ENSCORESW-3349 changes made loops in parser for better performance. #503
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… change in output
ameya1981
changed the title
magaliruffier
suggested changes
Sep 2, 2020
| $add_dependent_xref_sth->execute($xref_id, $dependent_xref_id); | ||
| } | ||
| } | ||
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| # Also store refseq protein as direct xref for ensembl translation, if translation exists | ||
| if (defined $tl && defined $tl_of) { | ||
| if ($tl_of->seq eq $tl->seq) { | ||
| if (md5($tl_of->seq) eq md5($tl->seq)) { |
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what advantage does using the md5 bring?
we still call the seq method, so I am assuming the same query is still being run underneath
| @@ -369,7 +387,7 @@ sub run_script { | |||
| # If a best match was defined for the refseq transcript, store it as direct xref for ensembl transcript | |||
| if ($best_id) { | |||
| my ($acc, $version) = split(/\./, $id); | |||
| $version =~ s/\D//g if $version; | |||
| $version =~ s/\D//g if $version; | |||
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cosmetic changes should be avoided, and if absolutely necessary, submitted as a separate commit to avoid masking the actual code changes
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can't confirm if changes are needed |
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Requirements
Description
Optimize loops in RefSeqCoordinateParser which runs for human xrefs. No change in output is expected.
Use case
Potential memory issues caused by holding objects in memory
Benefits
Lesser memory required for parsing
Possible Drawbacks
NA
Testing
There is no unit test for this parser.
Running the parser as a singlejob did not result into any memory failures(over multiple times).
The xref count from these changes is same as the xref count from e100 parser
If so, do the tests pass/fail?
NA