| More docs on the ARB website. See also index of helppages. Last update on 07. Sep 2018 .

Main topics:

- Search Database for Species
- Search Database for Genes
- Protection Level
- TAGS: Subfields

Related topics:

- Regular Expressions (REG)
- Search and Replace Tool (SRT)
- ARB Command Interpreter (ACI)

# MODIFY FIELDS OF LISTED SPECIES/GENES

- OCCURRENCE
- DESCRIPTION
- NOTES
- EXAMPLES
- NOTES
- WARNINGS
- BUGS

## OCCURRENCE

### ARB_NT/Species/Search/More Functions/Modify fields of listed

### ARB_NT/Genes/Search/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.

### 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.

## NOTES

### 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 contain special characters (such as ':').

## BUGS

### No bugs known