Name

SWISS::GNs.pm


Description

SWISS::GNs represents the GN lines within an SWISS-PROT + TrEMBL entry as specified in the user manual http://www.expasy.org/sprot/userman.html . The GNs object is a container object which holds a list of SWISS::GeneGroup objects.


Inherits from

SWISS::ListBase.pm


Attributes

list
  Each list element is a SWISS::GeneGroup object.
and (deprecated, for old format only)
  Delimiter used between genes. Defaults to " AND ".
or (deprecated, for old format only)
  Delimiter used between gene names. Defaults to " OR ".


Methods

Standard methods

new
fromText
toText

Reading/Writing methods

text [($newText)]

Sets the text of the GN line to the parameter if it is present, and returns the (unwrapped) text of the line. Also sets 'and' and 'or' delimiters to the first occurrences of the words "OR" and "AND" in the line, conserving the case.

lowercase (deprecated, for old format only)

Sets the GNs::and and GNs::or delimiters to their lower case values.

uppercase (deprecated, for old format only)

Sets the GNs::and and GNs::or delimiters to their upper case values.

getFirst()

Returns first gene name in gene line

getTags($target)

Returns evidence tags associated with $target

$target is a string

isPresent($target)

Returns 1 if $target is present in the GN line

$target is a string

needsReCasing($target)

If $target is present in the GN line, but wrongly cased, method returns the matching name in its current case

$target is a string

replace($newName, $target, $evidenceTag)

Replaces the first GN object in the GN line whose text attribute is $target with a new GN object whose text attribute is set to $newName and whose evidenceTags attribute is is set using values set by splitting $evidenceTag on /, / (as name is not being changed, programs should keep old tag and add new tag). Does nothing if $target is not found.

delete($target)

Removes synonym/single-member gene group matching $target. Note that if a "Name" is deleted, the first "Synonym" will be promoted to "Name"

addAsNewSynonym($newName, $target, $evidenceTag, $location)

Adds a new GN object (with text attribute set to new $newName, and evidenceTags attribute set to ($evidenceTag)), as a synonym to the first gene group in which $target is a gene name. Does nothing if $target is not found. Will not add a duplicate gene name. $location determines where in gene group new object is added: if $location == 1, 2, 3, ..., new object added in the 1st, 2nd, 3rd, ... position; if $location == 0, new object added before $target; if $location == -1, new object added after $target (default); if $location == -2, new object added at end of gene group. Note that if the new synonym is inserted in the first postion, it will become the "Name" and the previous "Name" will be downgraded to first "Synonym"

addAsNewGeneGroup($newName, $target, $evidenceTag, $location)

Adds a new GeneGroup object, comprising 1 GN object (with text attribute set to new $newName, and evidenceTags attribute set to ($evidenceTag)). Will not add a duplicate gene name. $location and $target determine where in GNs line new group is added: if $location == 1, 2, 3, ..., new object added in the 1st, 2nd, 3rd, ... position; if $location == 0, new object added before $target; if $location == -1, new object added after $target (default); if $location == -2, new object added at end of GNs line. Does nothing if $target is not found, and $location == 0 or -1; otherwise $target does not need to be set.

replaceGeneGroup($newGeneGroup, $target)

Replaces the first gene group containing $target with $newGeneGroup. Creating the $newGeneGroup correctly is the user's responsibility

getGeneGroup($target)

Returns the first gene group that contains $target

setToOr()

Retruns a new GNs object, but with all GNs objects in a single gene group. Needed when adding 'C' to 'A and B', when the relationship of 'C' to 'A' and 'B' is unknown: the universal use of ' or ' is the default delimeter for TrEMBL entries


TRANSITION

The format of the GN line will change in 2004 from:

 GN   (CYSA1 OR CYSA OR RV3117 OR MT3199 OR MTCY164.27) AND (CYSA2 OR
 GN   RV0815C OR MT0837 OR MTV043.07C).

to:

 GN   Name=CysA1; Synonyms=CysA; OrderedLocusNames=Rv3117, MT3199;
 GN   ORFNames=MtCY164.27;
 GN   and
 GN   Name=CysA2; OrderedLocusNames=Rv0815c, MT0837; ORFNames=MTV043.07c;

This module supports both formats. To convert an entry from the old to the new format, do:

 $entry->GNs->is_old_format(0);