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clindet / anor

anor: an annotation and visualization system based on R and Shiny framework
https://jhuanglab.github.io/anor/
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Difficult to understand documentation with regard to sqlite databases #2

Open allaway opened 6 years ago

allaway commented 6 years ago

I am trying to annotate some variants using the exac_03 database. I retrieved it using download.database(), but it retrieved the following database: hg19_exac03.sqlite.sql. It's now in my "annovar/humandb" directory.

When I try x <- annotation(dat = dat, anno.name = "exac03", database.dir = "annovar/humandb", db.type = "sqlite") I get the following error: 

Error in dbname.initial(anno.name, dbname.fixed, setdb.fun, buildver,  : 
  annovar/humandb/hg19_exac03.sqlite sqlite format database dose not exist.

Is there a step I am missing between retrieving the db and running annotation? Thanks!

Miachol commented 6 years ago

I'm sorry about this. The document of annovarR is incomplete now,

I guess you need to install the SQLite3 before installing the SQLite format exac03 database. If the sqlite or sqlite3 not in PATH, the converting step in download.database may not work.

# After installing SQLite3
annovarR::sql2sqlite('/path/hg19_exac03.sqlite.sql', dbname = '/path/hg19_exac03.sqlite')
# If you have downloaded the text format `hg19_exac03.txt`
sqlite.auto.build("exac03", buildver = hg19"", database.dir = "/path/humandb")`

In fact, you can also use the perl version ANNOVAR to do the exac03 annotation. 

x <- annotation(dat = dat, anno.name = "perl_annovar_exac03", database.dir = "~/.annovarR/db", annovar.dir = "/opt/bin/annotation/annovar/20170716/")
allaway commented 6 years ago

Dear Jianfeng, Thank you for the help! That makes sense. I'll make sure sqlite3 is in my path. In the interim, I used the perl version on the command line, which worked well. In the future, I'll try to incorporate annovarR into my workflow. Cheers, Robert

On Thu, Jun 28, 2018 at 7:32 PM Jianfeng notifications@github.com wrote:

I'm sorry about this. The document of annovarR is incomplete now,

I guess you need to install the SQLite3 https://www.sqlite.org/index.html before installing the SQLite format exac03 database. If the sqlite or sqlite3 not in PATH, the converting step in download.database may not work.

After installing SQLite3annovarR::sql2sqlite('/path/hg19_exac03.sqlite.sql', dbname = '/path/hg19_exac03.sqlite')# If you have downloaded the text format hg19_exac03.txt

sqlite.auto.build("exac03", buildver = hg19"", database.dir = "/path/humandb")`

In fact, you can also use the perl version ANNOVAR to do the exac03 annotation.

x <- annotation(dat = dat, anno.name = "perl_annovar_exac03", database.dir = "~/.annovarR/db", annovar.dir = "/opt/bin/annotation/annovar/20170716/")

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