Remove lca gather (#1307)

* remove lca gather
* remove lca gather from docs and comments

doc/classifying-signatures.md

@@ -81,9 +81,6 @@ differences between the `sourmash lca` subcommands and the basic
 output structured taxonomic information, and these are what you should look
 to if you are interested in doing classification.
 
-The command `lca gather` applies the `gather` algorithm to search an
-LCA database; it reports taxonomy.
-
 It's important to note that taxonomy based on k-mers is very, very
 specific and if you get a match, it's pretty reliable. On the
 converse, however, k-mer identification is very brittle with respect
@@ -120,8 +117,8 @@ containment queries against genome databases.  This will give you
 numbers that (approximately) match what you get from counting mapped
 reads.
 
-If you compute your input signatures with `--track-abundance`, both
-`sourmash gather` and `sourmash lca gather` will use that information
+If you compute your input signatures with `--track-abundance`,
+`sourmash gather` will use that information
 to calculate an abundance-weighted result.  This will weight
 each match to a hash value by the multiplicity of the hash value in
 the query signature.  You can turn off this behavior with

doc/command-line.md

@@ -77,7 +77,6 @@ walkthrough of these commands.
 
 * `lca classify` classifies many signatures against an LCA database.
 * `lca summarize` summarizes the content of metagenomes using an LCA database.
-* `lca gather` finds non-overlapping matches to a metagenome in an LCA database.
 * `lca index` creates a database for use with LCA subcommands.
 * `lca rankinfo` summarizes the content of a database.
 * `lca compare_csv` compares lineage spreadsheets, e.g. those output by `lca classify`.
@@ -261,8 +260,8 @@ Note:
 
 Use `sourmash gather` to classify a metagenome against a collection of
 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.
+lca summarize` to classify a metagenome using a collection of genomes
+with taxonomic information.
 
 ## `sourmash lca` subcommands for taxonomic classification
 
@@ -431,39 +430,6 @@ text file passed to `sourmash lca summarize` with the
 `--query-from-file` flag; these files will be appended to the `--query`
 input.
 
-### `sourmash lca gather` - find metagenome taxonomy (DEPRECATED for 4.0)
-
-The `sourmash lca gather` command finds all non-overlapping
-matches to the query, similar to the `sourmash gather` command.  This
-is specifically meant for metagenome and genome bin analysis.  (See
-[Classifying Signatures](classifying-signatures.md) for more
-information on the different approaches that can be used here.)
-
-If the input signature was computed with `--track-abundance`, output
-will be abundance weighted (unless `--ignore-abundances` is
-specified).  `-o/--output` will create a CSV file containing the
-matches.
-
-Usage:
-
-```
-sourmash lca gather query.sig [<lca database> ...]
-```
-
-Example output:
-
-```
-overlap     p_query p_match
----------   ------- --------
-1.8 Mbp      14.6%    9.1%      Fusobacterium nucleatum
-1.0 Mbp       7.8%   16.3%      Proteiniclasticum ruminis
-1.0 Mbp       7.7%   25.9%      Haloferax volcanii
-0.9 Mbp       7.4%   11.8%      Nostoc sp. PCC 7120
-0.9 Mbp       7.0%    5.8%      Shewanella baltica
-0.8 Mbp       6.0%    8.6%      Desulfovibrio vulgaris
-0.6 Mbp       4.9%   12.6%      Thermus thermophilus
-```
-
 ### `sourmash lca index` - build an LCA database
 
 The `sourmash lca index` command creates an LCA database from

src/sourmash/cli/lca/__init__.py

@@ -6,7 +6,6 @@
 
 from . import classify
 from . import compare_csv
-from . import gather
 from . import index
 from . import rankinfo
 from . import summarize

src/sourmash/lca/__init__.py

@@ -9,6 +9,5 @@
 from .command_classify import classify
 from .command_summarize import summarize_main
 from .command_rankinfo import rankinfo_main
-from .command_gather import gather_main
 from .__main__ import main
 

src/sourmash/lca/__main__.py

@@ -5,7 +5,7 @@
 import sys
 import argparse
 
-from . import classify, index, summarize_main, rankinfo_main, gather_main
+from . import classify, index, summarize_main, rankinfo_main
 from .command_compare_csv import compare_csv
 from ..logging import set_quiet, error
 
@@ -16,7 +16,6 @@
 
 index <taxonomy.csv> <output_db name> <signature [...]>  - create LCA database
 classify --db <db_name [...]> --query <signature [...]>  - classify genomes
-gather <signature> <db_name [...]>                       - classify metagenomes
 summarize --db <db_name [...]> --query <signature [...]> - summarize mixture
 rankinfo <db_name [...]>                                 - database rank info
 compare_csv <csv1> <csv2>                                - compare spreadsheets