Hi Ben, Thanks for the suggestions. The sorting by group worked pretty well.
There are some situations where alphabetical sorting would be helpful (to get all residues of a certain type together at the first position and then by the second position. I guess I can group on a single column but then that doesn't sort the second column. But I can work with the sorting by group. By the way, Jim Procter gave me some "Groovy" scripts to left-justify some selected columns or right-justify some selected columns. I am finding them really, really helpful in cleaning up alignments that are very gappy in some loop regions and I don't care about the pairwise alignments in that region; I can left-justify them and then delete empty columns. He said it was an idea to include that as a regular feature. It's a little time consuming to read in the left-script, and then the right-script, and then the left-script again since sometimes it takes a lot of both scripts to clean up an entire alignment in a way that makes sense. For my two cents, I think that would be great if it were just a preloaded tool that would make it easy to left and right justify and set of selected columns. Thanks, Roland --------------------------------------------- Roland Dunbrack (he/his/him/him) Institute for Cancer Research Fox Chase Cancer Center Philadelphia PA 19111 http://dunbrack.fccc.edu http://dunbrack.org On Sat, Jul 4, 2020 at 3:57 PM Benedict Soares (Staff) < [email protected]> wrote: > Hi Roland, > > Another possibility you might try (which for your first use case will do > exactly what you want, and for your second use case get you most of the > way): > > 1) Select the column(s) you are interested in: > to select a single column just click at the top of the column to > select a single column; > to select multiple contiguous columns click and drag at the top of the > columns; > to select multiple non-contiguous columns, select the first column(s), > then hold the Ctrl (or cmd if on a Mac) key down whilst selecting further > column(s). > > 2) Click on "Select" -> "Make Groups for Selection" which will create a > group for each different combination of residues/gaps _in your selected > columns_. The groups themselves will currently be scattered throughout the > sequences, so... > > 3) Click on "Calculate" -> "Sort" -> "By Group" which will then re-arrange > the sequences so that sequences in the same group are together. These > groups will be ordered from largest group to smallest group(s), or the > other way round. Select Sort By Group again to reverse the order they're in. > > In your first use case, you should have the sequences ordered with all the > sequences with a gap in the selected column, followed by the single > sequence with a residue in the column (or the other way round if you > reverse the order). > > In the second use case it won't be in alphabetical order, but in order of > size of groups (i.e. occurrences of each residue/gap combination). You > might find it easier to see what's going on in those groups/columns by > selecting "View" -> "Hide" -> "All but Selected Region" (assuming you still > have the relevant columns selected). When you've found your sequences of > interest, select them (click on the ID) and you can bring back the hidden > columns with "View" -> "Show" -> "All Columns". > > Hope I've understood correctly and this helps, > > Ben > ------------------------------ > *From:* [email protected] < > [email protected]> on behalf of Roland Dunbrack < > [email protected]> > *Sent:* 04 July 2020 11:34 > *To:* [email protected] <[email protected]> > *Subject:* [Jalview-discuss] sorting by sequence selection > > Hello, > > Is there a way to sort all the sequences or a set of them in a Jalview > session by some selected columns? For instance, I have a gapped column in > 1000 sequences and it's a pain to try to find the inserted residue. If I > can just sort by that column it would move to the top or the bottom of the > sequences. In other cases, I am looking for different mutations at some > positions in antibodies, and if I can select 3 columns from a set of > sequences and then reorder those whole sequences in alphabetical order of > the selected 3-residue segment in each. > > Thanks, > Roland > > --------------------------------------------- > Roland Dunbrack (he/his/him/him) > Institute for Cancer Research > Fox Chase Cancer Center > Philadelphia PA 19111 > http://dunbrack.fccc.edu > http://dunbrack.org > > The University of Dundee is a registered Scottish Charity, No: SC015096 >
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