SWISS::Knife Files

WELCOME 
   Welcome to Swissknife - an object oriented Perl library to handle
   entries in SWISS-PROT format.

VERSION
   This is version 1.3 - March 2003

LATEST
   The latest version is always available at
   ftp://ftp.ebi.ac.uk/pub/software/swissprot/Swissknife/
   http://swissknife.sf.net

INSTALLATION
   Use the following commands:
   gunzip Swissknife_1.3.tar.gz
   tar xf Swissknife_1.3.tar
   cd SWISS
   perl Makefile.PL
   make install

   Alternatively, you may simply copy the lib/SWISS directory (the
   directory itself with all the files it contains) to a directory in
   your PERLLIB.

REQUIREMENTS
   Perl version 5.004 or higher.
   External modules used: 
      Carp
      Data::Dumper
      Exporter
      strict
      vars  
   All of these are part of the Perl 5.005 distribution.

DOCUMENTATION
   The Swissknife modules are documented using the POD (plain old
   documentation format). When installed, the documentation is
   accessible by typing "perldoc SWISS::Entry" at the command
   prompt, and similarly for other modules.

COPYRIGHT
   Copyright (C) 1999, 2003, the European Bioinformatics Institute and 
   the Swiss Institute of Bioinformatics.

   The SWISS modules are free software; you can redistribute and/or
   modify them under the terms of the GNU General Public License
   as published by the Free Software Foundation; either version 2
   of the License, or (at your option) any later version.

   These modules are distributed in the hope that they will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.

   You should have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.

AUTHORS
   Wolfgang Fleischmann, wfl@ebi.ac.uk
   Alexandre Gattiker, gattiker@isb-sib.ch
   Henning Hermjakob, hhe@ebi.ac.uk
   Paul Kersey, pkersey@ebi.ac.uk

ACKNOWLEDGEMENTS
   The Swissknife modules have been built on the example of the prEMBL
   modules by Matthew Pocock, mrp@sanger.ac.uk

   Thanks to Christian Iseli for help with the perl module setup.

UPDATES 

** since release 1.2

The directory structure has been reorganized, the modules are now supplied in
the lib/SWISS directory in the tar.gz file, and a Makefile.PL is available.

Entry: support lines that are indented by one space. [gattiker]

GN: added method toMixedCase(). [gattiker]

IDs: support multiple ID lines in STANDARD entries. [gattiker]

KWs: more fine-grained keyword sorting rule. [gattiker]

FTs: The SP style evidence (PROBABLE etc) was not correctly parsed when
followed by an evidence tag. [hhe]
Changed wrapping rule after slash. [gattiker]
Changed sort order logic for some keys. [gattiker]

DRs: Changed DR line sort order logic. [gattiker]

CCs: Remodelled for new style ALTERNATIVE PRODUCTS section.  CC.pm,
CCcopyright.pm and CCalt_prod.pm added. [pkersey]

ACs: Updated sort() method to sort secondary AC numbers alphanumerically.
[gattiker]

DEs: Replaced children attribute with Contains and Includes,
to support lines with both Contains and Includes blocks. [gattiker]

** since release 1.1
IDs:
As announced in the release notes for Swiss-Prot release 40 
(http://www.expasy.org/sprot/relnotes/#forthcoming), Swiss-Prot IDs
will soon have an mnemonic code of up to 5 instead of up to 4
characters for the protein name. This release takes this change into account.

RPs:
As announced in the release notes for Swiss-Prot release 40 
(http://www.expasy.org/sprot/relnotes/#forthcoming), Swiss-Prot
entries will soon contain more than one RP line. This release takes
this into account. Previous Swissknife releases will DELETE all but
the first RP line!


** since release 1.0

* Format changes:

DRs: 
- changed order of DR lines. Now InterPro-related and MENDEL DR lines 
  are sorted alphabetically on the ID (if they have one). 
  All other DR lines are sorted on the AC, 
  except EMBL, these are never sorted.
  PROSITE lines are sorted as the last of the signature database lines,
  although SMART comes later in alphabetical sorting.
- added SMART to list of databases.

FTs:
- The FT line sort order has been updated.
- Minor changes in the line wrapping of multiline features.

KWs:
- sort() and update(1) will now sort the keywords alphabetically.

OSs:
OS lines now show only one organism per line.

* Added functionality:

DEs, DRs: 
Modules now do "lazy writing". A line object is only reformatted on
writing the entry if it has been modified. To force reformatting of an
object, use $entry->DEs->reformat();

GNs:
Introduction of several convenience methods.


* Bugfixes:

CCs: 
Now CCs->getObject works properly.

DEs: 
In some cases brackets '(' and ')' were incorrectly 
converted to '{-' and '-}'.

Ref:
Cases like
RC   STRAIN=12,714 / SCARLATINA;
are now correctly parsed as one strain.

Stars:
- $entry->Stars->update(1) now forces a resorting of all **XX lines.

SQs:
- CRC64 and molweight are now only recalculated when a sequence change
  has occurred.





** since release 0.9.5

Entry::isVariant

DEs : more complex parsing

GNs : more complex parsing resulting in interface changes

DRs : added PRODOM to list of databases,
      slightly changed handling of internal "**DR" lines.

new: SWISS/t: Tests.

Stars: Bugfix in formatting of special cases.
       Format change for section headers.

Stars::EV: Modified handling of evidence tags.

CRC64: A new, fast perl-only CRC64 module has been contributed by
Alexandre Gattiker. This makes the complicated installation of the
SPcrc package unnecessary and should allow easy installation of
Swissknife on Windows systems.

** since release 0.9.4
Introduction of Evidence tags. Due to this new concept,
interface changes to the KWS, OGs, OSs modules.

new: OXs, OX modules to handle new OX lines.

** since release 0.9.3:
ACs:: now uses multiple AC lines, conform to the format change in SWISS-PROT.

SQs::crc32 renamed to 
SQs::crc and now returns CRC64. Requires SPcrc. If SPcrc is not
installed, it falls back to CRC32. 

Minor bugfix: When building up an entry by adding first a ** line,
then the SQ line, the order was wrong. Fixed through an update of the
** line pattern.

Introduced new ** line format, e.g. 
**PM

Entry::isFragment added.
Entry::isCurated added.

Changed inclusion of modules from "use" to "require on demand".


** since release 0.9.2:
ListBase.pm: get now returns an empty list, not 0, if the object is empty.

ACs.pm: Updated pattern for ACs to take the new accession number
format into account. 
Now can read and write multiple AC lines.

CCs.pm, DEs.pm, FTs.pm, Ref.pm: Updated line wrapping algorithm.

Refs.pm: Major bugfix: When using Swissknife under Perl 5.005, all but the first reference were lost.
DRs.pm: Updated DR sort order.


** since release 0.9.1:
ListBase.pm: get now returns an empty list, not 0, if the object is empty.

TextFunc.pm, Stars.pm: Bugfix: Removed /x modifier in pattern matching expressions.

ACs.pm: Updated pattern for ACs to take the new accession number
format into account. 


** since release 0.9:
DRs.pm:
Modification:
DRs->pids now returns full pids, including the version number.
The version number is now only dropped if called as DRs->pids(1).

Bugfix:
DRs->emblacs has been fixed


ListBase.pm:
Bugfix:
ListBase->unique and ListBase->del now work properly if the list objects
are arrays.


In most line objects the URL for the SWISS-PROT user manual has been
updated to www.expasy.org