Removing sequences from mysql using bioentry-id

[cjfields]

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Author Name: Nikolay empty (Nikolay empty)
Original Redmine Issue: 1528, https://redmine.open-bio.org/issues/1528
Original Date: 2003-09-26
Original Assignee: Bioperl Guts

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Hi I have been using biosql with mysql database for analyzing genetic material.
You have included the script that gets data into the database called
load_seqdatabase.pl. However, the main problem is that there doesn’t seem to
exist a safe way of REMOVING sequences from this database. Can you write a
script that cleanly removes biosequence and information about it based on
Accession Number, or simply bioentry_id. Such script would allow a greater
control and order of the database.

Of course the easiest solution is not to add those unwanted sequences in the
first place, and that’s what I’ve been doing. However, proves to be extrememly
inconvenient.

Thanx

Nikolay

[cjfields]

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Original Redmine Comment
Author Name: Sendu Bala
Original Date: 2006-09-02T10:30:26Z

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We would welcome any contribution from you to resolve this: after all these years it doesn’t seem like anyone else has been interested.

[cjfields]

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Original Redmine Comment
Author Name: Chris Fields
Original Date: 2006-11-09T12:28:24Z

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Though there is no documentation, the test scripts in bioperl-db demonstrate how to remove persistent objects from the database. i.e. from 13remove.t:

# delete seq
foreach $pseq (@seqs) {
    ok ($pseq->remove(), 1);
}

from 03simpleseq.t:

# delete seq and namespace
ok ($pseq->remove(), 1);
my $ns = Bio::DB::Persistent::BioNamespace->new(-identifiable => $pseq);
ok $ns = $db->get_object_adaptor($ns)->find_by_unique_key($ns);
ok $ns->primary_key();
ok ($ns->remove(), 1);

[cjfields]

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Original Redmine Comment
Author Name: Chris Fields
Original Date: 2007-09-24T15:10:48Z

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I think this has been answered several times on the mail list and here. Maybe time to get a bioperl-db HOWTO up and going?