Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[WIP] CAMI profiling output for sourmash tax #1606

Closed
wants to merge 121 commits into from
Closed
Changes from 1 commit
Commits
Show all changes
121 commits
Select commit Hold shift + click to select a range
db32c56
provide a kind of ridiculous upgrade to lca index to better deal with…
ctb May 21, 2021
2c305ed
update load_taxonomy_assignments to be more flexible and pay attentio…
ctb May 21, 2021
1908205
init structure for taxonomy subcommand
bluegenes May 21, 2021
494dbbc
more init
bluegenes May 22, 2021
ac3a553
syntax and add tax to init
bluegenes May 22, 2021
1966afc
Merge branch 'latest' into add-taxonomy
bluegenes May 22, 2021
85ef9fa
Merge branch 'latest' into update/lca_index
ctb May 22, 2021
ce939e5
Merge branch 'latest' into add-taxonomy
bluegenes May 24, 2021
208a9b3
init tax tests
bluegenes May 25, 2021
7e822c6
Merge branch 'latest' into update/lca_index
bluegenes May 25, 2021
a5bc6f0
Merge branch 'update/lca_index' of https://github.com/dib-lab/sourmas…
bluegenes May 25, 2021
33c55f3
working tax summarize command
bluegenes May 25, 2021
850e4e4
fix main
bluegenes May 26, 2021
0029d51
init tests for new tax_utils
bluegenes May 27, 2021
ea2456a
add ascending taxlist
bluegenes May 27, 2021
1075b68
init classify cmd
bluegenes May 28, 2021
88b643b
init tax cli testing
bluegenes May 28, 2021
822d664
Merge branch 'latest' into add-taxonomy
bluegenes May 28, 2021
a26052d
fix filename
bluegenes May 28, 2021
d2fef53
Merge branch 'add-taxonomy' of https://github.com/dib-lab/sourmash in…
bluegenes May 28, 2021
1448985
change to function for classify threshold
bluegenes May 28, 2021
06daba4
add header
bluegenes May 28, 2021
bd26822
enable single gather result for summarize; mult for classify
bluegenes May 28, 2021
7b5fc72
add util script to take output of tax and format for krona viz (#1559)
taylorreiter May 28, 2021
63be068
Merge branch 'latest' into add-taxonomy
bluegenes May 28, 2021
2c5f864
get summarized working for summary and krona output
bluegenes May 28, 2021
c868e06
init test krona output
bluegenes May 28, 2021
bb04930
add write_summary function
bluegenes May 28, 2021
4fd6de0
get classify working again, both summary and krona output
bluegenes May 29, 2021
8d6f321
test write_classification
bluegenes May 29, 2021
147fed9
init classify cli tests
bluegenes May 29, 2021
b1a40a3
init tests for load_taxonomy_assignments
bluegenes May 31, 2021
6410f37
enable force for getting past duplicated entries in taxonomy csv
bluegenes May 31, 2021
454ca3a
handle and test missing taxonomy info
bluegenes May 31, 2021
65e7d5d
classify: handle, test empty gather results, gather results from csv
bluegenes May 31, 2021
eb980cd
split identifiers by default
bluegenes May 31, 2021
f83f741
standardize spacing
bluegenes May 31, 2021
28c5107
comments
bluegenes May 31, 2021
29b82e2
init add tax to docs
bluegenes Jun 1, 2021
0dbf6fb
[MRG] add a function to take multiple sourmash tax summarize csvs and…
taylorreiter Jun 1, 2021
277ab35
Merge branch 'add-taxonomy' of https://github.com/dib-lab/sourmash in…
bluegenes Jun 1, 2021
1625743
rework format_tax_to_frac for easier testing and use; add tests
bluegenes Jun 2, 2021
cbc4020
better name and docstring for agg_sumgather_csvs_by_lineage
bluegenes Jun 2, 2021
fc3de6d
init combine command
bluegenes Jun 2, 2021
b042aa4
Merge branch 'latest' into add-taxonomy
bluegenes Jun 2, 2021
6c117dd
Merge branch 'latest' into add-taxonomy
bluegenes Jun 2, 2021
721421d
debugging code to help track down SBT duplicates/loss problem
ctb Jun 4, 2021
0dd9fa3
fix, I think
ctb Jun 4, 2021
f4a5e2e
remove unnecessary code
ctb Jun 4, 2021
7c44fc7
add test for duplicate signatures in SBT creation
ctb Jun 4, 2021
9f7848f
Merge branch 'debug/sbt_dups_tests' into debug/sbt_dups
ctb Jun 4, 2021
61d88d2
see what happens when you run twice
ctb Jun 4, 2021
1074d62
add missing signatures, oops
ctb Jun 4, 2021
9fd5076
initial refactoring that passes many tests
ctb Jun 4, 2021
b9a63bb
factor filename generation out of actual writing
ctb Jun 4, 2021
aee6cf6
refactor and cleanup
ctb Jun 4, 2021
e4c69e3
add more sigs to test, add note of concern L)
ctb Jun 4, 2021
c909b00
fix --append tests, too
ctb Jun 4, 2021
cf1b74a
refactor out save_exact in favor if save(..., overwrite=True)
ctb Jun 4, 2021
15f02cd
fix some storage stuff in the tests
ctb Jun 4, 2021
578ba43
make test less confusing?
ctb Jun 4, 2021
b46b966
Update src/sourmash/sbt_storage.py
ctb Jun 4, 2021
5a61c0d
define list_sbts() on base Storage class
ctb Jun 4, 2021
2af87b6
Merge branch 'debug/sbt_dups' of github.com:dib-lab/sourmash into deb…
ctb Jun 4, 2021
6bf3b0a
Merge branch 'latest' of https://github.com/dib-lab/sourmash into upd…
ctb Jun 5, 2021
f362774
Merge branch 'debug/sbt_dups' into update/lca_index
ctb Jun 5, 2021
3b1063c
properly record duplicate signature names
ctb Jun 6, 2021
e9e275f
Merge branch 'latest' into add-taxonomy
bluegenes Jun 9, 2021
e9f4e46
move threshold arg parsing into cli/utils
bluegenes Jun 11, 2021
3ba3919
Merge branch 'add-taxonomy' of https://github.com/dib-lab/sourmash in…
bluegenes Jun 11, 2021
c796df3
init changes for multiquery input
bluegenes Jun 12, 2021
d50956b
use namedtuple for summarized gather results
bluegenes Jun 13, 2021
57d034e
init update for mult files
bluegenes Jun 13, 2021
6389a9d
adjust for namedtuple output
bluegenes Jun 13, 2021
b184baf
mods for namedtuple
bluegenes Jun 13, 2021
69e5d59
upd utils
bluegenes Jun 14, 2021
d4ee27d
add --from-file to summarize
bluegenes Jun 14, 2021
229c2da
working multifile summarize
bluegenes Jun 14, 2021
599f394
--from-csv to --from-file
bluegenes Jun 14, 2021
6e220f4
somewhat working classify again
bluegenes Jun 14, 2021
45a8dcd
updated classify
bluegenes Jun 14, 2021
25db3cb
finish fixing combine test
bluegenes Jun 14, 2021
3d33c13
make taxonomy_csv required
bluegenes Jun 14, 2021
bdb1628
cleanup
bluegenes Jun 14, 2021
165d750
more cleanup
bluegenes Jun 14, 2021
9bfc1b9
Merge branch 'latest' into add-taxonomy
bluegenes Jun 14, 2021
b79dc8b
use load_pathlist_from_file
bluegenes Jun 14, 2021
a1e5d87
test check_and_load_gather_csvs
bluegenes Jun 14, 2021
4f586b1
properly restrict kwargs with *
bluegenes Jun 14, 2021
0dfaba9
allow lineage summary table output from summarize
bluegenes Jun 14, 2021
c2cd08d
Merge branch 'latest' into add-taxonomy
bluegenes Jun 14, 2021
dce5940
fix merge
ctb Jun 15, 2021
443e122
require rank for krona, lineage summary output formats
bluegenes Jun 15, 2021
ed655b5
add test for lineage summary output with format_lineage
bluegenes Jun 15, 2021
98d3d39
add docstrings
bluegenes Jun 15, 2021
92f796a
punt cami to separate PR
bluegenes Jun 15, 2021
cba072e
raise ValueError on empty gather results
bluegenes Jun 15, 2021
9c5ff01
move notify
bluegenes Jun 15, 2021
13f5f00
cleanup
bluegenes Jun 16, 2021
891d951
remove tax combine; add tax label
bluegenes Jun 16, 2021
3e330b5
verson of load_taxonomy that strictly uses headers
bluegenes Jun 17, 2021
16d5d7f
use new tax fn; enable mult taxonomy inputs
bluegenes Jun 17, 2021
f884010
Merge branch 'latest' into add-taxonomy
bluegenes Jun 17, 2021
f46ab7d
init tax docs
bluegenes Jun 17, 2021
8a41e94
add classification status to classify output
bluegenes Jun 17, 2021
89e448b
add multi db gather test csv
bluegenes Jun 17, 2021
86a53f8
fix typo
bluegenes Jun 17, 2021
a9366bd
whoops, actually fix
bluegenes Jun 17, 2021
7044ae5
handle accession in lineage csv header
bluegenes Jun 17, 2021
24bea0f
fix line width
bluegenes Jun 17, 2021
3cbac9f
return available ranks from load_taxonomy_csv
bluegenes Jun 17, 2021
bee47fd
[MRG] add test to confirm failure when summarizing on empty gather (#…
hehouts Jun 17, 2021
7d41b87
init standardize errs
bluegenes Jun 17, 2021
b0501c2
Merge branch 'add-taxonomy' of https://github.com/sourmash-bio/sourma…
bluegenes Jun 17, 2021
643a62c
add good valueerror for empty lineage csv file
bluegenes Jun 17, 2021
43e3609
better catch errs in __main__; test all cmds: empty gather, lineage f…
bluegenes Jun 17, 2021
4b1ded4
check available ranks, bad gather headers, empty gather, etc
bluegenes Jun 18, 2021
4fdabb7
emit one (and only one) warning per 100% match
bluegenes Jun 18, 2021
0e6df72
Merge branch 'latest' into add-taxonomy
bluegenes Jun 18, 2021
e495d1d
add all functions to __all__ ...is this desired?
bluegenes Jun 18, 2021
a0fc0c8
start cami profiling output based on krona
luizirber Jun 18, 2021
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
Merge branch 'latest' into update/lca_index
  • Loading branch information
ctb authored May 22, 2021
commit 85ef9faf4bd07fbc7bdc130b0528815b109081e9

This merge commit was added into this branch cleanly.

There are no new changes to show, but you can still view the diff.