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Last update on 25. Nov 2018 .
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Export Selected Species and Sequences

OCCURRENCE

ARB_NT/File/Export Foreign Format

 

DESCRIPTION

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

Choose the 'EXPORT FOREIGN FORMAT' option from the 'File' menu to display the 'ARB EXPORT' window.

Select a formate from the corresponding subwindow.

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

EXPERT:

The program reads the selected format (formats is $ARBHOME/lib/export/*.eft) and replaces all references to species information by the value of the reference. See ´Export File Formats´ for more information.
 

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