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Add createdb support for sequence db input #545

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matchy233
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According to the source code of createdb, it should be able to accept MMSeqs databases as one of the input sources. But the current implementation fail to handle MMSeqs db input. This PR fixes this issue.

Probably need to edit MMSeqsBase.cpp with new instructions.

@@ -126,8 +129,11 @@ int createdb(int argc, const char **argv, const Command& command) {
}

KSeqWrapper* kseq = NULL;
std::string seq = ">";
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Can we move this into the if condition?

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No we can't :( we need to refer to the address of this string later. Variables defined inside if {} block is not accessible to the outer scope.

@matchy233
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I can modify MMseqsBase.cpp to add instructions for the fixed version of createdb later if needed

@milot-mirdita
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This feature was meant for turning a bunch of fasta files in form of a DB (e.g., produced by tar2db) into a normal MMseqs2 sequence databases. It is being used for this purpose in the databases downloader workflow.

If you want to consume sequence dbs and produce new sequence dbs, i would suggest to add a check for the presence of a header db and only then do your new code.

@matchy233
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Thanks for the explanation! I'll modify the code to support the old implementation as well as the new one. Maybe we can add the usage for database input to the usage text? so that some curious users (like me) would not get confused next time :P

@matchy233 matchy233 changed the title Fix createdb support for db input Add createdb support for sequence db input Mar 17, 2022
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3 participants