Better formatted error message for ancestral alleles #887
Conversation
hyanwong
force-pushed
the
aa-formatting
branch
2 times, most recently
from
5e282e4 to
7c47a9a
Compare
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #887 +/- ##
=======================================
Coverage 87.04% 87.04%
=======================================
Files 5 5
Lines 1767 1767
Branches 310 310
=======================================
Hits 1538 1538
Misses 140 140
Partials 89 89
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. |
hyanwong
force-pushed
the
aa-formatting
branch
2 times, most recently
from
af170e1 to
fd50a6f
Compare
tsinfer/formats.py
Outdated
| "The following alleles were not found in the variant_allele array " | ||
| "and will be treated as unknown:\n" | ||
| f"{unknown_alleles}" | ||
| "Ancestral alleles not found in the variant_allele " |
There was a problem hiding this comment.
What'll happen here if there's thousands of them? The warning may take very long to generate, and may not be helpful. I think just keep it to the overall summary.
There was a problem hiding this comment.
The summary is the same order of length, right? As in it was, {'aaa': 3, 'bbb':4}, and would now be 'aaa': 3 (x%)\n'bbb': 4 (y%).
I'm suggesting this because I would find it useful to know (a) the proportion of bad ancestral alleles and (b) if I accidentally wasn't e.g. converting them to uppercase etc in the right way. I think reporting this would help avoid lots of accidentally bad analysis, which is why we introduced it (see #870 and #683 (comment). But happy to be guided by user experience.
I've been testing on the default 1000 genomes VCFs, and seeing what would be useful.
There was a problem hiding this comment.
Ah, I didn't understand the code.
Can you do the computations outside of the string then? This is unnecessarily terse
There was a problem hiding this comment.
Refactored to move the calculations above the string construction. Thanks for the feedback @jeromekelleher
hyanwong
force-pushed
the
aa-formatting
branch
from
fd50a6f to
30cb691
Compare
hyanwong
force-pushed
the
aa-formatting
branch
from
30cb691 to
bb9570b
Compare
This is pretty useful information, so quoting percentages is helpful to debug issues, I think.