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Last update on 17. Sep 2019 .
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Export Selected Species and Sequences

OCCURRENCE

ARB_NT/File/Export/Export to external format

 

DESCRIPTION

Exports the selected 'alignment' of some or all 'species' in various formats.

Select a format from the format list.

Select a field transfer set (FTS) if you like to select or modify the data to be exported.

Choose whether to export all or only marked species.

Choose a filter to export only selected columns.

Select a compression method:

  • 'none' preserves the alignment information
  • 'vertical gaps' removes all columns containing only gaps
  • 'all gaps' completely remove the alignment information

Check 'Cut stop codon' to cut off the sequence at the stop codon.

Define whether the data should be written to one or to multiple files by clicking on the checkbox after the 'Should the data be written to multiple files:' prompt. In the multiple file mode, each 'species' is written to its own file.

Define an output file name by selecting from the 'Directories and Files' subwindow or by typing it to the 'Output File Name' subwindow. In the multiple file mode, the resulting filenames are created by appending the 'species name' to the specified output filename separated by underscores (filename_species name).

Press the <GO> button

 

Export filters

Default export filters available for all users are stored in directory $ARBHOME/lib/export/*.eft.

ARB reads the selected format and replaces all references to species fields by the value of the referred field. See ´Export File Formats´ for more information.

Specifying a FTS will (virtually) modify the contents of fields used in the export filter. Note: this will NOT affect the fields original content, it just is a temporary change, visible only to the export filter.

Simple example: if the export filter accesses the field 'author' and you use some arb database where the author is stored in the field 'autref', you may create a FTS containing one simple forwarding rule "autref -> author".
The content of field 'autref' will be exported whenever 'author' is accessed (but your database will not get modified).
This FTS can be used with any export form that uses 'author'.
 

Custom export filters

You may create and store your own private export filters in directory '~/.arb_prop/filter'. See ´Export File Formats´ for information about the export filter definition language.

Press the 'Test' button to modify and test the selected filter (see ´Test export filter´).

 

NOTES

None

 

EXAMPLES

None

 

BUGS

No bugs known