The latest release is always available from https://sourceforge.net/projects/swissknife/files/latest/download.
The current and development version are hosted at
[Swissknife project page]
[Browse Git 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 wallclock secs ( 0.03 usr + 0.01 sys = 0.04 CPU) @ 250.00/s (n=10) (warning: too few iterations for a reliable count) Read/Write NULL: : 0 wallclock secs ( 0.03 usr + 0.01 sys = 0.04 CPU) @ 250.00/s (n=10) (warning: too few iterations for a reliable count) Read/Write: : 0 wallclock secs ( 0.03 usr + 0.03 sys = 0.06 CPU) @ 166.67/s (n=10) (warning: too few iterations for a reliable count) Read/Write/addAC: : 0 wallclock secs ( 0.11 usr + 0.03 sys = 0.14 CPU) @ 71.43/s (n=10) (warning: too few iterations for a reliable count) Read/Write/Fullparse: : 10 wallclock secs ( 9.29 usr + 0.05 sys = 9.34 CPU) @ 1.07/s (n=10) Read/Write/Fp/Update: : 14 wallclock secs (14.22 usr + 0.04 sys = 14.26 CPU) @ 0.70/s (n=10) Read/equals: : 0 wallclock secs ( 0.26 usr + 0.01 sys = 0.27 CPU) @ 37.04/s (n=10) (warning: too few iterations for a reliable count) Read/Write/Modify: : 4 wallclock secs ( 3.71 usr + 0.04 sys = 3.75 CPU) @ 2.67/s (n=10)
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 ***
DEs.t ............. ok
FTId.t ............ ok
GNs.t ............. ok
annot.t ........... ok
crc64.t ........... ok
evidence.t ........ ok
fasta.t ........... ok
formatProblems.t .. ok
identity.t ........ ok
util.t ............ ok
All tests successful.
Files=10, Tests=20, 2 wallclock secs ( 0.05 usr 0.02 sys + 1.39 cusr 0.09 csys = 1.55 CPU)
Result: PASS
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. |
CCdisease.pm | CCdisease.html | One comment object of the topic DISEASE. |
CCsubcell_location.pm | CCsubcell_location.html | One comment object of the topic SUBCELLULAR LOCATION. |
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/DR.pm | Stars/DR.html | DR in the internal "annotator's section". See Stars.html |
Stars/EV.pm | Stars/EV.html | Evidence section. See Stars.html |
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.