[MRG] add an lca gather signature decomposition approach
#390
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ctb
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lca gather signature decomposition approachlca gather signature decomposition approach
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@@ Coverage Diff @@
## master #390 +/- ##
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- Coverage 90.14% 90.07% -0.08%
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Files 31 32 +1
Lines 4586 4824 +238
Branches 36 36
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+ Hits 4134 4345 +211
- Misses 451 478 +27
Partials 1 1
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5 tasks
This was referenced Feb 18, 2018
This was referenced Feb 19, 2018
luizirber
approved these changes
Feb 23, 2018
| @@ -15,7 +15,7 @@ | |||
| from sourmash_lib.lca.command_index import load_taxonomy_assignments | |||
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| def compare_csv(args): | |||
| p = argparse.ArgumentParser() | |||
| p = argparse.ArgumentParser(prog="sourmash lca compare_csv") | |||
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Oh, we can make a low-hanging fruit issue for this change (on other commands)
| from sourmash_lib.lca.lca_utils import debug, set_debug | ||
| from sourmash_lib.search import format_bp | ||
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| LCAGatherResult = namedtuple('LCAGatherResult', |
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I have a feeling that we might be reaching a point where we want a Result class to collect functionality from all these NamedTuples...
This was referenced Feb 23, 2018
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yay w00t!
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Ref #384. Unlike 'sourmash gather' this requires taxonomy information from an LCA database.
It is also
Unlike
sourmash gatherthis will not print out arbitrary genome names or anything - it's solely about taxonomic display. It also alerts the user to the number of equivalent matches and outputs it to the CSV (but only displays one match).other additions:
sourmash gather --output-unassignedsourmash lcasubcommands where subcommand was not output to helpsourmash lca classifydb error message isn't very friendly #387 - fail more nicely when failing to parse LCA DBschecklist:
make testDid it pass the tests?make coverageIs the new code covered?without a major version increment. Changing file formats also requires a
major version number increment.
changes were made?