Support for non mapped accession with taxid #1
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- Support for chunk number during data insertion
…sion number, the table exists in the database - Also surrounded call to yield in case a taxid is not found in the database (E.g.: 0), do not throw stack trace but print a small error message on stderr
…speed up a little bit - Chunk value can be passed with 'create' sub option - If a taxid is not found in the database, a message is thrown to the user
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Hi, Thank you for your comments and your improvements! Cheers, |
The line `for table, acc_file in acc_dl_dict.items():` was duplicated and caused the db with multiple accession tables to fail
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Everything looks ready to be merged. Thanks again for your contribution! |
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Thanks for merging 👍 and sorry for duplicated loop, a wrong copy/paste |
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Hi,
First of all, I've found your project very interesting and tried to use it. It works well except some case where an accession number is not mapped to a taxid, see method
_unmapped_taxid.So I've made some modifications to your code to try to support this and avoid a stack trace.
I've also tried to speed up a little bit the data loading using
insert_manywhen loading other files thannames.dmpandnodes.dmp.Have a look at the PR and let me know.
Best
Emmanuel