source: branches/stable/HELP_SOURCE/oldhelp/mg_species.hlp

Last change on this file was 18359, checked in by westram, 5 years ago
  • add new FTS transfer mode to merge-tool (implements #825)
    • allows to skip transport of sequence alignment data (i.e. allows plain metadata updates)
  • update+fix documentation
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 6.9 KB
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1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
4UP      arb_merge_workflow.hlp
5
6#Please insert subtopic references  (line starts with keyword SUB)
7SUB     del_list.hlp
8SUB     write_field_list.hlp
9SUB     mod_field_list.hlp
10SUB     mg_xfer_field_of_listed.hlp
11SUB     mg_xfer_field_of_sel.hlp
12
13# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
14
15#************* Title of helpfile !! and start of real helpfile ********
16TITLE           Compare and Transfer Species Entries
17
18OCCURRENCE      ARB_MERGE/Transfer species
19
20DESCRIPTION     Allows
21                        * database searching,
22                        * comparison of the two databases,
23                        * transferring data from left to right
24                        * realigning sequences to new alignment
25
26        Database Searching:
27
28                To perform database searching within the individual databases
29                use the left or right part of the 'TRANSFER SPECIES' window for
30                source and target database (DB), respectively.
31
32                The database is scanned for 'species' (see LINK{glossary.hlp})
33                which contain (or do not contain) the search string within the
34                specified 'field' (see LINK{glossary.hlp}). The corresponding
35                'species' and the respective 'field' entries are listed in the
36                'HIT LIST' subwindow. The number of hits is displayed after the
37                'Hits:' prompt.
38
39                Define whether matching or non matching species should be
40                listed by pressing the appropriate combination of left
41                and right buttons in the 'QUERY TYPE' area. Performing
42                multiple searches, define whether the list of 'species'
43                should be replaced by the new results, whether newly
44                found 'species' should be removed from or appended
45                to the existing list.
46
47                Select a 'field' from the 'Fields' subwindow.
48
49                Type the search string to the 'Search string' subwindow.
50
51                Press the 'RUN QUERY' button of the results area.
52
53                See also LINK{searching.hlp} and LINK{search_equal_fields.hlp}.
54
55        Data Transfer:
56
57                Transfer will always happen from source to target species
58                (i.e. from left to right side).
59
60                Select the transfer mode:
61                 * "whole species" will copy all fields,
62                 * "single field" will copy one single field (selectable, allows to append data) and
63                 * "using FTS" will use the "field transfer set" selected below (see LINK{xferset.hlp}).
64
65                   The "using FTS" mode has two flavors (with and w/o sequence data; see section below).
66                   The second mode can be used to update/synchronize metadata between two databases
67                   containing different alignments (e.g. update metadata of common species from
68                   a new SILVA release into your local databases).
69
70                Select the transfer scope:
71                 * "selected species" will copy (from) the selected species into
72                   a new species or to the species selected in the right-side
73                   hitlist.
74                 * "listed species" will copy all species listed in the left-side hitlist.
75
76                Click the 'Transfer species' button in the window center to transfer
77                according to selected transfer-type and -scope.
78
79                See LINK{save.hlp} for howto save the modified database(s).
80
81SECTION         Overwritten data
82
83                This section describes when and what data will be overwritten
84                and when data gets mixed into existing data.
85
86                In "whole species" transfer mode
87                 * any existing species (with the same ID, i.e. 'name') will be deleted and
88                 * a full copy of each source species will be created.
89
90                The "single field" and "using FTS" transfer modes
91                 * will copy from the selected source species to the selected target species
92                   when "selected species" scope is used (regardless whether their IDs match or not) or
93                 * will copy from each listed species to (a new or already existing) target species
94                   with the same ID.
95
96                Some fields are handled special:
97                 * the 'name' entry will always be transferred when missing at target.
98                 * the 'acc' entry will be transferred when missing at target (and when "using FTS" mode).
99                 * whether 'ali_*/data' entries (i.e. the sequence data) will be transferred,
100                   depends on the transfer mode:
101                   * "whole species" and "using FTS (with seq)" will transfer all existing sequence data
102                   * "single field" and "using FTS (w/o seq)" will not transfer any sequence data
103                 * all transferred sequence entries will be targeted by alignment adaption (see below).
104
105SECTION         Adapt Alignment
106
107                ARB Merge tries to keep the alignment correct. Normally people
108                have inserted new gaps in either the left or right database.
109                By entering the ID(s) of some reference species in the input
110                box in the upper center of the TRANSFER SPECIES window, the
111                program will try to find those species in both databases,
112                create a column reference list, and realign all transferred
113                sequences.
114
115                To enable this feature, enable the 'Adapt alignment' toggle.
116
117NOTES           You may mix data from source fields with data of existing target fields
118                using FTS as follows:
119
120                For example if you have a source field 's1' and an existing destination field 'd1'
121                you may merge the contents of these fields (into 'd1') using a simple rule
122                transferring 's1' to 'd1' and add one of the following LINK{aci.hlp} expressions:
123
124                    ACI                   does
125
126                    dd;readdb(d1)         prefix content of 's1' in front of 'd1'
127                    dd;" ";readdb(d1)     dito, but insert one space
128                    readdb(d1);dd         append content of 's1' behind 'd1'
129                    readdb(d1);" ";dd     dito, but insert one space
130
131
132EXAMPLES        For general examples of database searching see LINK{sp_search.hlp}.
133
134WARNINGS        The data will always be transferred from the source DB to
135                the target DB.
136
137                If you want to align sequences during transfer, it is recommended
138                that the left database has fewer gaps than the right one.
139
140                Entries in the target database will be overwritten w/o further consent
141                (applies to single transferred fields and complete transferred species).
142
143BUGS            No bugs known
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