source: branches/lib/HELP_SOURCE/source/arb_import.hlp

#       main topics:
UP      arb.hlp
UP      glossary.hlp
UP      save.hlp
UP      arb_intro.hlp

#       sub topics:

SUB     importift.hlp

SUB     universal_ift.hlp
SUB     dssp_ift.hlp
SUB     gde_flat_ift.hlp

SUB     arb_export.hlp

# format described in ../help.readme


TITLE           Import Foreign Data(bases)

OCCURRENCE      ARB_INTRO <Create and Import>,
                ARB_NT/File/Import/Import from external format

DESCRIPTION     Reads foreign data(base) formats, creates a new ARB database,
                and imports the foreign data. A selection of commonly used
                foreign formats can be automatically identified. Data can be
                imported from single or multiple files.

                Type a source file name to the 'Enter file name of foreign
                database' subwindow. Use '*' and '?' as multiple and single
                character wildcards to load a set of files, respectively.
                Alternatively you may select a file from the directories and
                files subwindow.

                Make a selection whether you want to import

                     - a full genome flatfile (in GENBANK or EMBL format) or
                     - normal sequence files.

                In the second case select the file format from the
                'Select foreign database format' subwindow
                or press the 'AUTO DETECT' button.

                If your file type is not in the list and you are only
                interested in the sequence, try 'universal'.

                Enter the name and type of the destination alignment (see LINK{alignment.hlp}).

                   Use different alignment names for different genes
                   to be able to store them in the same datebase while
                   still being able to distinguish them.

                Choose the default protection used for the imported data.

                Check "Create selection?" to store the names of all imported
                species in a LINK{species_configs.hlp}.

                Click the 'FTS' selection button to define or select LINK{xferset.hlp}.

                Press the 'GO' button.

SECTION         Custom import filters

                You may create and store your own private import filters in
                directory '~/.arb_prop/filter'. See LINK{importift.hlp} for information
                about the import filter definition language.

                Press the 'Test' button to modify and test the selected filter
                (see LINK{import_test.hlp}).

                If you want to import only parts of the data provided by an
                existing import filter, use LINK{xferset.hlp}.

NOTES           Following file formats currently can be detected and loaded:
                GENBANK, RDP: GENBANK, EBI and FastA

                Several uncommon file formats (including AE2, GCG and DSSP)
                are kept in directory '$ARBHOME/lib/import/older'. To
                make them available, copy or symlink them into ''$ARBHOME/lib/import' or into
                your local filter directory '~/.arb_prop/filter/'.

                To import big new databases into an existing ARB database, convert it
                to the ARB format first, save and merge it with the
                ARB_MERGE tool.

                For importing other formats such as PHYLIP or PAUP into an
                existing ARB database use the 'Import sequences using Readseq'
                function accessible via the 'File' menu of the 'ARB_NT' main menu.
                See LINK{agde_readseq.hlp}.

                If 'AUTO DETECT' does not find any format, selecting a format
                by hand most likely wont help you (exception: universal format).

WARNINGS        When using 'AUTO DETECT', check if the correct format is detected.
                RDP files may for instance be identified as GenBank. In such case
                choose 'rdp.ift' manually.

BUGS            'AUTO DETECT' looks for certain key-words in the files. If it can't
                find these words, it does not accept the file, even if the file has
                the correct format. This is especially true for the gcg format.