_test_data('track_abund/47.fa.sig') + sig63abund = utils.get_test_data('track_abund/63.fa.sig') + + c.run_sourmash('sig', 'merge', sig47abund, sig63abund) + actual_merge_sig = sourmash.load_one_signature(c.last_result.out) + # @CTB: should check that this merge did what we think it should do! + + +@utils.in_tempdir +def test_sig_merge_3_abund_ab(c): + # merge of 47 with abund, with 63 without, should fail; and vice versa + sig47 = utils.get_test_data('47.fa.sig') + sig63abund = utils.get_test_data('track_abund/63.fa.sig') + + with pytest.raises(ValueError) as e: + c.run_sourmash('sig', 'merge', sig47, sig63abund) + + print(c.last_result) + assert 'incompatible signatures: track_abundance is False in first sig, True in second' in c.last_result.err + + +@utils.in_tempdir +def test_sig_merge_3_abund_ba(c): + # merge of 47 without abund, with 63 with, should fail + sig47 = utils.get_test_data('47.fa.sig') + sig63abund = utils.get_test_data('track_abund/63.fa.sig') + + with pytest.raises(ValueError) as e: + c.run_sourmash('sig', 'merge', sig63abund, sig47) + + print(c.last_result) + assert 'incompatible signatures: track_abundance is True in first sig, False in second' in c.last_result.err + + +@utils.in_tempdir +def test_sig_merge_flatten(c): + # merge of 47 without abund, with 63 with, will succeed with --flatten + sig47 = utils.get_test_data('47.fa.sig') + sig63abund = utils.get_test_data('track_abund/63.fa.sig') + sig47and63 = utils.get_test_data('47+63.fa.sig') + + c.run_sourmash('sig', 'merge', sig63abund, sig47, '--flatten') + + print(c.last_result) + out = c.last_result.out + + test_merge_sig = sourmash.load_one_signature(sig47and63) + actual_merge_sig = sourmash.load_one_signature(out) + + print(test_merge_sig.minhash) + print(actual_merge_sig.minhash) + print(out) + + assert actual_merge_sig.minhash == test_merge_sig.minhash + + +@utils.in_tempdir +def test_sig_merge_flatten_2(c): + # merge of 47 with abund, with 63 with, will succeed with --flatten + sig47abund = utils.get_test_data('track_abund/47.fa.sig') + sig63 = utils.get_test_data('63.fa.sig') + sig47and63 = utils.get_test_data('47+63.fa.sig') + + c.run_sourmash('sig', 'merge', sig63, sig47abund, '--flatten') + + print(c.last_result) + out = c.last_result.out + + test_merge_sig = sourmash.load_one_signature(sig47and63) + actual_merge_sig = sourmash.load_one_signature(out) + + print(test_merge_sig.minhash) + print(actual_merge_sig.minhash) + print(out) + + assert actual_merge_sig.minhash == test_merge_sig.minhash + + +@utils.in_tempdir +def test_sig_intersect_1(c): + # intersect of 47 and 63 should be intersection of mins + sig47 = utils.get_test_data('47.fa.sig') + sig63 = utils.get_test_data('63.fa.sig') + sig47and63 = utils.get_test_data('47+63-intersect.fa.sig') + c.run_sourmash('sig', 'intersect', sig47, sig63) + + # stdout should be new signature + out = c.last_result.out + + test_intersect_sig = sourmash.load_one_signature(sig47and63) + actual_intersect_sig = sourmash.load_one_signature(out) + + print(test_intersect_sig.minhash) + print(actual_intersect_sig.minhash) + print(out) + + assert actual_intersect_sig.minhash == test_intersect_sig.minhash + + +@utils.in_tempdir +def test_sig_intersect_2(c): + # intersect of 47 with abund and 63 with abund should be same + # as without abund, i.e. intersect 'flattens' + sig47 = utils.get_test_data('track_abund/47.fa.sig') + sig63 = utils.get_test_data('track_abund/63.fa.sig') + sig47and63 = utils.get_test_data('47+63-intersect.fa.sig') + c.run_sourmash('sig', 'intersect', sig47, sig63) + + # stdout should be new signature + out = c.last_result.out + + test_intersect_sig = sourmash.load_one_signature(sig47and63) + actual_intersect_sig = sourmash.load_one_signature(out) + + print(test_intersect_sig.minhash) + print(actual_intersect_sig.minhash) + print(out) + + assert actual_intersect_sig.minhash == test_intersect_sig.minhash + + +@utils.in_tempdir +def test_sig_subtract_1(c): + # subtract of 63 from 47 + sig47 = utils.get_test_data('47.fa.sig') + sig63 = utils.get_test_data('63.fa.sig') + c.run_sourmash('sig', 'subtract', sig47, sig63) + + # stdout should be new signature + out = c.last_result.out + + test1_sig = sourmash.load_one_signature(sig47) + test2_sig = sourmash.load_one_signature(sig63) + actual_subtract_sig = sourmash.load_one_signature(out) + + mins = set(test1_sig.minhash.get_mins()) + mins -= set(test2_sig.minhash.get_mins()) + + assert set(actual_subtract_sig.minhash.get_mins()) == set(mins) + + +@utils.in_tempdir +def test_sig_subtract_1_multisig(c): + # subtract of everything from 47 + sig47 = utils.get_test_data('47.fa.sig') + multisig = utils.get_test_data('47+63-multisig.sig') + c.run_sourmash('sig', 'subtract', sig47, multisig, '--flatten') + + # stdout should be new signature + out = c.last_result.out + + actual_subtract_sig = sourmash.load_one_signature(out) + + assert not set(actual_subtract_sig.minhash.get_mins()) + + +@utils.in_tempdir +def test_sig_subtract_2(c): + # subtract of 63 from 47 should fail if 47 has abund + sig47 = utils.get_test_data('track_abund/47.fa.sig') + sig63 = utils.get_test_data('63.fa.sig') + + with pytest.raises(ValueError): + c.run_sourmash('sig', 'subtract', sig47, sig63) + + +@utils.in_tempdir +def test_sig_subtract_3(c): + # subtract of 63 from 47 should fail if 63 has abund + sig47 = utils.get_test_data('47.fa.sig') + sig63 = utils.get_test_data('track_abund/63.fa.sig') + + with pytest.raises(ValueError): + c.run_sourmash('sig', 'subtract', sig47, sig63) + + +@utils.in_tempdir +def test_sig_intersect_2(c): + # intersect of 47 and nothing should be self + sig47 = utils.get_test_data('47.fa.sig') + c.run_sourmash('sig', 'intersect', sig47) + + # stdout should be new signature + out = c.last_result.out + + test_intersect_sig = sourmash.load_one_signature(sig47) + actual_intersect_sig = sourmash.load_one_signature(out) + + print(test_intersect_sig.minhash) + print(actual_intersect_sig.minhash) + print(out) + + assert actual_intersect_sig.minhash == test_intersect_sig.minhash + + +@utils.in_tempdir +def test_sig_intersect_2_multisig(c): + # intersect of all the multisig stuff should be nothing + sig47 = utils.get_test_data('47+63-multisig.sig') + c.run_sourmash('sig', 'intersect', sig47) + + # stdout should be new signature + out = c.last_result.out + + actual_intersect_sig = sourmash.load_one_signature(out) + + assert not len(actual_intersect_sig.minhash) + + +@utils.in_tempdir +def test_sig_rename_1(c): + # set new name for 47 + sig47 = utils.get_test_data('47.fa.sig') + c.run_sourmash('sig', 'rename', sig47, 'fiz bar') + + # stdout should be new signature + out = c.last_result.out + + test_rename_sig = sourmash.load_one_signature(sig47) + actual_rename_sig = sourmash.load_one_signature(out) + + print(test_rename_sig.minhash) + print(actual_rename_sig.minhash) + + assert actual_rename_sig.minhash == test_rename_sig.minhash + assert test_rename_sig.name() != actual_rename_sig.name() + assert actual_rename_sig.name() == 'fiz bar' + + +@utils.in_tempdir +def test_sig_extract_1(c): + # extract 47 from 47... :) + sig47 = utils.get_test_data('47.fa.sig') + c.run_sourmash('sig', 'extract', sig47) + + # stdout should be new signature + out = c.last_result.out + + test_extract_sig = sourmash.load_one_signature(sig47) + actual_extract_sig = sourmash.load_one_signature(out) + + assert actual_extract_sig == test_extract_sig + + +@utils.in_tempdir +def test_sig_extract_2(c): + # extract matches to 47's md5sum from among several + sig47 = utils.get_test_data('47.fa.sig') + sig63 = utils.get_test_data('63.fa.sig') + c.run_sourmash('sig', 'extract', sig47, sig63, '--md5', '09a0869') + + # stdout should be new signature + out = c.last_result.out + + test_extract_sig = sourmash.load_one_signature(sig47) + actual_extract_sig = sourmash.load_one_signature(out) + + print(test_extract_sig.minhash) + print(actual_extract_sig.minhash) + + assert actual_extract_sig == test_extract_sig + + +@utils.in_tempdir +def test_sig_extract_3(c): + # extract nothing (no md5 match) + sig47 = utils.get_test_data('47.fa.sig') + with pytest.raises(ValueError) as exc: + c.run_sourmash('sig', 'extract', sig47, '--md5', 'FOO') + + +@utils.in_tempdir +def test_sig_extract_4(c): + # extract matches to 47's name from among several signatures + sig47 = utils.get_test_data('47.fa.sig') + sig63 = utils.get_test_data('63.fa.sig') + c.run_sourmash('sig', 'extract', sig47, sig63, '--name', 'NC_009665.1') + + # stdout should be new signature + out = c.last_result.out + + test_extract_sig = sourmash.load_one_signature(sig47) + actual_extract_sig = sourmash.load_one_signature(out) + + print(test_extract_sig.minhash) + print(actual_extract_sig.minhash) + + assert actual_extract_sig == test_extract_sig + + +@utils.in_tempdir +def test_sig_extract_5(c): + # extract nothing (no name match) + sig47 = utils.get_test_data('47.fa.sig') + with pytest.raises(ValueError) as exc: + c.run_sourmash('sig', 'extract', sig47, '--name', 'FOO') + + +@utils.in_tempdir +def test_sig_extract_6(c): + # extract matches to several names from among several signatures + sig47 = utils.get_test_data('47.fa.sig') + sig63 = utils.get_test_data('63.fa.sig') + c.run_sourmash('sig', 'extract', sig47, sig63, '--name', 'Shewanella') + + # stdout should be new signature + out = c.last_result.out + + siglist = sourmash.load_signatures(out) + siglist = list(siglist) + + assert len(siglist) == 2 + + +@utils.in_tempdir +def test_sig_flatten_1(c): + # extract matches to several names from among several signatures & flatten + sig47abund = utils.get_test_data('track_abund/47.fa.sig') + sig47 = utils.get_test_data('47.fa.sig') + c.run_sourmash('sig', 'flatten', sig47abund, '--name', 'Shewanella') + + # stdout should be new signature + out = c.last_result.out + + siglist = sourmash.load_signatures(out) + siglist = list(siglist) + + assert len(siglist) == 1 + + test_flattened = sourmash.load_one_signature(sig47) + assert test_flattened.minhash == siglist[0].minhash + + +@utils.in_tempdir +def test_sig_downsample_1_scaled(c): + # downsample a scaled signature + sig47 = utils.get_test_data('47.fa.sig') + c.run_sourmash('sig', 'downsample', '--scaled', '10000', sig47) + + # stdout should be new signature + out = c.last_result.out + + test_downsample_sig = sourmash.load_one_signature(sig47) + actual_downsample_sig = sourmash.load_one_signature(out) + + test_mh = test_downsample_sig.minhash.downsample_scaled(10000) + + assert actual_downsample_sig.minhash == test_mh + + +@utils.in_tempdir +def test_sig_downsample_1_scaled_downsample_multisig(c): + # downsample many scaled signatures in one file + multisig = utils.get_test_data('47+63-multisig.sig') + c.run_sourmash('sig', 'downsample', '--scaled', '10000', multisig) + + # stdout should be new signatures + out = c.last_result.out + + for sig in sourmash.load_signatures(out): + assert sig.minhash.scaled == 10000 + + +@utils.in_tempdir +def test_sig_downsample_1_scaled_to_num(c): + # downsample a scaled signature + sig47 = utils.get_test_data('47.fa.sig') + c.run_sourmash('sig', 'downsample', '--num', '500', sig47) + + # stdout should be new signature + out = c.last_result.out + + actual_downsample_sig = sourmash.load_one_signature(out) + actual_mins = actual_downsample_sig.minhash.get_mins() + actual_mins = list(actual_mins) + actual_mins.sort() + + test_downsample_sig = sourmash.load_one_signature(sig47) + test_mins = test_downsample_sig.minhash.get_mins() + test_mins = list(test_mins) + test_mins.sort() + test_mins = test_mins[:500] # take 500 smallest + + assert actual_mins == test_mins + + +@utils.in_tempdir +def test_sig_downsample_1_scaled_to_num_fail(c): + # downsample a scaled signature + sig47 = utils.get_test_data('47.fa.sig') + + with pytest.raises(ValueError): + c.run_sourmash('sig', 'downsample', '--num', '50000', sig47) + + +@utils.in_tempdir +def test_sig_downsample_1_scaled_empty(c): + # downsample a scaled signature + sig47 = utils.get_test_data('47.fa.sig') + + with pytest.raises(ValueError): + c.run_sourmash('sig', 'downsample', sig47) + + +@utils.in_tempdir +def test_sig_downsample_2_num(c): + # downsample a num signature + sigs11 = utils.get_test_data('genome-s11.fa.gz.sig') + c.run_sourmash('sig', 'downsample', '--num', '500', + '-k', '21', '--dna', sigs11) + + # stdout should be new signature + out = c.last_result.out + + test_downsample_sig = sourmash.load_one_signature(sigs11, ksize=21, + select_moltype='DNA') + actual_downsample_sig = sourmash.load_one_signature(out) + test_mh = test_downsample_sig.minhash.downsample_n(500) + + assert actual_downsample_sig.minhash == test_mh + + +@utils.in_tempdir +def test_sig_downsample_2_num_to_scaled(c): + # downsample a num signature and convert it into a scaled sig + sigs11 = utils.get_test_data('genome-s11.fa.gz.sig') + c.run_sourmash('sig', 'downsample', '--scaled', '10000', + '-k', '21', '--dna', sigs11) + + # stdout should be new signature + out = c.last_result.out + + test_downsample_sig = sourmash.load_one_signature(sigs11, ksize=21, + select_moltype='DNA') + actual_downsample_sig = sourmash.load_one_signature(out) + + test_mins = test_downsample_sig.minhash.get_mins() + actual_mins = actual_downsample_sig.minhash.get_mins() + + # select those mins that are beneath the new max hash... + max_hash = actual_downsample_sig.minhash.max_hash + test_mins_down = { k for k in test_mins if k < max_hash } + assert test_mins_down == set(actual_mins) + + +@utils.in_tempdir +def test_sig_downsample_2_num_to_scaled_fail(c): + # downsample a num signature and FAIL to convert it into a scaled sig + # because new scaled is too low + sigs11 = utils.get_test_data('genome-s11.fa.gz.sig') + + with pytest.raises(ValueError): + c.run_sourmash('sig', 'downsample', '--scaled', '100', + '-k', '21', '--dna', sigs11) + + +@utils.in_tempdir +def test_sig_downsample_2_num_empty(c): + # downsample a num signature + sigs11 = utils.get_test_data('genome-s11.fa.gz.sig') + + with pytest.raises(ValueError): + c.run_sourmash('sig', 'downsample', '-k', '21', '--dna', sigs11) + + +@utils.in_tempdir +def test_sig_describe_1(c): + # get basic info on a signature + sig47 = utils.get_test_data('47.fa.sig') + c.run_sourmash('sig', 'describe', sig47) + + 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_describe_1_multisig(c): + # get basic info on multiple signatures in a single file + sigs = utils.get_test_data('47+63-multisig.sig') + c.run_sourmash('sig', 'describe', sigs) + + out = c.last_result.out + print(c.last_result) + + expected_output = """\ +signature: NC_009665.1 Shewanella baltica OS185, complete genome +signature: NC_009661.1 Shewanella baltica OS185 plasmid pS18501, complete sequence +signature: NC_011663.1 Shewanella baltica OS223, complete genome +signature: NC_011664.1 Shewanella baltica OS223 plasmid pS22301, complete sequence +signature: NC_011668.1 Shewanella baltica OS223 plasmid pS22302, complete sequence +signature: NC_011665.1 Shewanella baltica OS223 plasmid pS22303, complete sequence""".splitlines() + for line in expected_output: + assert line.strip() in out + + +@utils.in_tempdir +def test_sig_describe_2(c): + # get info in CSV spreadsheet + sig47 = utils.get_test_data('47.fa.sig') + sig63 = utils.get_test_data('63.fa.sig') + c.run_sourmash('sig', 'describe', sig47, sig63, '--csv', 'out.csv') + + expected_md5 = ['09a08691ce52952152f0e866a59f6261', + '38729c6374925585db28916b82a6f513'] + + with open(c.output('out.csv'), 'rt') as fp: + r = csv.DictReader(fp) + + n = 0 + + for row, md5 in zip(r, expected_md5): + assert row['md5'] == md5 + n += 1 + + assert n == 2 + + +@utils.in_tempdir +def test_sig_overlap(c): + # get overlap details + sig47 = utils.get_test_data('47.fa.sig') + sig63 = utils.get_test_data('63.fa.sig') + c.run_sourmash('sig', 'overlap', sig47, sig63) + out = c.last_result.out + + print(out) + + # md5s + assert '09a08691ce52952152f0e866a59f6261' in out + assert '38729c6374925585db28916b82a6f513' in out + + assert 'similarity: 0.32069' in out + assert 'number of hashes in common: 2529' in out + + +@utils.in_tempdir +def test_import_export_1(c): + # check to make sure we can import what we've exported! + inp = utils.get_test_data('genome-s11.fa.gz.sig') + outp = c.output('export.json') + + c.run_sourmash('sig', 'export', inp, '-o', outp, '-k', '21', '--dna') + c.run_sourmash('sig', 'import', outp) + + original = sourmash.load_one_signature(inp, ksize=21, select_moltype='DNA') + roundtrip = sourmash.load_one_signature(c.last_result.out) + + assert original.minhash == roundtrip.minhash + + +@utils.in_tempdir +def test_import_export_2(c): + # check to make sure we can import a mash JSON dump file. + # NOTE: msh.json_dump file calculated like so: + # mash sketch -s 500 -k 21 ./tests/test-data/genome-s11.fa.gz + # mash info -d ./tests/test-data/genome-s11.fa.gz.msh > tests/test-data/genome-s11.fa.gz.msh.json_dump + # + sig1 = utils.get_test_data('genome-s11.fa.gz.sig') + msh_sig = utils.get_test_data('genome-s11.fa.gz.msh.json_dump') + + c.run_sourmash('sig', 'import', msh_sig) + imported = sourmash.load_one_signature(c.last_result.out) + compare = sourmash.load_one_signature(sig1, ksize=21, select_moltype='DNA') + + assert imported.minhash == compare.minhash diff --git a/tests/test_jaccard.py b/tests/test_jaccard.py index 940cde74d7..93bda700b9 100644 --- a/tests/test_jaccard.py +++ b/tests/test_jaccard.py @@ -6,7 +6,7 @@ from __future__ import print_function, unicode_literals import pytest -from sourmash_lib import MinHash +from sourmash import MinHash from . import sourmash_tst_utils as utils # below, 'track_abundance' is toggled to both True and False by py.test -- @@ -174,7 +174,7 @@ def test_abund_similarity_zero(): #### def test_jaccard_on_real_data(): - from sourmash_lib.signature import load_signatures + from sourmash.signature import load_signatures afile = 'n10000/GCF_000005845.2_ASM584v2_genomic.fna.gz.sig.gz' a = utils.get_test_data(afile) @@ -206,7 +206,7 @@ def test_jaccard_on_real_data(): def test_scaled_on_real_data(): - from sourmash_lib.signature import load_signatures + from sourmash.signature import load_signatures afile = 'scaled100/GCF_000005845.2_ASM584v2_genomic.fna.gz.sig.gz' a = utils.get_test_data(afile) @@ -244,7 +244,7 @@ def test_scaled_on_real_data(): def test_scaled_on_real_data_2(): - from sourmash_lib.signature import load_signatures + from sourmash.signature import load_signatures afile = 'scaled100/GCF_000005845.2_ASM584v2_genomic.fna.gz.sig.gz' a = utils.get_test_data(afile) diff --git a/tests/test_lca.py b/tests/test_lca.py index 74fea16e90..09a56caf53 100644 --- a/tests/test_lca.py +++ b/tests/test_lca.py @@ -13,7 +13,7 @@ import pytest from . import sourmash_tst_utils as utils -import sourmash_lib +import sourmash from sourmash_lib.lca import lca_utils from sourmash_lib.lca.lca_utils import * @@ -888,7 +888,7 @@ def test_gather_unknown_hashes(): assert '88.5% (2.1 Mbp) of hashes have no assignment.' in out -def test_gather_equiv_results(): +def test_gather_combined_results(): with utils.TempDirectory() as location: query_sig = utils.get_test_data('47+63.fa.sig') lca_db = utils.get_test_data('lca/47+63.lca.json') @@ -901,6 +901,23 @@ def test_gather_equiv_results(): print(out) print(err) + assert '5.5 Mbp 69.4% 100.0% Shewanella baltica OS223' in out + assert '2.4 Mbp 30.6% 47.1% Shewanella baltica OS185' in out + + +def test_gather_equiv_results(): + with utils.TempDirectory() as location: + query_sig = utils.get_test_data('47+63-intersect.fa.sig') + lca_db = utils.get_test_data('lca/47+63.lca.json') + + cmd = ['lca', 'gather', query_sig, lca_db, '-o', 'matches.csv'] + status, out, err = utils.runscript('sourmash', cmd, + in_directory=location) + + print(cmd) + print(out) + print(err) + assert '2.7 Mbp 100.0%' in out assert 'Shewanella baltica' in out assert '(** 1 equal matches)' in out diff --git a/tests/test_sbt.py b/tests/test_sbt.py index e806ef3f0e..8589c6aa71 100644 --- a/tests/test_sbt.py +++ b/tests/test_sbt.py @@ -4,11 +4,11 @@ import pytest -from sourmash_lib import signature -from sourmash_lib.sbt import SBT, GraphFactory, Leaf, Node -from sourmash_lib.sbtmh import (SigLeaf, search_minhashes, +from sourmash import signature +from sourmash.sbt import SBT, GraphFactory, Leaf, Node +from sourmash.sbtmh import (SigLeaf, search_minhashes, search_minhashes_containment) -from sourmash_lib.sbt_storage import (FSStorage, TarStorage, +from sourmash.sbt_storage import (FSStorage, TarStorage, RedisStorage, IPFSStorage) from . import sourmash_tst_utils as utils diff --git a/tests/test_signature.py b/tests/test_signature.py index 2c7a67b3c8..d53b845008 100644 --- a/tests/test_signature.py +++ b/tests/test_signature.py @@ -4,19 +4,19 @@ import pytest -import sourmash_lib -from sourmash_lib.signature import SourmashSignature, save_signatures, \ +import sourmash +from sourmash.signature import SourmashSignature, save_signatures, \ load_signatures, load_one_signature from . import sourmash_tst_utils as utils def test_compare(track_abundance): # same content, same name -> equal - e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) e.add("AT" * 10) sig1 = SourmashSignature(e, name='foo') - f = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + f = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) f.add("AT" * 10) sig2 = SourmashSignature(f, name='foo') @@ -25,11 +25,11 @@ def test_compare(track_abundance): def test_compare_ne(track_abundance): # same content, different names -> different - e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) e.add("AT" * 10) sig1 = SourmashSignature(e, name='foo') - f = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + f = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) f.add("AT" * 10) sig2 = SourmashSignature(f, name='bar') @@ -38,11 +38,11 @@ def test_compare_ne(track_abundance): def test_compare_ne2(track_abundance): # same content, different filename -> different - e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) e.add("AT" * 10) sig1 = SourmashSignature(e, name='foo', filename='a') - f = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + f = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) f.add("AT" * 10) sig2 = SourmashSignature(f, name='foo', filename='b') @@ -52,11 +52,11 @@ def test_compare_ne2(track_abundance): def test_compare_ne2_reverse(track_abundance): # same content, one has filename, other does not -> different - e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) e.add("AT" * 10) sig1 = SourmashSignature(e, name='foo') - f = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + f = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) f.add("AT" * 10) sig2 = SourmashSignature(f, filename='b') @@ -66,7 +66,7 @@ def test_compare_ne2_reverse(track_abundance): def test_hashable(track_abundance): # check: can we use signatures as keys in dictionaries and sets? - e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) e.add("AT" * 10) sig = SourmashSignature(e) @@ -77,7 +77,7 @@ def test_hashable(track_abundance): def test_str(track_abundance): # signatures should be printable - e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) e.add("AT" * 10) sig = SourmashSignature(e) @@ -92,7 +92,7 @@ def test_str(track_abundance): def test_roundtrip(track_abundance): - e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) e.add("AT" * 10) sig = SourmashSignature(e) s = save_signatures([sig]) @@ -105,7 +105,7 @@ def test_roundtrip(track_abundance): def test_load_signature_ksize_nonint(track_abundance): - e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) e.add("AT" * 10) sig = SourmashSignature(e) s = save_signatures([sig]) @@ -119,7 +119,7 @@ def test_load_signature_ksize_nonint(track_abundance): def test_roundtrip_empty(track_abundance): # edge case, but: empty minhash? :) - e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) sig = SourmashSignature(e) s = save_signatures([sig]) @@ -132,7 +132,7 @@ def test_roundtrip_empty(track_abundance): def test_roundtrip_max_hash(track_abundance): - e = sourmash_lib.MinHash(n=0, ksize=20, track_abundance=track_abundance, + e = sourmash.MinHash(n=0, ksize=20, track_abundance=track_abundance, max_hash=10) e.add_hash(5) sig = SourmashSignature(e) @@ -148,7 +148,7 @@ def test_roundtrip_max_hash(track_abundance): def test_roundtrip_seed(track_abundance): - e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance, + e = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance, seed=10) e.add_hash(5) sig = SourmashSignature(e) @@ -164,9 +164,9 @@ def test_roundtrip_seed(track_abundance): def test_similarity_downsample(track_abundance): - e = sourmash_lib.MinHash(n=0, ksize=20, track_abundance=track_abundance, + e = sourmash.MinHash(n=0, ksize=20, track_abundance=track_abundance, max_hash=2**63) - f = sourmash_lib.MinHash(n=0, ksize=20, track_abundance=track_abundance, + f = sourmash.MinHash(n=0, ksize=20, track_abundance=track_abundance, max_hash=2**2) e.add_hash(1) @@ -188,7 +188,7 @@ def test_similarity_downsample(track_abundance): def test_md5(track_abundance): - e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) e.add_hash(5) sig = SourmashSignature(e) print(sig._save()) @@ -196,35 +196,35 @@ def test_md5(track_abundance): def test_name(track_abundance): - e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) sig = SourmashSignature(e, name='foo') assert sig.name() == 'foo' def test_name_2(track_abundance): - e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) sig = SourmashSignature(e, filename='foo.txt') assert sig.name() == 'foo.txt' def test_name_3(track_abundance): - e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) sig = SourmashSignature(e, name='foo', filename='foo.txt') assert sig.name() == 'foo' def test_name_4(track_abundance): - e = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) sig = SourmashSignature(e) assert sig.name() == sig.md5sum()[:8] def test_save_load_multisig(track_abundance): - e1 = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e1 = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) sig1 = SourmashSignature(e1) - e2 = sourmash_lib.MinHash(n=1, ksize=25, track_abundance=track_abundance) + e2 = sourmash.MinHash(n=1, ksize=25, track_abundance=track_abundance) sig2 = SourmashSignature(e2) x = save_signatures([sig1, sig2]) @@ -246,7 +246,7 @@ def test_load_one_fail_nosig(track_abundance): def test_load_one_succeed(track_abundance): - e1 = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e1 = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) sig1 = SourmashSignature(e1) x = save_signatures([sig1]) @@ -256,10 +256,10 @@ def test_load_one_succeed(track_abundance): def test_load_one_fail_multisig(track_abundance): - e1 = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e1 = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) sig1 = SourmashSignature(e1) - e2 = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e2 = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) sig2 = SourmashSignature(e2) x = save_signatures([sig1, sig2]) @@ -269,10 +269,10 @@ def test_load_one_fail_multisig(track_abundance): def test_save_minified(track_abundance): - e1 = sourmash_lib.MinHash(n=1, ksize=20, track_abundance=track_abundance) + e1 = sourmash.MinHash(n=1, ksize=20, track_abundance=track_abundance) sig1 = SourmashSignature(e1, name="foo") - e2 = sourmash_lib.MinHash(n=1, ksize=25, track_abundance=track_abundance) + e2 = sourmash.MinHash(n=1, ksize=25, track_abundance=track_abundance) sig2 = SourmashSignature(e2, name="bar baz") x = save_signatures([sig1, sig2]) diff --git a/tests/test_signature_json.py b/tests/test_signature_json.py index e561a72950..7112d0963f 100644 --- a/tests/test_signature_json.py +++ b/tests/test_signature_json.py @@ -2,9 +2,9 @@ import io import json import ijson -import sourmash_lib -from sourmash_lib.signature import SourmashSignature -from sourmash_lib.signature_json import (_json_next_atomic_array, +import sourmash +from sourmash.signature import SourmashSignature +from sourmash.signature_json import (_json_next_atomic_array, _json_next_signature, load_signature_json, load_signatures_json, @@ -112,10 +112,10 @@ def test_load_signaturesset_json_iter(): def test_save_load_multisig_json(): - e1 = sourmash_lib.MinHash(n=1, ksize=20) + e1 = sourmash.MinHash(n=1, ksize=20) sig1 = SourmashSignature(e1) - e2 = sourmash_lib.MinHash(n=1, ksize=25) + e2 = sourmash.MinHash(n=1, ksize=25) sig2 = SourmashSignature(e2) x = save_signatures_json([sig1, sig2]) diff --git a/tests/test_sourmash.py b/tests/test_sourmash.py index e343dd3364..2ea8eb6860 100644 --- a/tests/test_sourmash.py +++ b/tests/test_sourmash.py @@ -13,18 +13,18 @@ import pytest from . import sourmash_tst_utils as utils -import sourmash_lib -from sourmash_lib import MinHash -from sourmash_lib.sbt import SBT, Node -from sourmash_lib.sbtmh import SigLeaf, load_sbt_index +import sourmash +from sourmash import MinHash +from sourmash.sbt import SBT, Node +from sourmash.sbtmh import SigLeaf, load_sbt_index try: import matplotlib matplotlib.use('Agg') except ImportError: pass -from sourmash_lib import signature -from sourmash_lib import VERSION +from sourmash import signature +from sourmash import VERSION def test_run_sourmash(): status, out, err = utils.runscript('sourmash', [], fail_ok=True) @@ -457,7 +457,7 @@ def test_do_sourmash_compute_with_scaled_1(): max_hashes = [ x.minhash.max_hash for x in siglist ] assert len(max_hashes) == 2 - assert set(max_hashes) == { sourmash_lib.MAX_HASH } + assert set(max_hashes) == { sourmash.MAX_HASH } def test_do_sourmash_compute_with_scaled_2(): @@ -700,7 +700,7 @@ def test_do_basic_compare(c): sigs = [] for fn in testsigs: - sigs.append(sourmash_lib.load_one_signature(fn, ksize=21, + sigs.append(sourmash.load_one_signature(fn, ksize=21, select_moltype='dna')) cmp_calc = numpy.zeros([len(sigs), len(sigs)]) @@ -708,6 +708,10 @@ def test_do_basic_compare(c): for j, sj in enumerate(sigs): cmp_calc[i][j] = si.similarity(sj) + sigs = [] + for fn in testsigs: + sigs.append(sourmash.load_one_signature(fn, ksize=21, + select_moltype='dna')) assert (cmp_out == cmp_calc).all() @@ -726,7 +730,7 @@ def test_do_basic_compare_using_rna_arg(c): sigs = [] for fn in testsigs: - sigs.append(sourmash_lib.load_one_signature(fn, ksize=21, + sigs.append(sourmash.load_one_signature(fn, ksize=21, select_moltype='dna')) cmp_calc = numpy.zeros([len(sigs), len(sigs)]) @@ -1175,7 +1179,7 @@ def test_gather_lca_db(c): c.run_sourmash('gather', query, lca_db) print(c) - assert 'NC_009665.1 Shewanella baltica OS185' in str(c) + assert 'NC_009665.1 Shewanella baltica OS185' in str(c.last_result.out) @utils.in_tempdir