BIRCH
blastdbkit.py -
Technical Description
update April 21, 2016


blastdbkit.py - manual page
blastdbkit.py - pydoc documentation

SUMMARY

blastdbkit.py is a Python script that performs the tasks necessary to install and update a local copy of NCBI Blast-formatted databases. As described in the manual page, blastdbkit.py can

Critical information regarding local copies of databases is found in two BLASTDB.list files, the master copy in $BIRCH/admin, and the local copy in $BIRCH/local/admin. The local copy in generated from the master copy, but the local copy lists in field 4 a '1' for databases locally-installed, or '0' for those not installed. This file is used to add a '+' or '-' to the menus in birchadmin that perform Add, Delete or Update functions.

After each Add, Delete or Update operation, the following operations are performed:

blastdbkit.py --reportlocal writes a spreadsheet report on the locally-installed databases to $BLASTDB/localreport.tsv. This file, which can be imported by any spreadsheet, lists the sum of all files in a database, and the dates of the last update.

blastdbkit.py --reportftp
writes a spreadsheet report on database files at a remote FTP server (eg. ftp.ncbi.nlm.nih.gov) to $BLASTDB/ftpreport.tsv. This file, which can be imported by any spreadsheet, lists the sum of all compressed files in a database, an estimate of total uncompressed sizes, and the dates of the files on the FTP server.







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