#33 Get sequence for SAM/BAM track from mysql

open
Lincoln Stein
Gbrowse (28)
5
2009-12-01
2009-11-30
Keiran Raine
No

Would it be possible to make this component accept a 'sub-adaptor' for the fasta reference?

e.g.

[humansam:database]
db_adaptor = Bio::DB::Sam
db_args = -bam /Library/WebServer/Documents/gbrowse2/databases/homosapiens/bam/PD2125b.bam
-fasta [
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor DBI::mysql
-dsn GRC37
-user nobody
]
search options = default

This has a two fold benefit if possible:

1. You only need to maintain the sequence in your DB rather than one on disk and one in the DB (especially useful if you will have multiple builds of the genome).
2. The DB should be faster, especially if you don't have local disk (e.g. virtual servers).

Discussion

  • Scott Cain
    Scott Cain
    2009-12-01

    • assigned_to: scottcain --> lstein
     
  • Keiran Raine
    Keiran Raine
    2010-07-29

    Just a note to mention that Lincoln did implement this.