3.1 fetch and dump

A number of fetch and dump operators are available, with slightly varying functionality. Essentially, all the fetch operations act on one or more entries (that may be specified by queries), while the dump operations act on a whole database.

Consequently, the fetch operators accept a list of names (i.e. “entry identifiers sensu largo”) as argument:

[seq|mot|cla]_fetch_name <name> ...

show unique name and ID

[seq|mot|cla]_fetch_entry <name> ...

full text of single entry (by name, AC or ID)

[seq|mot|cla]_fetch_prop <name>

... accession of entry by name, AC or ID

[seq|mot|cla]_fetch_desc <name> ...

show name and description

[seq|mot]_fetch_nr <name> ...

show non-redundant part of entry and corresponding ID(s)

The dump operators accept a list of database IDs as argument:

[seq|mot|cla]_dump_name <db> ...

- show unique name of all entries in <db>

[seq|mot|cla]_dump_entry <db> ...

- full text of all entries in <db>

[seq|mot|cla]_dump_prop <db> ...

- accession of entry by name, AC or ID of all entries in <db>

[seq|mot|cla]_dump_prop <db> ...

- description of all entries in <db>

[seq|mot]_dump_nr <db> ...

- show non-redundant part of entry that takes part in the computation and corresponding ID(s), AC(s) and md5. Note that there is no such thing for cla.

As an example, the function seq_fetch_name accepts the argument seq_name=NAME... ; if this is not given, the default is seq_name. The following two queries are thus equivalent:

> seq_fetch_name seq_name=sw:AAS_ECOLI,sw:DPO1_ECOLI 
sw:AAS_ECOLI 
sw:DPO1_ECOLI 
 
> seq_fetch_name sw:AAS_ECOLI,sw:DPO1_ECOLI 
sw:AAS_ECOLI  
sw:DPO1_ECOLI 

3.2 Output Formats

Please refer to section 13 for details about the possible output formats, output redirection, and related issues.