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Last update on 25. Nov 2018 .
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Modify fields of listed

OCCURRENCE

ARB_NT/Species/Search and Query/More Functions/Modify fields of listed

ARB_NT/Genome/Search and query/More Functions/Modify fields of listed

ARB_NT/Genome/Experiment/Search and query/More Functions/Modify fields of listed

ARB_NT/Tree/NDS

 

DESCRIPTION

Finds and replaces substrings within fields/tagged subfields of all listed species/genes. The entries within the selected fields of all listed species/genes can be modified either individually or globally.

 

Target field

Select the target field to modify by pressing the button in the upper part of the window.

Target field related options:

  • 'Create missing target fields' with type=STRING if checked. Bail out with error otherwise.
  • 'Accept conversion errors':
    • if checked, accepts modifications like writing "hello" to a numeric field (which will be written as '0')
    • otherwise arb will abort with an error in such cases (Note that writing "4711" to numeric fields will work w/o error)


 

Expert options

  • 'Use Tags' allows to tag entries or modify only tagged parts of entries. See ´TAGS: Subfields´ for details.
  • 'Double Pars' causes the result of the 'Command' to be interpreted and executed as command once again (special; in doubt don't use)

 

Command

Three different languages can be used to modify an entry:

SRT:    indicated by a leading ':' character
ACI:    indicated by a leading '|' character
REG:    indicated by sourrounding '/' characters

Details:

REG: Simple Regular Expressions (not for beginners)
'/Search RegExpr/Replace String/'  or
'/Search RegExpr/'
(see ´Regular Expressions (REG)´ for more details)
SRT: Replaces substrings
Syntax: ':old_string=new_string' (see ´Search and Replace Tool (SRT)´ for more details)
Example: remove all spaces with SRT ': ='
Different search/replace commands can be performed simultaneously and have to be separated by ':'
':search1=replace1:search2=replace2:  ...  :searchn=replacen'.
'*' and '?' are wild cards for multiple and single characters, respectively.
ACI: More sophisticated string manipulations
Read ´ARB Command Interpreter (ACI)´ for more information.
 

Predefined commands

Clicking on one of the predefined commands in the list at the bottom of the window

  • will set the content of the 'Command' field and
  • may change the selected target field (!!!)

 

Defining custom commands

You may add new commands by editing one of the files:

$ARBHOME/lib/sellists/mod_fields.sellst
$ARBHOME/lib/sellists/mod_gene_fields.sellst

You should save this file to another location when installing new versions of ARB or it will be overwritten.

A better way is to create your own list(s). All list matching 'mod_fields*.sellst' will be loaded, where 'mod_fields.sellst' is loaded.

If you have created any scripts which might be useful for other ARB users send them to devel@arb-home.de.

 

EXAMPLES

':p?r=p?1w'      replaces       par to paw
                                pbr to pbw
                                pcr to pcw ...
':p??r=p?2?1r'   swaps the two letters between p and r
':a*=b*1'        replaces only the first 'a' by 'b'
':?* *=?1. *2'   Replaces the first word by its first
                 letter + '.'
':\:=\n'         replaces all ':' by <newline>
':*=*1 *(key1)'  appends the database field <key1>
':*=*1 *(key1|nothing found)'
                appends the database field <key1>
                if <key1> does not contain entries
                append 'nothing  found'
  1. Global modification: Replace 'spec.' by 'sp.' within the field full_name of all listed species:
    Press:          'MODIFY FIELDS OF LISTED SPECIES'
    Select Field:   'full_name'
    Type Command:   ':spec.=sp.'
    Press:          'GO'
  2. Individual modification: Append the particular entries of fields 'title' and 'journal' to that of the fields 'author' of all listed species if there are any entries:
    Press:          'MODIFY FIELDS OF LISTED SPECIES'
    Select Field:   'author'
    Type Command:   ':*=*1 *(title) *(journal)'
    Press:          'GO'

 

NOTES

Undo does work.

 

WARNINGS

Be careful if search or replace string contains special characters (such as ':').

 

BUGS

No bugs known