Bystro comes with several small programs to fetch and modify source files
TL;DR : Fetches from some remote repository or SQL server. Provide the remote file path or SQL statement, and Bystro will fetch the data.
type: gene
utils:
- name: fetch
args:
sql_statement: SELECT * FROM refGene r LEFT JOIN kgXref k ON r.name = k.refseq WHERE chrom = %chromosomes%;
connection:
host: genome-mysql.cse.ucsc.edu
user: 'genome'
database: 'hg19'
- args:
geneFile: /mnt/db_backup/dbnsfp/dbNSFP3.5_gene.complete
completed: 2017-11-23T19:25:00
name: refGeneXdbnsfp
Any valid SQL statement can be used. In order to pre-split the fetched data per chromosome, simply provide the %chromosomes%
macro (ex: WHERE chrom = %chromosomes%
)
- All
args
exceptsql
are optional for SQL fetch. The following options will be assumed:
args:
connection:
host: genome-mysql.cse.ucsc.edu
user: 'genome'
database: //The `assembly` (ex: hg19)