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SilverTools: Conversion of sequence database flat files to GCG format

Nicole Redaschi redaschi at comp.bioz.unibas.ch
Fri Jun 21 06:39:15 EST 1996


SilverTools: Conversion of sequence database flat files to GCG format
---------------------------------------------------------------------

The SilverTools software was developed to facilitate the conversion of
EMBL, GenBank, SwissProt, and PIR flat files to GCG format. For the
nucleotide sequence databases, the scripts allow you to generate either
EMBL + GenBank exclusion set or vice versa.
The distribution includes scripts to copy the flat files from a remote
ftp server to your site (using mirror on UNIX or ftp on VMS, resp.).
SilverTools was designed for sites that make the formatted data available
by anonymous ftp for further distribution. Therefore, the data formatting
process was split into two steps: Step 1 generates a partial set of gcg-
formatted files in an operating system-independent format (*.seq, *.ref
and *.header files). These data can be copied by ftp to any UNIX or VMS
machine. Step 2 will then produce the full set of gcg-formatted files. 

+------+----------------+---------------------------------------------+
| step | script*        | purpose                                     |
+------+----------------+---------------------------------------------+
| 0    | mirror_xxx.csh | mirror raw data (UNIX)/                     |
|      |    GET_XXX.COM | get raw data by ftp (VMS)                   |
+------+----------------+---------------------------------------------+
| 1    |    gcg_xxx.csh | generate partial set of gcg-formatted files |
|      |    GCG_XXX.COM | (operating system-independent format)       |
+------+----------------+---------------------------------------------+
| 2    |    ftp_xxx.csh | generate full set of gcg-formatted files    |
|      |    FTP_XXX.COM | (operating system-dependent format)         |
+------+----------------+---------------------------------------------+
  * C-shell scripts in lower case, DCL scripts in upper case,
    where xxx/XXX stands for the name of the database

There are separate scripts for the formatting of database releases and
updates. By adding apropriate entries to a crontab file (UNIX), or using
self-submitting procedures (VMS), database updates can be processed
automatically at regular intervals. Incremental EMBL updates are merged
into a cumulative update file using the SynCron tools (see article in
bionet.molbio.embldatabank) to help you maintaining synchronised copies
of the EMBL updates. 

A UNIX and VMS version of SilverTools is available by anonymous ftp from:

 ftp.ch.embnet.org  directory: bioftp-sw/silvertools


Nicole Redaschi

(ex-EMBnet Switzerland, Email redaschi at biox.embnet.unibas.ch)


PS: The first set-up of SilverTools may seem a bit though, but once done
    it will save you a lot of work :-)

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