| 1 | #Please insert up references in the next lines (line starts with keyword UP) |
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| 2 | UP arb.hlp |
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| 3 | UP glossary.hlp |
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| 4 | UP save.hlp |
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| 5 | UP arb_intro.hlp |
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| 6 | |
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| 7 | #Please insert subtopic references (line starts with keyword SUB) |
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| 8 | |
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| 9 | SUB importift.hlp |
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| 10 | |
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| 11 | SUB universal_ift.hlp |
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| 12 | SUB dssp_ift.hlp |
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| 13 | SUB gde_flat_ift.hlp |
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| 14 | |
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| 15 | SUB arb_export.hlp |
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| 16 | |
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| 17 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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| 18 | |
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| 19 | #************* Title of helpfile !! and start of real helpfile ******** |
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| 20 | TITLE Import Foreign Data(bases) |
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| 21 | |
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| 22 | OCCURRENCE ARB_INTRO <Create and Import>, |
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| 23 | ARB_NT/File/Import/Import from external format |
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| 24 | |
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| 25 | DESCRIPTION Reads foreign data(base) formats, creates a new ARB database, |
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| 26 | and imports the foreign data. A selection of commonly used |
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| 27 | foreign formats can be automatically identified. Data can be |
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| 28 | imported from single or multiple files. |
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| 29 | |
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| 30 | Type a source file name to the 'Enter file name of foreign |
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| 31 | database' subwindow. Use '*' and '?' as multiple and single |
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| 32 | character wildcards to load a set of files, respectively. |
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| 33 | Alternatively you may select a file from the directories and |
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| 34 | files subwindow. |
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| 35 | |
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| 36 | Make a selection whether you want to import |
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| 37 | |
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| 38 | - a full genome flatfile (in GENBANK or EMBL format) or |
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| 39 | - normal sequence files. |
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| 40 | |
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| 41 | In the second case select the file format from the |
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| 42 | 'Select foreign database format' subwindow |
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| 43 | or press the 'AUTO DETECT' button. |
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| 44 | |
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| 45 | If your file type is not in the list and you are only |
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| 46 | interested in the sequence, try 'universal'. |
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| 47 | |
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| 48 | Enter the name and type of the destination alignment (see LINK{alignment.hlp}). |
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| 49 | |
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| 50 | Use different alignment names for different genes |
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| 51 | to be able to store them in the same datebase while |
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| 52 | still being able to distinguish them. |
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| 53 | |
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| 54 | Choose the default protection used for the imported data. |
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| 55 | |
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| 56 | Check "Create selection?" to store the names of all imported |
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| 57 | species in a LINK{species_configs.hlp}. |
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| 58 | |
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| 59 | Click the 'FTS' selection button to define or select LINK{xferset.hlp}. |
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| 60 | |
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| 61 | Press the 'GO' button. |
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| 62 | |
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| 63 | SECTION Custom import filters |
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| 64 | |
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| 65 | You may create and store your own private import filters in |
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| 66 | directory '~/.arb_prop/filter'. See LINK{importift.hlp} for information |
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| 67 | about the import filter definition language. |
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| 68 | |
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| 69 | Press the 'Test' button to modify and test the selected filter |
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| 70 | (see LINK{import_test.hlp}). |
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| 71 | |
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| 72 | If you want to import only parts of the data provided by an |
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| 73 | existing import filter, use LINK{xferset.hlp}. |
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| 74 | |
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| 75 | NOTES Following file formats currently can be detected and loaded: |
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| 76 | GENBANK, RDP: GENBANK, EBI and FastA |
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| 77 | |
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| 78 | Several uncommon file formats (including AE2, GCG and DSSP) |
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| 79 | are kept in directory '$ARBHOME/lib/import/older'. To |
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| 80 | make them available, copy or symlink them into ''$ARBHOME/lib/import' or into |
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| 81 | your local filter directory '~/.arb_prop/filter/'. |
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| 82 | |
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| 83 | To import big new databases into an existing ARB database, convert it |
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| 84 | to the ARB format first, save and merge it with the |
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| 85 | ARB_MERGE tool. |
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| 86 | |
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| 87 | For importing other formats such as PHYLIP or PAUP into an |
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| 88 | existing ARB database use the 'Import sequences using Readseq' |
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| 89 | function accessible via the 'File' menu of the 'ARB_NT' main menu. |
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| 90 | See LINK{agde_readseq.hlp}. |
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| 91 | |
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| 92 | If 'AUTO DETECT' does not find any format, selecting a format |
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| 93 | by hand most likely wont help you (exception: universal format). |
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| 94 | |
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| 95 | WARNINGS When using 'AUTO DETECT', check if the correct format is detected. |
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| 96 | RDP files may for instance be identified as GenBank. In such case |
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| 97 | choose 'rdp.ift' manually. |
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| 98 | |
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| 99 | BUGS 'AUTO DETECT' looks for certain key-words in the files. If it can't |
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| 100 | find these words, it does not accept the file, even if the file has |
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| 101 | the correct format. This is especially true for the gcg format. |
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| 102 | |
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