[387] | 1 | #Please insert up references in the next lines (line starts with keyword UP) |
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[10159] | 2 | UP arb.hlp |
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| 3 | UP glossary.hlp |
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| 4 | UP arb_merge_workflow.hlp |
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[387] | 5 | |
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| 6 | #Please insert subtopic references (line starts with keyword SUB) |
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[10159] | 7 | SUB del_list.hlp |
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| 8 | SUB write_field_list.hlp |
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| 9 | SUB mod_field_list.hlp |
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[18126] | 10 | SUB mg_xfer_field_of_listed.hlp |
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| 11 | SUB mg_xfer_field_of_sel.hlp |
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[387] | 12 | |
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[2986] | 13 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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[387] | 14 | |
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| 15 | #************* Title of helpfile !! and start of real helpfile ******** |
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[10159] | 16 | TITLE Compare and Transfer Species Entries |
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[387] | 17 | |
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[10159] | 18 | OCCURRENCE ARB_MERGE/Transfer species |
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[387] | 19 | |
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[10159] | 20 | DESCRIPTION Allows |
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[5785] | 21 | * database searching, |
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[10159] | 22 | * comparison of the two databases, |
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| 23 | * transferring data from left to right |
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| 24 | * realigning sequences to new alignment |
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[387] | 25 | |
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[10159] | 26 | Database Searching: |
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[387] | 27 | |
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[10159] | 28 | To perform database searching within the individual databases |
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| 29 | use the left or right part of the 'TRANSFER SPECIES' window for |
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| 30 | source and target database (DB), respectively. |
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[387] | 31 | |
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[10159] | 32 | The database is scanned for 'species' (see LINK{glossary.hlp}) |
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| 33 | which contain (or do not contain) the search string within the |
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| 34 | specified 'field' (see LINK{glossary.hlp}). The corresponding |
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| 35 | 'species' and the respective 'field' entries are listed in the |
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| 36 | 'HIT LIST' subwindow. The number of hits is displayed after the |
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| 37 | 'Hits:' prompt. |
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[387] | 38 | |
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[10159] | 39 | Define whether matching or non matching species should be |
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| 40 | listed by pressing the appropriate combination of left |
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| 41 | and right buttons in the 'QUERY TYPE' area. Performing |
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| 42 | multiple searches, define whether the list of 'species' |
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| 43 | should be replaced by the new results, whether newly |
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| 44 | found 'species' should be removed from or appended |
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| 45 | to the existing list. |
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[387] | 46 | |
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[10159] | 47 | Select a 'field' from the 'Fields' subwindow. |
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[387] | 48 | |
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[10159] | 49 | Type the search string to the 'Search string' subwindow. |
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[387] | 50 | |
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[10159] | 51 | Press the 'RUN QUERY' button of the results area. |
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[387] | 52 | |
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[5785] | 53 | See also LINK{searching.hlp} and LINK{search_equal_fields.hlp}. |
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| 54 | |
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[10159] | 55 | Data Transfer: |
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[433] | 56 | |
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[18126] | 57 | Transfer will always happen from source to target species |
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| 58 | (i.e. from left to right side). |
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[387] | 59 | |
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[18126] | 60 | Select the transfer mode: |
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| 61 | * "whole species" will copy all fields, |
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| 62 | * "single field" will copy one single field (selectable, allows to append data) and |
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| 63 | * "using FTS" will use the "field transfer set" selected below (see LINK{xferset.hlp}). |
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[387] | 64 | |
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[18126] | 65 | Select the transfer scope: |
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| 66 | * "selected species" will copy (from) the selected species into |
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| 67 | a new species or to the species selected in the right-side |
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| 68 | hitlist. |
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| 69 | * "listed species" will copy all species listed in the left-side hitlist. |
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[433] | 70 | |
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[18126] | 71 | Click the 'Transfer species' button in the window center to transfer |
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| 72 | according to selected transfer-type and -scope. |
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| 73 | |
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[16574] | 74 | See LINK{save.hlp} for howto save the modified database(s). |
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[387] | 75 | |
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[18126] | 76 | SECTION Adapt Alignment |
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[433] | 77 | |
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[10159] | 78 | ARB Merge tries to keep the alignment correct. Normally people |
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| 79 | have inserted new gaps in either the left or right database. |
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| 80 | By entering the ID(s) of some reference species in the input |
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| 81 | box in the upper center of the TRANSFER SPECIES window, the |
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| 82 | program will try to find those species in both databases, |
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| 83 | create a column reference list, and realign all transferred |
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| 84 | sequences. |
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[18126] | 85 | |
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[3045] | 86 | To enable this feature, enable the 'Adapt alignment' toggle. |
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[387] | 87 | |
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[18126] | 88 | SECTION Overwritten data |
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[387] | 89 | |
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[18126] | 90 | This section describes when and what data will be overwritten |
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| 91 | and when data gets mixed into existing data. |
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| 92 | |
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| 93 | In "whole species" transfer mode |
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| 94 | * any existing species (with the same ID, i.e. 'name') will be deleted and |
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| 95 | * a full copy of each source species will be created. |
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| 96 | |
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| 97 | The "single field" and "using FTS" transfer modes |
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| 98 | * will copy from the selected source species to the selected target species |
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| 99 | when "selected species" scope is used or |
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| 100 | * will copy from each listed species to (a new or already existing) target species |
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| 101 | with the same ID. |
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| 102 | |
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| 103 | Some fields are handled special: |
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| 104 | * the 'name' entry will always be transferred when missing at target. |
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| 105 | * the 'acc' entry will be transferred when missing at target (and when "using FTS" mode). |
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| 106 | * all transferred 'ali_*/data' entries will be targeted by alignment adaption (see section above). |
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| 107 | |
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[10159] | 108 | NOTES None |
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[387] | 109 | |
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[433] | 110 | |
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[10159] | 111 | EXAMPLES For examples for database searching see LINK{sp_search.hlp}. |
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[387] | 112 | |
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| 113 | |
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[10159] | 114 | WARNINGS The data will always be transferred from the source DB to |
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| 115 | the target DB. |
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| 116 | If you want to align sequences during transfer, it is recommended |
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| 117 | that the left database has fewer gaps than the right one. |
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[387] | 118 | |
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[10159] | 119 | If there are entries (for selected data) in both databases, |
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| 120 | those in the target DB will be overwritten! |
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[387] | 121 | |
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| 122 | |
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[10159] | 123 | BUGS No bugs known |
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