The latest release is always available from ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/.
The development version is now hosted at
[Swissknife project page]
[Browse CVS tree].
General information on installation etc. is contained in the file README. This document is the starting point to the usage documentation of the Swissknife modules.
use SWISS::Entry;
A small program using Swissknife is example.pl.
The program benchmark.pl can be used to test
the Swissknife components and to give a rough idea of the
system performance. The program can be called with the Swiss-Prot
example file SWISS100.dat.
Usage example:
cd SWISS/examples
perl benchmark.pl -file SWISS100.dat -repeats 10
The output should look similar to:
*** Swissknife Benchmark and Test suite *** Read only: : 0 secs ( 0.39 usr + 0.01 sys = 0.40 CPU) (warning: too few iterations for a reliable count) Read/Write NULL: : 1 secs ( 0.95 usr 0.05 sys = 1.00 cpu) Read/Write: : 1 secs ( 0.97 usr 0.10 sys = 1.07 cpu) Read/Write/addAC: : 2 secs ( 1.62 usr 0.08 sys = 1.70 cpu) Read/Write/Fullparse: : 23 secs (22.48 usr 0.17 sys = 22.65 cpu) Read/Write/Fp/Update: : 35 secs (34.40 usr 0.18 sys = 34.58 cpu) Read/equals: : 13 secs (13.67 usr 0.03 sys = 13.70 cpu) Read/Write/Modify: : 10 secs ( 9.52 usr 0.12 sys = 9.63 cpu)
A more comprehensive test set is provided in the t/ directory:
cd SWISS/t
perl test.pl *.t
should produce an output similar to
*** Swissknife test suite ***
crc64...............ok
DEs.................ok
evidence............ok
formatProblems......ok
GNs.................ok
identity............ok
All tests successful.
Files=6, Tests=12, 3 wallclock secs ( 3.19 cusr + 0.14 csys = 3.33 CPU)
Module | Documentation | Comment |
---|---|---|
The main module | ||
Entry.pm | Entry.html | The main module to handle Swiss-Prot entries. One Entry object represents one Swiss-Prot entry and provides an API for its modification. |
Line objects | Each line object implements a class to handle one line object of an entry or (e.g. Ref.pm) a group of related line objects. | |
ACs.pm | ACs.html | Representation of the AC line. |
DTs.pm | DTs.html | The date lines. |
DEs.pm | DEs.html | The description lines. |
DE.pm | DE.html | A single name for the protein. |
DRs.pm | DRs.html | The DR lines, crossreferences to other databases. |
CCs.pm | CCs.html | Comment lines. |
CCcopyright.pm | CCcopyright.html | The copyright statement (part of the comment lines). |
CCalt_prod.pm | CCalt_prod.html | One comment object of the topic ALTERNATIVE PRODUCTS. |
CCrna_editing.pm | CCrna_editing.html | One comment object of the topic RNA EDITING. |
CCbpc_properties.pm | CCbpc_properties.html | One comment object of the topic BIOPHYSICOCHEMICAL PROPERTIES. |
CCinteraction.pm | CCinteraction.html | One comment object of the topic INTERACTION. |
CC.pm | CC.html | One comment object of any other topic. |
FTs.pm | FTs.html | The feature lines. |
GNs.pm | GNs.html | The gene lines. |
GeneGroup.pm | GeneGroup.html | The different synonyms for a single gene name. |
GN.pm | GN.html | One single gene name. |
IDs.pm | IDs.html | The ID line. |
KWs.pm | KWs.html | The keyword lines. KWs is a container object, it holds an array of KW objects. |
KW.pm | KW.html | One keyword object. |
OCs.pm | OCs.html | The OC line encoding the taxonomy of the source organism. |
OGs.pm | OGs.html | The OG lines. OGs is a container object, it holds an array of OG objects. |
OG.pm | OG.html | One organism name. |
OSs.pm | OSs.html | The OS lines. OSs is a container object, it holds an array of OS objects. |
OS.pm | OS.html | One organism name. |
OXs.pm | OXs.html | The OX lines. OXs is a container object, for each valid taxonomic resource it contains a ListBase object which holds a list of OX objects. |
OX.pm | OX.html | One tax id object. |
Ref.pm | Ref.html | Represents one literature reference. |
Refs.pm | Refs.html | Represents the list of literature references. |
Stars.pm | Stars.html | The "annotator's section" (See note) |
Stars/aa.pm | Stars/aa.html | Unstructured notes in the internal "annotator's section". See Stars.html |
Stars/EV.pm | Stars/EV.html | Evidence section. |
Stars/default.pm | Stars/default.html | Default class for structured information in the internal "annotator's section". See Stars.html |
SQs.pm | SQs.html | The sequence lines. |
Base objects | These modules implement the base classes from which all line object classes are derived. | |
BaseClass.pm | BaseClass.html | The base class, implementing common methods, e.g. equals |
ListBase.pm | ListBase.html | Provides methods to manipulate list-based objects like KWs.pm |
Auxiliary modules | ||
TextFunc.pm | TextFunc.html | Auxiliary functions, mainly for text formatting. |
CRC64.pm | CRC64.html | Provides a method to calculate the CRC64 checksum. |
Please report any bugs and suggestions for improvement to sk at ebi dot ac dot uk.