hssp-get

hssp-get [-pdbdir dir] [-cat] pdbid

Get the path to a HSSP file. If the file already exists in the specified HSSP directory, it is used, otherwise the file is downloaded. The resulting file will be named in the form pdbid.hssp.gz and will always be gzipped.

Arguments

-hsspdir dir - Specifies an alternate HSSP directory. The default is /projects/compbio/data/hssp.
-cat - Instead of returning the file name, uncompress the file to stdout.
pdbid - PDB four character identifier of the file to get. Trailing chain identifiers and other garbage is dropped. Maybe upper or lower case.

Output

If successful, the full path to the HSSP file or the contents of the file if -cat is specified is written to stdout. If an error occurs, a message is written to stderr. This idea is that the output of this script is used to get the file name to open or to the actual data stream. For example:

       hssp-get -cat 1ceo | egrep '^AUTHOD
       some-prog `hssp-get 1ceo`

Exit codes

1 - file not found.
2 - Other ftp error.
3 - Error uncompressing, compressing or installing file.
4 - bad command line argument.

Source

CVS module xssp-tools.

Contact

Mark Diekhans